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rAKA/src/mesh/group_manager.cc
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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 << "_nodes");
}
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
Array<UInt>::iterator<Vector<UInt> > pairs_it = total_pairs.begin(2);
Array<UInt>::iterator<Vector<UInt> > pairs_end = total_pairs.end(2);
/// 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);
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__
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