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model.cc
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			/**
			* @file model.cc
			*
			* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
			* @author David Simon Kammer <david.kammer@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			*
			* @date creation: Mon Oct 03 2011
			* @date last modification: Thu Nov 19 2015
			*
			* @brief implementation of model common parts
			*
			* @section LICENSE
			*
			* Copyright (©) 2010-2012, 2014, 2015 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 "model.hh"
			#include "communicator.hh"
			#include "data_accessor.hh"
			#include "element_group.hh"
			#include "element_synchronizer.hh"
			#include "synchronizer_registry.hh"
			/* -------------------------------------------------------------------------- */

			namespace akantu {

			/* -------------------------------------------------------------------------- */
			Model::Model(Mesh & mesh, UInt dim, const ID & id, const MemoryID & memory_id)
			: Memory(id, memory_id), ModelSolver(mesh, id, memory_id), mesh(mesh),
			spatial_dimension(dim == _all_dimensions ? mesh.getSpatialDimension()
			: dim),
			is_pbc_slave_node(0, 1, "is_pbc_slave_node"), parser(getStaticParser()) {
			AKANTU_DEBUG_IN();

			this->mesh.registerEventHandler(*this, _ehp_model);

			AKANTU_DEBUG_OUT();
			}

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

			/* -------------------------------------------------------------------------- */
			// void Model::setParser(Parser & parser) { this->parser = &parser; }

			/* -------------------------------------------------------------------------- */
			void Model::initFullImpl(const ModelOptions & options) {
			AKANTU_DEBUG_IN();

			method = options.analysis_method;
			if (!this->hasDefaultSolver()) {
			this->initNewSolver(this->method);
			}
			initModel();

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void Model::initNewSolver(const AnalysisMethod & method) {
			ID solver_name;
			TimeStepSolverType tss_type;
			std::tie(solver_name, tss_type) = this->getDefaultSolverID(method);

			if (not this->hasSolver(solver_name)) {
			ModelSolverOptions options = this->getDefaultSolverOptions(tss_type);
			this->getNewSolver(solver_name, tss_type, options.non_linear_solver_type);

			for(auto && is_type : options.integration_scheme_type) {
			if (!this->hasIntegrationScheme(solver_name, is_type.first)) {
			this->setIntegrationScheme(solver_name, is_type.first, is_type.second,
			options.solution_type[is_type.first]);
			}
			}
			}

			this->method = method;
			this->setDefaultSolver(solver_name);
			}

			/* -------------------------------------------------------------------------- */
			void Model::initPBC() {
			auto it = pbc_pair.begin();
			auto end = pbc_pair.end();

			is_pbc_slave_node.resize(mesh.getNbNodes());
			#ifndef AKANTU_NDEBUG
			Array<Real>::const_vector_iterator coord_it =
			mesh.getNodes().begin(this->spatial_dimension);
			#endif

			while (it != end) {
			UInt i1 = (*it).first;

			is_pbc_slave_node(i1) = true;

			#ifndef AKANTU_NDEBUG
			UInt i2 = (*it).second;
			UInt slave = mesh.isDistributed() ? mesh.getGlobalNodesIds()(i1) : i1;
			UInt master = mesh.isDistributed() ? mesh.getGlobalNodesIds()(i2) : i2;

			AKANTU_DEBUG_INFO("pairing " << slave << " (" << Vector<Real>(coord_it[i1])
			<< ") with " << master << " ("
			<< Vector<Real>(coord_it[i2]) << ")");
			#endif
			++it;
			}
			}

			/* -------------------------------------------------------------------------- */
			void Model::dumpGroup(const std::string & group_name) {
			ElementGroup & group = mesh.getElementGroup(group_name);
			group.dump();
			}

			/* -------------------------------------------------------------------------- */
			void Model::dumpGroup(const std::string & group_name,
			const std::string & dumper_name) {
			ElementGroup & group = mesh.getElementGroup(group_name);
			group.dump(dumper_name);
			}

			/* -------------------------------------------------------------------------- */
			void Model::dumpGroup() {
			auto bit = mesh.element_group_begin();
			auto bend = mesh.element_group_end();
			for (; bit != bend; ++bit) {
			bit->second->dump();
			}
			}

			/* -------------------------------------------------------------------------- */
			void Model::setGroupDirectory(const std::string & directory) {
			auto bit = mesh.element_group_begin();
			auto bend = mesh.element_group_end();
			for (; bit != bend; ++bit) {
			bit->second->setDirectory(directory);
			}
			}

			/* -------------------------------------------------------------------------- */
			void Model::setGroupDirectory(const std::string & directory,
			const std::string & group_name) {
			ElementGroup & group = mesh.getElementGroup(group_name);
			group.setDirectory(directory);
			}

			/* -------------------------------------------------------------------------- */
			void Model::setGroupBaseName(const std::string & basename,
			const std::string & group_name) {
			ElementGroup & group = mesh.getElementGroup(group_name);
			group.setBaseName(basename);
			}

			/* -------------------------------------------------------------------------- */
			DumperIOHelper & Model::getGroupDumper(const std::string & group_name) {
			ElementGroup & group = mesh.getElementGroup(group_name);
			return group.getDumper();
			}

			/* -------------------------------------------------------------------------- */
			// DUMPER stuff
			/* -------------------------------------------------------------------------- */
			void Model::addDumpGroupFieldToDumper(const std::string & field_id,
			dumper::Field * field,
			DumperIOHelper & dumper) {
			#ifdef AKANTU_USE_IOHELPER
			dumper.registerField(field_id, field);
			#endif
			}

			/* -------------------------------------------------------------------------- */
			void Model::addDumpField(const std::string & field_id) {

			this->addDumpFieldToDumper(mesh.getDefaultDumperName(), field_id);
			}
			/* -------------------------------------------------------------------------- */

			void Model::addDumpFieldVector(const std::string & field_id) {

			this->addDumpFieldVectorToDumper(mesh.getDefaultDumperName(), field_id);
			}

			/* -------------------------------------------------------------------------- */
			void Model::addDumpFieldTensor(const std::string & field_id) {

			this->addDumpFieldTensorToDumper(mesh.getDefaultDumperName(), field_id);
			}

			/* -------------------------------------------------------------------------- */

			void Model::setBaseName(const std::string & field_id) {

			mesh.setBaseName(field_id);
			}
			/* -------------------------------------------------------------------------- */

			void Model::setBaseNameToDumper(const std::string & dumper_name,
			const std::string & basename) {
			mesh.setBaseNameToDumper(dumper_name, basename);
			}
			/* -------------------------------------------------------------------------- */

			void Model::addDumpFieldToDumper(const std::string & dumper_name,
			const std::string & field_id) {

			this->addDumpGroupFieldToDumper(dumper_name, field_id, "all", _ek_regular,
			false);
			}

			/* -------------------------------------------------------------------------- */
			void Model::addDumpGroupField(const std::string & field_id,
			const std::string & group_name) {

			ElementGroup & group = mesh.getElementGroup(group_name);
			this->addDumpGroupFieldToDumper(group.getDefaultDumperName(), field_id,
			group_name, _ek_regular, false);
			}

			/* -------------------------------------------------------------------------- */
			void Model::removeDumpGroupField(const std::string & field_id,
			const std::string & group_name) {
			ElementGroup & group = mesh.getElementGroup(group_name);
			this->removeDumpGroupFieldFromDumper(group.getDefaultDumperName(), field_id,
			group_name);
			}

			/* -------------------------------------------------------------------------- */
			void Model::removeDumpGroupFieldFromDumper(const std::string & dumper_name,
			const std::string & field_id,
			const std::string & group_name) {
			ElementGroup & group = mesh.getElementGroup(group_name);
			group.removeDumpFieldFromDumper(dumper_name, field_id);
			}

			/* -------------------------------------------------------------------------- */
			void Model::addDumpFieldVectorToDumper(const std::string & dumper_name,
			const std::string & field_id) {
			this->addDumpGroupFieldToDumper(dumper_name, field_id, "all", _ek_regular,
			true);
			}

			/* -------------------------------------------------------------------------- */
			void Model::addDumpGroupFieldVector(const std::string & field_id,
			const std::string & group_name) {
			ElementGroup & group = mesh.getElementGroup(group_name);
			this->addDumpGroupFieldVectorToDumper(group.getDefaultDumperName(), field_id,
			group_name);
			}

			/* -------------------------------------------------------------------------- */
			void Model::addDumpGroupFieldVectorToDumper(const std::string & dumper_name,
			const std::string & field_id,
			const std::string & group_name) {
			this->addDumpGroupFieldToDumper(dumper_name, field_id, group_name,
			_ek_regular, true);
			}
			/* -------------------------------------------------------------------------- */

			void Model::addDumpFieldTensorToDumper(const std::string & dumper_name,
			const std::string & field_id) {
			this->addDumpGroupFieldToDumper(dumper_name, field_id, "all", _ek_regular,
			true);
			}

			/* -------------------------------------------------------------------------- */
			void Model::addDumpGroupFieldToDumper(const std::string & dumper_name,
			const std::string & field_id,
			const std::string & group_name,
			const ElementKind & element_kind,
			bool padding_flag) {
			this->addDumpGroupFieldToDumper(dumper_name, field_id, group_name,
			this->spatial_dimension, element_kind,
			padding_flag);
			}

			/* -------------------------------------------------------------------------- */
			void Model::addDumpGroupFieldToDumper(const std::string & dumper_name,
			const std::string & field_id,
			const std::string & group_name,
			UInt spatial_dimension,
			const ElementKind & element_kind,
			bool padding_flag) {

			#ifdef AKANTU_USE_IOHELPER
			dumper::Field * field = nullptr;

			if (!field)
			field = this->createNodalFieldReal(field_id, group_name, padding_flag);
			if (!field)
			field = this->createNodalFieldUInt(field_id, group_name, padding_flag);
			if (!field)
			field = this->createNodalFieldBool(field_id, group_name, padding_flag);
			if (!field)
			field = this->createElementalField(field_id, group_name, padding_flag,
			spatial_dimension, element_kind);
			if (!field)
			field = this->mesh.createFieldFromAttachedData<UInt>(field_id, group_name,
			element_kind);
			if (!field)
			field = this->mesh.createFieldFromAttachedData<Real>(field_id, group_name,
			element_kind);

			if (!field)
			AKANTU_DEBUG_WARNING("No field could be found based on name: " << field_id);
			if (field) {
			DumperIOHelper & dumper = mesh.getGroupDumper(dumper_name, group_name);
			this->addDumpGroupFieldToDumper(field_id, field, dumper);
			}

			#endif
			}

			/* -------------------------------------------------------------------------- */

			void Model::dump() { mesh.dump(); }

			/* -------------------------------------------------------------------------- */

			void Model::setDirectory(const std::string & directory) {
			mesh.setDirectory(directory);
			}

			/* -------------------------------------------------------------------------- */

			void Model::setDirectoryToDumper(const std::string & dumper_name,
			const std::string & directory) {
			mesh.setDirectoryToDumper(dumper_name, directory);
			}

			/* -------------------------------------------------------------------------- */

			void Model::setTextModeToDumper() { mesh.setTextModeToDumper(); }

			/* -------------------------------------------------------------------------- */

			} // namespace akantu

rAKA/src/model/model.cc1aa85b4c82dabugfixes/39-the-python…

model.ccView Options

rAKA/src/model/model.cc
1aa85b4c82dabugfixes/39-the-python…

model.cc
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