group_manager.cc
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group_manager.cc
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	/**
	* @file group_manager.cc
	*
	* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
	* @author Dana Christen <dana.christen@gmail.com>
	* @author David Simon Kammer <david.kammer@epfl.ch>
	* @author Nicolas Richart <nicolas.richart@epfl.ch>
	* @author Marco Vocialta <marco.vocialta@epfl.ch>
	*
	* @date creation: Wed Nov 13 2013
	* @date last modification: Tue Feb 20 2018
	*
	* @brief Stores information about ElementGroup and NodeGroup
	*
	* @section LICENSE
	*
	* Copyright (©) 2014-2018 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 "group_manager.hh"
	#include "aka_csr.hh"
	#include "data_accessor.hh"
	#include "element_group.hh"
	#include "element_synchronizer.hh"
	#include "mesh.hh"
	#include "mesh_accessor.hh"
	#include "mesh_utils.hh"
	#include "node_group.hh"
	/* -------------------------------------------------------------------------- */
	#include <algorithm>
	#include <iterator>
	#include <list>
	#include <numeric>
	#include <queue>
	#include <sstream>
	#include <utility>
	/* -------------------------------------------------------------------------- */

	namespace 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() = default;

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

	auto it = node_groups.find(group_name);

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

	std::stringstream sstr;
	sstr << this->id << ":" << group_name << "_node_group";

	auto && ptr =
	std::make_unique<NodeGroup>(group_name, mesh, sstr.str(), memory_id);

	auto & node_group = *ptr;

	// \todo insert_or_assign in c++17
	if (it != node_groups.end()) {
	it->second = std::move(ptr);
	} else {
	node_groups[group_name] = std::move(ptr);
	}

	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_ERROR("ElementFilter cannot be applied to NodeGroup yet."
	<< " Needs to be implemented.");
	}

	AKANTU_DEBUG_OUT();
	return node_group;
	}

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

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

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

	auto && ptr = std::make_unique<ElementGroup>(
	group_name, mesh, new_node_group, dimension,
	this->id + ":" + group_name + "_element_group", memory_id);

	auto & element_group = *ptr;

	if (it != element_groups.end()) {
	it->second = std::move(ptr);
	} else {
	element_groups[group_name] = std::move(ptr);
	}

	AKANTU_DEBUG_OUT();

	return element_group;
	}

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

	auto eit = element_groups.find(group_name);
	if (eit != element_groups.end()) {
	if (destroy_node_group)
	destroyNodeGroup(eit->second->getNodeGroup().getName());
	element_groups.erase(eit);
	}

	AKANTU_DEBUG_OUT();
	}

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

	auto nit = node_groups.find(group_name);
	if (nit != node_groups.end()) {
	node_groups.erase(nit);
	}

	AKANTU_DEBUG_OUT();
	}

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

	// if (destroy_node_groups)
	// for (auto && data : element_groups) {
	// destroyNodeGroup(std::get<1>(data)->getNodeGroup().getName());
	// }

	// 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);

	auto && ptr = std::make_unique<ElementGroup>(
	group_name, mesh, node_group, dimension,
	id + ":" + group_name + "_element_group", memory_id);

	auto & element_group = *ptr;
	element_groups[group_name] = std::move(ptr);

	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();

	if (T::type == FilterFunctor::_node_filter_functor) {
	auto & filtered_node_group = this->createFilteredNodeGroup(
	group_name + "_nodes", node_group, filter);

	AKANTU_DEBUG_OUT();
	return this->createElementGroup(group_name, dimension, filtered_node_group);
	} else if (T::type == FilterFunctor::_element_filter_functor) {
	AKANTU_ERROR(
	"Cannot handle an ElementFilter yet. Needs to be implemented.");
	}

	AKANTU_DEBUG_OUT();
	}

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

	public:
	ClusterSynchronizer(GroupManager & group_manager, UInt element_dimension,
	std::string cluster_name_prefix,
	ElementTypeMapArray<UInt> & element_to_fragment,
	const ElementSynchronizer & element_synchronizer,
	UInt nb_cluster)
	: group_manager(group_manager), element_dimension(element_dimension),
	cluster_name_prefix(std::move(cluster_name_prefix)),
	element_to_fragment(element_to_fragment),
	element_synchronizer(element_synchronizer), nb_cluster(nb_cluster) {}

	UInt synchronize() {
	Communicator & comm = Communicator::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);

	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
	element_synchronizer.synchronizeOnce(*this,
	SynchronizationTag::_gm_clusters);

	/// count total number of pairs
	Array<int> nb_pairs(nb_proc); // This is potentially a bug for more than
	// 2**31 pairs, but due to a all gatherv after
	// it must be int to match MPI interfaces
	nb_pairs(rank) = distant_ids.size();
	comm.allGather(nb_pairs);

	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);

	for (auto & ids : distant_ids) {
	total_pairs(local_pair_index, 0) = ids.first;
	total_pairs(local_pair_index, 1) = ids.second;
	++local_pair_index;
	}

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

	/// 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.size() != 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.size() * 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);

	auto it = global_clusters[c].begin();
	auto 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;

	AKANTU_DEBUG_ASSERT(group_manager.elementGroupExists(tmp_sstr.str()),
	"Temporary fragment \"" << tmp_sstr.str()
	<< "\" not found");

	cluster.append(group_manager.getElementGroup(tmp_sstr.str()));
	group_manager.destroyElementGroup(tmp_sstr.str(), true);
	}
	}

	return total_nb_cluster;
	}

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

	return 0;
	}

	inline void packData(CommunicationBuffer & buffer,
	const Array<Element> & elements,
	const SynchronizationTag & tag) const override {
	if (tag != SynchronizationTag::_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 unpackData(CommunicationBuffer & buffer,
	const Array<Element> & elements,
	const SynchronizationTag & tag) override {
	if (tag != SynchronizationTag::_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;
	const ElementSynchronizer & element_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");
	}

	/* -------------------------------------------------------------------------- */
	UInt GroupManager::createClusters(
	UInt element_dimension, Mesh & mesh_facets, std::string cluster_name_prefix,
	const GroupManager::ClusteringFilter & filter) {
	return createClusters(element_dimension, std::move(cluster_name_prefix),
	filter, mesh_facets);
	}

	/* -------------------------------------------------------------------------- */
	UInt GroupManager::createClusters(
	UInt element_dimension, std::string cluster_name_prefix,
	const GroupManager::ClusteringFilter & filter) {
	std::unique_ptr<Mesh> mesh_facets;
	if (!mesh_facets && element_dimension > 0) {
	MeshAccessor mesh_accessor(const_cast<Mesh &>(mesh));
	mesh_facets = std::make_unique<Mesh>(mesh.getSpatialDimension(),
	mesh_accessor.getNodesSharedPtr(),
	"mesh_facets_for_clusters");

	mesh_facets->defineMeshParent(mesh);

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

	return createClusters(element_dimension, std::move(cluster_name_prefix),
	filter, *mesh_facets);
	}

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

	UInt nb_proc = mesh.getCommunicator().getNbProc();
	std::string tmp_cluster_name_prefix = cluster_name_prefix;

	ElementTypeMapArray<UInt> * element_to_fragment = nullptr;

	if (nb_proc > 1 && mesh.isDistributed()) {
	element_to_fragment =
	new ElementTypeMapArray<UInt>("element_to_fragment", id, memory_id);

	element_to_fragment->initialize(
	mesh, _nb_component = 1, _spatial_dimension = element_dimension,
	_element_kind = _ek_not_defined, _with_nb_element = true);
	// mesh.initElementTypeMapArray(*element_to_fragment, 1, element_dimension,
	// false, _ek_not_defined, true);
	tmp_cluster_name_prefix = "tmp_" + tmp_cluster_name_prefix;
	}

	ElementTypeMapArray<bool> seen_elements("seen_elements", id, memory_id);
	seen_elements.initialize(mesh, _spatial_dimension = element_dimension,
	_element_kind = _ek_not_defined,
	_with_nb_element = true);
	// mesh.initElementTypeMapArray(seen_elements, 1, element_dimension, false,
	// _ek_not_defined, true);

	for (auto ghost_type : ghost_types) {
	Element el;
	el.ghost_type = ghost_type;
	for (auto type :
	mesh.elementTypes(_spatial_dimension = element_dimension,
	_ghost_type = ghost_type, _element_kind = _ek_not_defined)) {
	el.type = type;
	UInt nb_element = mesh.getNbElement(type, ghost_type);
	Array<bool> & seen_elements_array = seen_elements(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;

	for (auto ghost_type : ghost_types) {
	Element uns_el;
	uns_el.ghost_type = ghost_type;
	for (auto type :
	mesh.elementTypes(_spatial_dimension = element_dimension,
	_ghost_type = ghost_type, _element_kind = _ek_not_defined)) {
	uns_el.type = type;
	Array<bool> & seen_elements_vec =
	seen_elements(uns_el.type, uns_el.ghost_type);

	for (UInt e = 0; e < seen_elements_vec.size(); ++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 && mesh.isDistributed())
	(*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 && mesh.isDistributed()) {
	ClusterSynchronizer cluster_synchronizer(
	this, element_dimension, cluster_name_prefix, element_to_fragment,
	this->mesh.getElementSynchronizer(), nb_cluster);
	nb_cluster = cluster_synchronizer.synchronize();
	delete element_to_fragment;
	}

	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 auto & datas = mesh.getData<T>(dataset_name);

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

	for (auto ghost_type : ghost_types) {
	for (auto type : datas.elementTypes(_ghost_type = ghost_type)) {
	const Array<T> & dataset = datas(type, ghost_type);
	UInt nb_element = mesh.getNbElement(type, ghost_type);
	AKANTU_DEBUG_ASSERT(dataset.size() == nb_element,
	"Not the same number of elements ("
	<< type << ":" << ghost_type
	<< ") in the map from MeshData ("
	<< dataset.size() << ") " << 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);

	auto it = group_dim.find(gname);
	if (it == group_dim.end()) {
	group_dim[gname] = mesh.getSpatialDimension(type);
	} else {
	it->second = std::max(it->second, mesh.getSpatialDimension(type));
	}
	}
	}
	}

	auto git = group_names.begin();
	auto gend = group_names.end();
	for (; git != gend; ++git)
	createElementGroup(git, group_dim[git]);

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

	Element el;
	for (auto ghost_type : ghost_types) {
	el.ghost_type = ghost_type;
	for (auto type : datas.elementTypes(_ghost_type = ghost_type)) {
	el.type = type;
	const Array<T> & dataset = datas(type, ghost_type);
	UInt nb_element = mesh.getNbElement(type, ghost_type);
	AKANTU_DEBUG_ASSERT(dataset.size() == 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, ghost_type).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);

	group.fillFromNodeGroup();
	}

	/* -------------------------------------------------------------------------- */
	void GroupManager::printself(std::ostream & stream, int indent) const {
	std::string space(indent, AKANTU_INDENT);

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

	std::set<std::string> node_group_seen;
	for (auto & group : iterateElementGroups()) {
	group.printself(stream, indent + 1);
	node_group_seen.insert(group.getNodeGroup().getName());
	}

	for (auto &group : iterateNodeGroups()) {
	if (node_group_seen.find(group.getName()) == node_group_seen.end())
	group.printself(stream, indent + 1);
	}

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

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

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

	/* -------------------------------------------------------------------------- */
	void GroupManager::checkAndAddGroups(DynamicCommunicationBuffer & 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");

	auto nnames_it = node_groups.begin();
	auto 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");
	auto gnames_it = this->element_groups.begin();
	auto 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();

	const Communicator & comm = mesh.getCommunicator();
	Int nb_proc = comm.getNbProc();
	Int my_rank = comm.whoAmI();

	if (nb_proc == 1)
	return;

	if (my_rank == 0) {
	for (Int p = 1; p < nb_proc; ++p) {
	DynamicCommunicationBuffer recv_buffer;
	auto tag = Tag::genTag(p, 0, Tag::_ELEMENT_GROUP);
	comm.receive(recv_buffer, p, tag);
	AKANTU_DEBUG_INFO("Got " << printMemorySize<char>(recv_buffer.size())
	<< " from proc " << p << " " << tag);
	this->checkAndAddGroups(recv_buffer);
	}

	DynamicCommunicationBuffer comm_buffer;
	this->fillBufferWithGroupNames(comm_buffer);

	AKANTU_DEBUG_INFO("Initiating broadcast with "
	<< printMemorySize<char>(comm_buffer.size()));
	comm.broadcast(comm_buffer);

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

	auto tag = Tag::genTag(my_rank, 0, Tag::_ELEMENT_GROUP);
	AKANTU_DEBUG_INFO("Sending " << printMemorySize<char>(comm_buffer.size())
	<< " to proc " << 0 << " " << tag);
	comm.send(comm_buffer, 0, tag);

	DynamicCommunicationBuffer recv_buffer;
	comm.broadcast(recv_buffer);
	AKANTU_DEBUG_INFO("Receiving broadcast with "
	<< printMemorySize<char>(recv_buffer.size()));

	this->checkAndAddGroups(recv_buffer);
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	const ElementGroup &
	GroupManager::getElementGroup(const std::string & name) const {
	auto it = element_groups.find(name);
	if (it == element_groups.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) {
	auto it = element_groups.find(name);
	if (it == element_groups.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 {
	auto it = node_groups.find(name);
	if (it == node_groups.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) {
	auto it = node_groups.find(name);
	if (it == node_groups.end()) {
	AKANTU_EXCEPTION("There are no node groups named "
	<< name << " associated to the group manager: " << id);
	}

	return *(it->second);
	}

	/* -------------------------------------------------------------------------- */
	template <typename GroupsType>
	void GroupManager::renameGroup(GroupsType & groups, const std::string & name,
	const std::string & new_name) {
	auto it = groups.find(name);
	if (it == groups.end()) {
	AKANTU_EXCEPTION("There are no group named "
	<< name << " associated to the group manager: " << id);
	}

	auto && group_ptr = std::move(it->second);

	group_ptr->name = new_name;

	groups.erase(it);
	groups[new_name] = std::move(group_ptr);
	}

	/* -------------------------------------------------------------------------- */
	void GroupManager::renameElementGroup(const std::string & name,
	const std::string & new_name) {
	renameGroup(element_groups, name, new_name);
	}

	/* -------------------------------------------------------------------------- */
	void GroupManager::renameNodeGroup(const std::string & name,
	const std::string & new_name) {
	renameGroup(node_groups, name, new_name);
	}

	/* -------------------------------------------------------------------------- */
	void GroupManager::copyElementGroup(const std::string & name,
	const std::string & new_name) {
	const auto & grp = getElementGroup(name);
	auto & new_grp = createElementGroup(new_name, grp.getDimension());

	new_grp.getElements().copy(grp.getElements());
	}

	/* -------------------------------------------------------------------------- */
	void GroupManager::copyNodeGroup(const std::string & name,
	const std::string & new_name) {
	const auto & grp = getNodeGroup(name);
	auto & new_grp = createNodeGroup(new_name);

	new_grp.getNodes().copy(grp.getNodes());
	}

	} // namespace akantu

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