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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 creation: Fri Apr 13 2012
			* @date last modification: Tue Jan 16 2018
			*
			* @brief Implementation of non-local manager
			*
			*
			* Copyright (©) 2010-2018 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 "non_local_manager.hh"
			#include "grid_synchronizer.hh"
			#include "model.hh"
			#include "non_local_neighborhood.hh"
			/* -------------------------------------------------------------------------- */
			#include <numeric>
			/* -------------------------------------------------------------------------- */

			namespace akantu {

			/* -------------------------------------------------------------------------- */
			NonLocalManager::NonLocalManager(Model & model,
			NonLocalManagerCallback & callback,
			const ID & id)
			: Parsable(ParserType::_neighborhoods, id),
			spatial_dimension(model.getMesh().getSpatialDimension()), id(id), model(model),
			integration_points_positions("integration_points_positions", id),
			volumes("volumes", id), compute_stress_calls(0),
			dummy_registry(nullptr), dummy_grid(nullptr) {
			/// 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(ParserType::_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->callback = &callback;
			}

			/* -------------------------------------------------------------------------- */
			NonLocalManager::~NonLocalManager() = default;

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::initialize() {
			volumes.initialize(this->model.getFEEngine(),
			_spatial_dimension = spatial_dimension);

			AKANTU_DEBUG_ASSERT(this->callback,
			"A callback should be registered prior to this call");
			this->callback->insertIntegrationPointsInNeighborhoods(_not_ghost);

			auto & mesh = this->model.getMesh();
			mesh.registerEventHandler(*this, _ehp_non_local_manager);

			/// store the number of current ghost elements for each type in the mesh
			// ElementTypeMap<UInt> nb_ghost_protected;
			// for (auto type : mesh.elementTypes(spatial_dimension, _ghost))
			// nb_ghost_protected(mesh.getNbElement(type, _ghost), type, _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
			this->callback->insertIntegrationPointsInNeighborhoods(_ghost);

			FEEngine & fee = this->model.getFEEngine();
			this->updatePairLists();

			/// cleanup the unneccessary ghost elements
			this->cleanupExtraGhostElements(); // nb_ghost_protected);

			this->callback->initializeNonLocal();

			this->setJacobians(fee, _ek_regular);

			this->initNonLocalVariables();
			this->computeWeights();
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::setJacobians(const FEEngine & fe_engine,
			ElementKind kind) {
			Mesh & mesh = this->model.getMesh();
			for (auto ghost_type : ghost_types) {
			for (auto type : mesh.elementTypes(spatial_dimension, ghost_type, kind)) {
			jacobians(type, ghost_type) =
			&fe_engine.getIntegratorInterface().getJacobians(type, ghost_type);
			}
			}
			}

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

			AKANTU_DEBUG_IN();

			auto weight_func_it = this->weight_function_types.find(weight_func);
			AKANTU_DEBUG_ASSERT(weight_func_it != weight_function_types.end(),
			"No info found in the input file for the weight_function "
			<< weight_func << " in the neighborhood "
			<< neighborhood_id);

			const ParserSection & section = weight_func_it->second;
			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] =
			std::make_unique<NonLocalNeighborhood<BaseWeightFunction>>(
			*this, this->integration_points_positions, sstr.str());
			#if defined(AKANTU_DAMAGE_NON_LOCAL)
			} else if (weight_func_type == "remove_wf") {
			neighborhoods[neighborhood_id] =
			std::make_unique<NonLocalNeighborhood<RemoveDamagedWeightFunction>>(
			*this, this->integration_points_positions, sstr.str());
			} else if (weight_func_type == "stress_wf") {
			neighborhoods[neighborhood_id] =
			std::make_unique<NonLocalNeighborhood<StressBasedWeightFunction>>(
			*this, this->integration_points_positions, sstr.str());
			} else if (weight_func_type == "damage_wf") {
			neighborhoods[neighborhood_id] =
			std::make_unique<NonLocalNeighborhood<DamagedWeightFunction>>(
			*this, this->integration_points_positions, sstr.str());
			#endif
			} 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
			const Communicator & static_communicator = model.getMesh().getCommunicator();
			static_communicator.allReduce(max_id_size, SynchronizerOperation::_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);

			/// 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, buffer_size);

			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,
			std::numeric_limits<Real>::max());
			Vector<Real> spacing(this->spatial_dimension, 0.);

			dummy_grid = std::make_unique<SpatialGrid<IntegrationPoint>>(
			this->spatial_dimension, spacing, grid_center);

			for (const auto & neighborhood_id : global_neighborhoods) {
			it = neighborhoods.find(neighborhood_id);
			if (it != neighborhoods.end()) {
			it->second->createGridSynchronizer();
			} else {
			dummy_synchronizers[neighborhood_id] = std::make_unique<GridSynchronizer>(
			this->model.getMesh(), *dummy_grid,
			std::string(this->id + ":" + neighborhood_id + ":grid_synchronizer"),
			false);
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::synchronize(DataAccessor<Element> & data_accessor,
			const SynchronizationTag & tag) {
			for (const auto & neighborhood_id : global_neighborhoods) {
			auto it = neighborhoods.find(neighborhood_id);
			if (it != neighborhoods.end()) {
			it->second->synchronize(data_accessor, tag);
			} else {
			auto synchronizer_it = dummy_synchronizers.find(neighborhood_id);
			if (synchronizer_it == dummy_synchronizers.end()) {
			continue;
			}

			synchronizer_it->second->synchronizeOnce(data_accessor, tag);
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::averageInternals(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
			for (auto & neighborhood : neighborhoods) {
			/// loop over all the non-local variables of the given neighborhood
			for (auto & non_local_variable : non_local_variables) {
			NonLocalVariable & non_local_var = *non_local_variable.second;
			neighborhood.second->weightedAverageOnNeighbours(
			non_local_var.local, non_local_var.non_local,
			non_local_var.nb_component, ghost_type);
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::computeWeights() {
			AKANTU_DEBUG_IN();

			this->updateWeightFunctionInternals();
			this->volumes.zero();

			for (const auto & global_neighborhood : global_neighborhoods) {
			auto it = neighborhoods.find(global_neighborhood);

			if (it != neighborhoods.end()) {
			it->second->updateWeights();
			} else {
			dummy_synchronizers[global_neighborhood]->synchronize(
			dummy_accessor, SynchronizationTag::_mnl_weight);
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::updatePairLists() {
			AKANTU_DEBUG_IN();

			integration_points_positions.initialize(
			this->model.getFEEngine(), _nb_component = spatial_dimension,
			_spatial_dimension = spatial_dimension);

			/// compute the position of the quadrature points
			this->model.getFEEngine().computeIntegrationPointsCoordinates(
			integration_points_positions);

			for (auto & pair : neighborhoods) {
			pair.second->updatePairList();
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::registerNonLocalVariable(const ID & variable_name,
			const ID & nl_variable_name,
			UInt nb_component) {

			AKANTU_DEBUG_IN();

			auto non_local_variable_it = non_local_variables.find(variable_name);

			if (non_local_variable_it == non_local_variables.end()) {
			non_local_variables[nl_variable_name] = std::make_unique<NonLocalVariable>(
			variable_name, nl_variable_name, this->id, nb_component);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			ElementTypeMapReal &
			NonLocalManager::registerWeightFunctionInternal(const ID & field_name) {

			AKANTU_DEBUG_IN();

			auto it = this->weight_function_internals.find(field_name);
			if (it == weight_function_internals.end()) {
			weight_function_internals[field_name] =
			std::make_unique<ElementTypeMapReal>(field_name, this->id);
			}

			AKANTU_DEBUG_OUT();

			return *(weight_function_internals[field_name]);
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::updateWeightFunctionInternals() {
			for (auto & pair : this->weight_function_internals) {
			auto & internals = *pair.second;
			internals.zero();
			for (auto ghost_type : ghost_types) {
			this->callback->updateLocalInternal(internals, ghost_type, _ek_regular);
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::initNonLocalVariables() {
			/// loop over all the non-local variables
			for (auto & pair : non_local_variables) {
			auto & variable = *pair.second;
			variable.non_local.initialize(this->model.getFEEngine(),
			_nb_component = variable.nb_component,
			_spatial_dimension = spatial_dimension);
			}
			}

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

			/// update the flattened version of the internals
			for (auto & pair : non_local_variables) {
			auto & variable = *pair.second;
			variable.local.zero();
			variable.non_local.zero();
			for (auto ghost_type : ghost_types) {
			this->callback->updateLocalInternal(variable.local, ghost_type,
			_ek_regular);
			}
			}

			this->volumes.zero();

			for (auto & pair : neighborhoods) {
			auto & neighborhood = *pair.second;
			neighborhood.asynchronousSynchronize(SynchronizationTag::_mnl_for_average);
			}

			this->averageInternals(_not_ghost);

			AKANTU_DEBUG_INFO("Wait distant non local stresses");

			for (auto & pair : neighborhoods) {
			auto & neighborhood = *pair.second;
			neighborhood.waitEndSynchronize(SynchronizationTag::_mnl_for_average);
			}

			this->averageInternals(_ghost);

			/// copy the results in the materials
			for (auto & pair : non_local_variables) {
			auto & variable = *pair.second;
			for (auto ghost_type : ghost_types) {
			this->callback->updateNonLocalInternal(variable.non_local, ghost_type,
			_ek_regular);
			}
			}

			this->callback->computeNonLocalStresses(_not_ghost);

			++this->compute_stress_calls;
			}

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

			using ElementSet = std::set<Element>;
			ElementSet relevant_ghost_elements;

			/// loop over all the neighborhoods and get their protected ghosts
			for (auto & pair : neighborhoods) {
			auto & neighborhood = *pair.second;
			ElementSet to_keep_per_neighborhood;

			neighborhood.getRelevantGhostElements(to_keep_per_neighborhood);
			relevant_ghost_elements.insert(to_keep_per_neighborhood.begin(),
			to_keep_per_neighborhood.end());
			}

			for (auto & pair : neighborhoods) {
			auto & neighborhood = *pair.second;
			neighborhood.cleanupExtraGhostElements(relevant_ghost_elements);
			}

			// /// 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;

			// RemovedElementsEvent remove_elem(mesh);
			// auto & new_numberings = remove_elem.getNewNumbering();
			// Element element;
			// element.ghost_type = _ghost;

			// for (auto & type : mesh.elementTypes(spatial_dimension, _ghost)) {
			// element.type = type;
			// UInt nb_ghost_elem = mesh.getNbElement(type, _ghost);
			// // UInt nb_ghost_elem_protected = 0;
			// // try {
			// // nb_ghost_elem_protected = nb_ghost_protected(type, _ghost);
			// // } catch (...) {
			// // }

			// if (!new_numberings.exists(type, _ghost))
			// new_numberings.alloc(nb_ghost_elem, 1, type, _ghost);
			// else
			// new_numberings(type, _ghost).resize(nb_ghost_elem);

			// Array<UInt> & new_numbering = new_numberings(type, _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;
			// }
			// }
			// }

			// for (auto & type : mesh.elementTypes(spatial_dimension, _not_ghost)) {
			// UInt nb_elem = mesh.getNbElement(type, _not_ghost);
			// if (!new_numberings.exists(type, _not_ghost))
			// new_numberings.alloc(nb_elem, 1, type, _not_ghost);
			// Array<UInt> & new_numbering = new_numberings(type, _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();
			NonLocalManager::removeIntegrationPointsFromMap(
			event.getNewNumbering(), spatial_dimension, integration_points_positions,
			fee, _ek_regular);
			NonLocalManager::removeIntegrationPointsFromMap(event.getNewNumbering(), 1,
			volumes, fee, _ek_regular);

			/// loop over all the neighborhoods and call onElementsRemoved
			auto 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(const Array<Element> & /unused/,
			const NewElementsEvent & /unused/) {
			this->resizeElementTypeMap(1, volumes, model.getFEEngine());
			this->resizeElementTypeMap(spatial_dimension, integration_points_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 (auto gt : ghost_types) {
			for (auto type : mesh.elementTypes(spatial_dimension, gt, el_kind)) {
			UInt nb_element = mesh.getNbElement(type, gt);
			UInt nb_quads = fee.getNbIntegrationPoints(type, gt);
			if (!element_map.exists(type, gt)) {
			element_map.alloc(nb_element * nb_quads, nb_component, type, gt);
			} else {
			element_map(type, 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 (auto gt : ghost_types) {
			for (auto type : new_numbering.elementTypes(_all_dimensions, gt, el_kind)) {
			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.size() * nb_quad_per_elem, nb_component);

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

			UInt new_size = 0;
			for (UInt i = 0; i < renumbering.size(); ++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);
			}
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			UInt NonLocalManager::getNbData(const Array<Element> & elements,
			const ID & id) const {
			UInt size = 0;
			UInt nb_quadrature_points = this->model.getNbIntegrationPoints(elements);
			auto it = non_local_variables.find(id);

			AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
			"The non-local variable " << id << " is not registered");

			size += it->second->nb_component * sizeof(Real) * nb_quadrature_points;
			return size;
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::packData(CommunicationBuffer & buffer,
			const Array<Element> & elements,
			const ID & id) const {

			auto it = non_local_variables.find(id);

			AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
			"The non-local variable " << id << " is not registered");

			DataAccessor<Element>::packElementalDataHelper<Real>(
			it->second->local, buffer, elements, true, this->model.getFEEngine());
			}

			/* -------------------------------------------------------------------------- */
			void NonLocalManager::unpackData(CommunicationBuffer & buffer,
			const Array<Element> & elements,
			const ID & id) const {
			auto it = non_local_variables.find(id);

			AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
			"The non-local variable " << id << " is not registered");

			DataAccessor<Element>::unpackElementalDataHelper<Real>(
			it->second->local, buffer, elements, true, this->model.getFEEngine());
			}

			} // namespace akantu

rAKA/src/model/common/non_local_toolbox/non_local_manager.ccba9e2713a380features/28-getelementi…

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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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