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non_local_manager.cc
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			/**
			* @file non_local_manager.cc
			* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			* @date Mon Sep 21 15:32:10 2015
			*
			* @brief Implementation of non-local manager
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2011 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 "non_local_manager.hh"
			#include "non_local_neighborhood.hh"
			#include "material_non_local.hh"
			#include "base_weight_function.hh"
			/* -------------------------------------------------------------------------- */
			__BEGIN_AKANTU__

			/* -------------------------------------------------------------------------- */
			NonLocalManager::NonLocalManager(SolidMechanicsModel & model,
			const ID & id,
			const MemoryID & memory_id) :
			Memory(id, memory_id),
			Parsable(_st_neighborhoods, id),
			model(model),
			quad_positions("quad_positions", id),
			volumes("volumes", id),
			spatial_dimension(this->model.getSpatialDimension()),
			compute_stress_calls(0),
			dummy_registry(NULL),
			dummy_grid(NULL) {
			Mesh & mesh = this->model.getMesh();
			mesh.registerEventHandler(*this);

			/// initialize the element type map array
			/// it will be resized to nb_quad * nb_element during the computation of coords
			mesh.initElementTypeMapArray(quad_positions, spatial_dimension, spatial_dimension, false, _ek_regular, true);
			this->initElementTypeMap(1, volumes, this->model.getFEEngine());

			/// parse the neighborhood information from the input file
			const Parser & parser = getStaticParser();

			/// iterate over all the non-local sections and store them in a map
			std::pair<Parser::const_section_iterator, Parser::const_section_iterator>
			weight_sect = parser.getSubSections(_st_non_local);
			Parser::const_section_iterator it = weight_sect.first;
			for (; it != weight_sect.second; ++it) {
			const ParserSection & section = *it;
			ID name = section.getName();
			this->weight_function_types[name] = section;
			}

			this->dummy_registry = new SynchronizerRegistry(this->dummy_accessor);
			}

			/* -------------------------------------------------------------------------- */
			NonLocalManager::~NonLocalManager() {

			/// delete neighborhoods
			NeighborhoodMap::iterator it;
			for (it = neighborhoods.begin(); it != neighborhoods.end(); ++it) {
			if(it->second) delete it->second;
			}

			/// delete non-local variables
			std::map<ID, NonLocalVariable *>::iterator it_variables;
			for (it_variables = non_local_variables.begin(); it_variables != non_local_variables.end(); ++it_variables) {
			if(it_variables->second) delete it_variables->second;
			}

			std::map<ID, ElementTypeMapReal *>::iterator it_internals;
			for (it_internals = weight_function_internals.begin(); it_internals != weight_function_internals.end(); ++it_internals) {
			if(it_internals->second) delete it_internals->second;
			}

			std::map<ID, GridSynchronizer * >::iterator grid_synch_it;
			for (grid_synch_it = dummy_synchronizers.begin(); grid_synch_it != dummy_synchronizers.end(); ++grid_synch_it) {
			if(grid_synch_it->second) delete grid_synch_it->second;
			}
			/// delete all objects related to the dummy synchronizers
			delete dummy_registry;
			delete dummy_grid;
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::setJacobians(const FEEngine & fe_engine, const ElementKind & kind) {
			Mesh & mesh = this->model.getMesh();
			for(UInt g = _not_ghost; g <= _ghost; ++g) {
			GhostType gt = (GhostType) g;
			Mesh::type_iterator it = mesh.firstType(spatial_dimension, gt, kind);
			Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, gt, kind);
			for(; it != last_type; ++it) {
			jacobians(it, gt) = &fe_engine.getIntegratorInterface().getJacobians(it, gt);
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::createNeighborhood(const ID & weight_func, const ID & neighborhood_id) {

			AKANTU_DEBUG_IN();


			const ParserSection & section = this->weight_function_types[weight_func];
			const ID weight_func_type = section.getOption();
			/// create new neighborhood for given ID
			std::stringstream sstr; sstr << id << ":neighborhood:" << neighborhood_id;

			if (weight_func_type == "base_wf")
			neighborhoods[neighborhood_id] = new NonLocalNeighborhood<BaseWeightFunction>(*this, this->quad_positions, sstr.str());
			else if (weight_func_type == "remove_wf")
			neighborhoods[neighborhood_id] = new NonLocalNeighborhood<RemoveDamagedWeightFunction>(*this, this->quad_positions, sstr.str());
			else if (weight_func_type == "stress_wf")
			neighborhoods[neighborhood_id] = new NonLocalNeighborhood<StressBasedWeightFunction>(*this, this->quad_positions, sstr.str());
			else if (weight_func_type == "damage_wf")
			neighborhoods[neighborhood_id] = new NonLocalNeighborhood<DamagedWeightFunction>(*this, this->quad_positions, sstr.str());
			else
			AKANTU_EXCEPTION("error in weight function type provided in material file");

			neighborhoods[neighborhood_id]->parseSection(section);
			neighborhoods[neighborhood_id]->initNeighborhood();

			AKANTU_DEBUG_OUT();

			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::createNeighborhoodSynchronizers() {
			/// exchange all the neighborhood IDs, so that every proc knows how many neighborhoods exist globally
			/// First: Compute locally the maximum ID size
			UInt max_id_size = 0;
			UInt current_size = 0;
			NeighborhoodMap::const_iterator it;
			for (it = neighborhoods.begin(); it != neighborhoods.end(); ++it) {
			current_size = it->first.size();
			if (current_size > max_id_size)
			max_id_size = current_size;
			}

			/// get the global maximum ID size on each proc
			StaticCommunicator & static_communicator = akantu::StaticCommunicator::getStaticCommunicator();
			static_communicator.allReduce(&max_id_size, 1, _so_max);

			/// get the rank for this proc and the total nb proc
			UInt prank = static_communicator.whoAmI();
			UInt psize = static_communicator.getNbProc();

			/// exchange the number of neighborhoods on each proc
			Array<Int> nb_neighborhoods_per_proc(psize);
			nb_neighborhoods_per_proc(prank) = neighborhoods.size();
			static_communicator.allGather(nb_neighborhoods_per_proc.storage(), 1);

			/// compute the total number of neighborhoods
			UInt nb_neighborhoods_global = std::accumulate(nb_neighborhoods_per_proc.begin(),
			nb_neighborhoods_per_proc.end(), 0);

			/// allocate an array of chars to store the names of all neighborhoods
			Array<char> buffer(nb_neighborhoods_global, max_id_size);

			/// starting index on this proc
			UInt starting_index = std::accumulate(nb_neighborhoods_per_proc.begin(),
			nb_neighborhoods_per_proc.begin() + prank, 0);


			it = neighborhoods.begin();
			/// store the names of local neighborhoods in the buffer
			for (UInt i = 0; i < neighborhoods.size(); ++i, ++it) {
			UInt c = 0;
			for (; c < it->first.size(); ++c)
			buffer(i + starting_index, c) = it->first[c];

			for (; c < max_id_size; ++c)
			buffer(i + starting_index, c) = char( 0 );
			}

			/// store the nb of data to send in the all gather
			Array<Int> buffer_size(nb_neighborhoods_per_proc);
			buffer_size *= max_id_size;
			/// exchange the names of all the neighborhoods with all procs
			static_communicator.allGatherV(buffer.storage(), buffer_size.storage());



			for (UInt i = 0; i < nb_neighborhoods_global; ++i) {
			std::stringstream neighborhood_id;
			for(UInt c = 0; c < max_id_size; ++c) {
			if (buffer(i,c) == char( 0 )) break;
			neighborhood_id << buffer(i,c);
			}
			global_neighborhoods.insert(neighborhood_id.str());
			}



			/// this proc does not know all the neighborhoods -> create dummy
			/// grid so that this proc can participate in the all gather for
			/// detecting the overlap of neighborhoods this proc doesn't know
			Vector<Real> grid_center(this->spatial_dimension);
			for(UInt s = 0; s < this->spatial_dimension; ++s)
			grid_center(s) = std::numeric_limits<Real>::max();
			dummy_grid = new SpatialGrid<IntegrationPoint>(spatial_dimension, 0., grid_center);
			std::set<SynchronizationTag> tags;
			tags.insert(_gst_mnl_for_average);
			tags.insert(_gst_mnl_weight);


			std::set<ID>::const_iterator global_neighborhoods_it = global_neighborhoods.begin();
			for (; global_neighborhoods_it != global_neighborhoods.end(); ++global_neighborhoods_it) {
			it = neighborhoods.find(*global_neighborhoods_it);
			if (it != neighborhoods.end()) {
			it->second->createGridSynchronizer();
			}
			else {
			ID neighborhood_name = *global_neighborhoods_it;
			std::stringstream sstr; sstr << getID() << ":" << neighborhood_name << ":grid_synchronizer";
			dummy_synchronizers[neighborhood_name] = GridSynchronizer::createGridSynchronizer(this->model.getMesh(),
			*dummy_grid,
			sstr.str(),
			dummy_registry,
			tags, 0, false);
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::flattenInternal(ElementTypeMapReal & internal_flat,
			const GhostType & ghost_type,
			const ElementKind & kind) {

			const ID field_name = internal_flat.getName();
			for (UInt m = 0; m < this->non_local_materials.size(); ++m) {
			Material & material = *(this->non_local_materials[m]);
			if (material.isInternal<Real>(field_name, kind))
			material.flattenInternal(field_name, internal_flat, ghost_type, kind);
			}
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::averageInternals(const GhostType & ghost_type) {
			/// update the weights of the weight function
			if (ghost_type == _not_ghost)
			this->computeWeights();

			/// loop over all neighborhoods and compute the non-local variables
			NeighborhoodMap::iterator neighborhood_it = neighborhoods.begin();
			NeighborhoodMap::iterator neighborhood_end = neighborhoods.end();
			for (; neighborhood_it != neighborhood_end; ++neighborhood_it) {
			/// loop over all the non-local variables of the given neighborhood
			std::map<ID, NonLocalVariable *>::iterator non_local_variable_it = non_local_variables.begin();
			std::map<ID, NonLocalVariable *>::iterator non_local_variable_end = non_local_variables.end();
			for(; non_local_variable_it != non_local_variable_end; ++non_local_variable_it) {
			NonLocalVariable * non_local_var = non_local_variable_it->second;
			neighborhood_it->second->weightedAverageOnNeighbours(non_local_var->local, non_local_var->non_local, non_local_var->nb_component, ghost_type);

			}
			}

			if (ghost_type == _ghost) {
			/// compute the non-local stresses in the materials
			for(UInt m = 0; m < this->non_local_materials.size(); ++m) {
			switch (spatial_dimension) {
			case 1:
			dynamic_cast<MaterialNonLocal<1> &>(*(this->non_local_materials[m])).computeNonLocalStresses(_not_ghost);
			break;
			case 2:
			dynamic_cast<MaterialNonLocal<2> &>(*(this->non_local_materials[m])).computeNonLocalStresses(_not_ghost);
			break;
			case 3:
			dynamic_cast<MaterialNonLocal<3> &>(*(this->non_local_materials[m])).computeNonLocalStresses(_not_ghost);
			break;
			}
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::init(){

			/// store the number of current ghost elements for each type in the mesh
			ElementTypeMap<UInt> nb_ghost_protected;
			Mesh & mesh = this->model.getMesh();
			Mesh::type_iterator it = mesh.firstType(spatial_dimension, _ghost);
			Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, _ghost);
			for(; it != last_type; ++it)
			nb_ghost_protected(mesh.getNbElement(it, _ghost), it, _ghost);

			/// exchange the missing ghosts for the non-local neighborhoods
			this->createNeighborhoodSynchronizers();

			/// insert the ghost quadrature points of the non-local materials into the non-local neighborhoods
			for(UInt m = 0; m < this->non_local_materials.size(); ++m) {
			switch (spatial_dimension) {
			case 1:
			dynamic_cast<MaterialNonLocal<1> &>(*(this->non_local_materials[m])).insertQuadsInNeighborhoods(_ghost);
			break;
			case 2:
			dynamic_cast<MaterialNonLocal<2> &>(*(this->non_local_materials[m])).insertQuadsInNeighborhoods(_ghost);
			break;
			case 3:
			dynamic_cast<MaterialNonLocal<3> &>(*(this->non_local_materials[m])).insertQuadsInNeighborhoods(_ghost);
			break;
			}

			}

			FEEngine & fee = this->model.getFEEngine();
			this->updatePairLists();
			/// cleanup the unneccessary ghost elements
			this->cleanupExtraGhostElements(nb_ghost_protected);
			this->setJacobians(fee, _ek_regular);
			this->initNonLocalVariables();
			this->computeWeights();
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::initNonLocalVariables(){
			/// loop over all the non-local variables
			std::map<ID, NonLocalVariable *>::iterator non_local_variable_it = non_local_variables.begin();
			std::map<ID, NonLocalVariable *>::iterator non_local_variable_end = non_local_variables.end();

			for(; non_local_variable_it != non_local_variable_end; ++non_local_variable_it) {
			NonLocalVariable & variable = *(non_local_variable_it->second);
			this->initElementTypeMap(variable.nb_component, variable.non_local, this->model.getFEEngine());
			}
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::initElementTypeMap(UInt nb_component, ElementTypeMapReal & element_map,
			const FEEngine & fee, const ElementKind el_kind) {
			Mesh & mesh = this->model.getMesh();
			/// need to resize the arrays
			for(UInt g = _not_ghost; g <= _ghost; ++g) {
			GhostType gt = (GhostType) g;
			Mesh::type_iterator it = mesh.firstType(spatial_dimension, gt, el_kind);
			Mesh::type_iterator end = mesh.lastType(spatial_dimension, gt, el_kind);
			for(; it != end; ++it) {
			ElementType el_type = *it;
			UInt nb_element = mesh.getNbElement(*it, gt);
			UInt nb_quads = fee.getNbIntegrationPoints(*it, gt);
			if (!element_map.exists(el_type, gt)) {
			element_map.alloc(nb_element * nb_quads,
			nb_component,
			el_type,
			gt);
			}
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::distributeInternals(ElementKind kind) {

			/// loop over all the non-local variables and copy back their values into the materials
			std::map<ID, NonLocalVariable *>::iterator non_local_variable_it = non_local_variables.begin();
			std::map<ID, NonLocalVariable *>::iterator non_local_variable_end = non_local_variables.end();
			for(; non_local_variable_it != non_local_variable_end; ++non_local_variable_it) {
			NonLocalVariable * non_local_var = non_local_variable_it->second;
			const ID field_name = non_local_var->non_local.getName();
			/// loop over all the materials
			for (UInt m = 0; m < this->non_local_materials.size(); ++m) {
			if (this->non_local_materials[m]->isInternal<Real>(field_name, kind))

			switch (spatial_dimension) {
			case 1:
			dynamic_cast<MaterialNonLocal<1> &>(*(this->non_local_materials[m])).updateNonLocalInternals(non_local_var->non_local, field_name, non_local_var->nb_component);
			break;
			case 2:
			dynamic_cast<MaterialNonLocal<2> &>(*(this->non_local_materials[m])).updateNonLocalInternals(non_local_var->non_local, field_name, non_local_var->nb_component);
			break;
			case 3:
			dynamic_cast<MaterialNonLocal<3> &>(*(this->non_local_materials[m])).updateNonLocalInternals(non_local_var->non_local, field_name, non_local_var->nb_component);
			break;
			}
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::computeAllNonLocalStresses() {

			/// update the flattened version of the internals
			std::map<ID, NonLocalVariable *>::iterator non_local_variable_it = non_local_variables.begin();
			std::map<ID, NonLocalVariable *>::iterator non_local_variable_end = non_local_variables.end();

			for(; non_local_variable_it != non_local_variable_end; ++non_local_variable_it) {
			non_local_variable_it->second->local.clear();
			non_local_variable_it->second->non_local.clear();
			for(UInt gt = _not_ghost; gt <= _ghost; ++gt) {
			GhostType ghost_type = (GhostType) gt;
			this->flattenInternal(non_local_variable_it->second->local, ghost_type, _ek_regular);
			}
			}

			this->volumes.clear();
			///loop over all the neighborhoods and compute intiate the
			/// exchange of the non-local_variables
			// std::set<ID>::const_iterator global_neighborhood_it = global_neighborhoods.begin();
			// NeighborhoodMap::iterator it;
			// for(; global_neighborhood_it != global_neighborhoods.end(); ++global_neighborhood_it) {
			// it = neighborhoods.find(*global_neighborhood_it);
			// if (it != neighborhoods.end())
			// it->second->getSynchronizerRegistry().asynchronousSynchronize(_gst_mnl_for_average);
			// else
			// dummy_synchronizers[*global_neighborhood_it]->asynchronousSynchronize(dummy_accessor, _gst_mnl_for_average);
			// }

			NeighborhoodMap::iterator neighborhood_it = neighborhoods.begin();
			//NeighborhoodMap::iterator neighborhood_end = neighborhoods.end();

			for(; neighborhood_it != neighborhoods.end(); ++neighborhood_it) {
			neighborhood_it->second->getSynchronizerRegistry().asynchronousSynchronize(_gst_mnl_for_average);
			}

			this->averageInternals(_not_ghost);

			AKANTU_DEBUG_INFO("Wait distant non local stresses");

			/// loop over all the neighborhoods and block until all non-local
			/// variables have been exchanged
			// global_neighborhood_it = global_neighborhoods.begin();
			// for(; global_neighborhood_it != global_neighborhoods.end(); ++global_neighborhood_it) {
			// it = neighborhoods.find(*global_neighborhood_it);
			// if (it != neighborhoods.end())
			// it->second->getSynchronizerRegistry().waitEndSynchronize(_gst_mnl_for_average);
			// else
			// dummy_synchronizers[*global_neighborhood_it]->waitEndSynchronize(dummy_accessor, _gst_mnl_for_average);
			// }

			neighborhood_it = neighborhoods.begin();
			for(; neighborhood_it != neighborhoods.end(); ++neighborhood_it) {
			neighborhood_it->second->getSynchronizerRegistry().waitEndSynchronize(_gst_mnl_for_average);
			}


			this->averageInternals(_ghost);

			/// copy the results in the materials
			this->distributeInternals(_ek_regular);
			/// loop over all the materials and update the weights
			for (UInt m = 0; m < this->non_local_materials.size(); ++m) {
			switch (spatial_dimension) {
			case 1:
			dynamic_cast<MaterialNonLocal<1> &>(*(this->non_local_materials[m])).computeNonLocalStresses(_not_ghost); break;
			case 2:
			dynamic_cast<MaterialNonLocal<2> &>(*(this->non_local_materials[m])).computeNonLocalStresses(_not_ghost); break;
			case 3:
			dynamic_cast<MaterialNonLocal<3> &>(*(this->non_local_materials[m])).computeNonLocalStresses(_not_ghost); break;
			}
			}

			++this->compute_stress_calls;
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::cleanupExtraGhostElements(ElementTypeMap<UInt> & nb_ghost_protected) {

			typedef std::set<Element> ElementSet;
			ElementSet relevant_ghost_elements;
			ElementSet to_keep_per_neighborhood;
			/// loop over all the neighborhoods and get their protected ghosts
			NeighborhoodMap::iterator neighborhood_it = neighborhoods.begin();
			NeighborhoodMap::iterator neighborhood_end = neighborhoods.end();
			for (; neighborhood_it != neighborhood_end; ++neighborhood_it) {
			neighborhood_it->second->cleanupExtraGhostElements(to_keep_per_neighborhood);
			ElementSet::const_iterator it = to_keep_per_neighborhood.begin();
			for(; it != to_keep_per_neighborhood.end(); ++it)
			relevant_ghost_elements.insert(*it);
			to_keep_per_neighborhood.clear();
			}

			/// remove all unneccessary ghosts from the mesh
			/// Create list of element to remove and new numbering for element to keep
			Mesh & mesh = this->model.getMesh();
			ElementSet ghost_to_erase;

			Mesh::type_iterator it = mesh.firstType(spatial_dimension, _ghost);
			Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, _ghost);

			RemovedElementsEvent remove_elem(mesh);
			Element element;
			element.ghost_type = _ghost;

			for(; it != last_type; ++it) {
			element.type = *it;
			UInt nb_ghost_elem = mesh.getNbElement(*it, _ghost);
			UInt nb_ghost_elem_protected = 0;
			try {
			nb_ghost_elem_protected = nb_ghost_protected(*it, _ghost);
			} catch (...) {}

			if(!remove_elem.getNewNumbering().exists(*it, _ghost))
			remove_elem.getNewNumbering().alloc(nb_ghost_elem, 1, *it, _ghost);
			else remove_elem.getNewNumbering(*it, _ghost).resize(nb_ghost_elem);
			Array<UInt> & new_numbering = remove_elem.getNewNumbering(*it, _ghost);
			for (UInt g = 0; g < nb_ghost_elem; ++g) {
			element.element = g;
			if (element.element >= nb_ghost_elem_protected &&
			relevant_ghost_elements.find(element) == relevant_ghost_elements.end()) {
			remove_elem.getList().push_back(element);
			new_numbering(element.element) = UInt(-1);
			}
			}
			/// renumber remaining ghosts
			UInt ng = 0;
			for (UInt g = 0; g < nb_ghost_elem; ++g) {
			if (new_numbering(g) != UInt(-1)) {
			new_numbering(g) = ng;
			++ng;
			}
			}
			}


			it = mesh.firstType(spatial_dimension, _not_ghost);
			last_type = mesh.lastType(spatial_dimension, _not_ghost);
			for(; it != last_type; ++it) {
			UInt nb_elem = mesh.getNbElement(*it, _not_ghost);
			if(!remove_elem.getNewNumbering().exists(*it, _not_ghost))
			remove_elem.getNewNumbering().alloc(nb_elem, 1, *it, _not_ghost);
			Array<UInt> & new_numbering = remove_elem.getNewNumbering(*it, _not_ghost);
			for (UInt e = 0; e < nb_elem; ++e) {
			new_numbering(e) = e;
			}
			}
			mesh.sendEvent(remove_elem);
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::onElementsRemoved(const Array<Element> & element_list,
			const ElementTypeMapArray<UInt> & new_numbering,
			__attribute__((unused)) const RemovedElementsEvent & event) {

			FEEngine & fee = this->model.getFEEngine();
			this->removeIntegrationPointsFromMap(event.getNewNumbering(), spatial_dimension, quad_positions, fee, _ek_regular);
			this->removeIntegrationPointsFromMap(event.getNewNumbering(), 1, volumes, fee, _ek_regular);

			/// loop over all the neighborhoods and call onElementsRemoved
			std::set<ID>::const_iterator global_neighborhood_it = global_neighborhoods.begin();
			NeighborhoodMap::iterator it;
			for(; global_neighborhood_it != global_neighborhoods.end(); ++global_neighborhood_it) {
			it = neighborhoods.find(*global_neighborhood_it);
			if (it != neighborhoods.end())
			it->second->onElementsRemoved(element_list, new_numbering, event);
			else
			dummy_synchronizers[*global_neighborhood_it]->onElementsRemoved(element_list, new_numbering, event);
			}
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::onElementsAdded(__attribute__((unused)) const Array<Element> & element_list,
			__attribute__((unused)) const NewElementsEvent & event) {
			this->resizeElementTypeMap(1, volumes, model.getFEEngine());
			this->resizeElementTypeMap(spatial_dimension, quad_positions, model.getFEEngine());

			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::resizeElementTypeMap(UInt nb_component, ElementTypeMapReal & element_map,
			const FEEngine & fee, const ElementKind el_kind) {
			Mesh & mesh = this->model.getMesh();
			for(UInt g = _not_ghost; g <= _ghost; ++g) {
			GhostType gt = (GhostType) g;
			Mesh::type_iterator it = mesh.firstType(spatial_dimension, gt, el_kind);
			Mesh::type_iterator end = mesh.lastType(spatial_dimension, gt, el_kind);
			for(; it != end; ++it) {
			UInt nb_element = mesh.getNbElement(*it, gt);
			UInt nb_quads = fee.getNbIntegrationPoints(*it, gt);
			if(!element_map.exists(*it, gt))
			element_map.alloc(nb_element * nb_quads, nb_component, *it, gt);
			else
			element_map(it, gt).resize(nb_element nb_quads);
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::removeIntegrationPointsFromMap(const ElementTypeMapArray<UInt> & new_numbering,
			UInt nb_component, ElementTypeMapReal & element_map,
			const FEEngine & fee, const ElementKind el_kind) {

			for(UInt g = _not_ghost; g <= _ghost; ++g) {
			GhostType gt = (GhostType) g;
			ElementTypeMapArray<UInt>::type_iterator it = new_numbering.firstType(_all_dimensions, gt, el_kind);
			ElementTypeMapArray<UInt>::type_iterator end = new_numbering.lastType(_all_dimensions, gt, el_kind);
			for (; it != end; ++it) {
			ElementType type = *it;
			if(element_map.exists(type, gt)){
			const Array<UInt> & renumbering = new_numbering(type, gt);

			Array<Real> & vect = element_map(type, gt);

			UInt nb_quad_per_elem = fee.getNbIntegrationPoints(type, gt);

			Array<Real> tmp(renumbering.getSize()*nb_quad_per_elem, nb_component);

			AKANTU_DEBUG_ASSERT(tmp.getSize() == vect.getSize(), "Something strange append some mater was created from nowhere!!");

			AKANTU_DEBUG_ASSERT(tmp.getSize() == vect.getSize(), "Something strange append some mater was created or disappeared in "<< vect.getID() << "("<< vect.getSize() <<"!=" << tmp.getSize() <<") ""!!");

			UInt new_size = 0;
			for (UInt i = 0; i < renumbering.getSize(); ++i) {
			UInt new_i = renumbering(i);
			if(new_i != UInt(-1)) {
			memcpy(tmp.storage() + new_i * nb_component * nb_quad_per_elem,
			vect.storage() + i * nb_component * nb_quad_per_elem,
			nb_component * nb_quad_per_elem * sizeof(Real));
			++new_size;
			}
			}
			tmp.resize(new_size * nb_quad_per_elem);
			vect.copy(tmp);
			}
			}
			}
			}


			__END_AKANTU__

rAKA/src/model/common/non_local_toolbox/non_local_manager.cc686ac09f1c08bugfixes/python_interfa…

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rAKA/src/model/common/non_local_toolbox/non_local_manager.cc
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non_local_manager.cc
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