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heat_transfer_model.cc
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			/**
			* @file heat_transfer_model.cc
			*
			* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
			* @author Lucas Frerot <lucas.frerot@epfl.ch>
			* @author Emil Gallyamov <emil.gallyamov@epfl.ch>
			* @author David Simon Kammer <david.kammer@epfl.ch>
			* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
			* @author Nicolas Richart <nicolas.richart@epfl.ch>
			* @author Rui Wang <rui.wang@epfl.ch>
			*
			* @date creation: Sun May 01 2011
			* @date last modification: Tue Feb 20 2018
			*
			* @brief Implementation of HeatTransferModel class
			*
			* @section LICENSE
			*
			* 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 "heat_transfer_model.hh"
			#include "dumpable_inline_impl.hh"
			#include "element_synchronizer.hh"
			#include "fe_engine_template.hh"
			#include "generalized_trapezoidal.hh"
			#include "group_manager_inline_impl.cc"
			#include "integrator_gauss.hh"
			#include "mesh.hh"
			#include "parser.hh"
			#include "shape_lagrange.hh"

			#ifdef AKANTU_USE_IOHELPER
			#include "dumper_element_partition.hh"
			#include "dumper_elemental_field.hh"
			#include "dumper_internal_material_field.hh"
			#include "dumper_iohelper_paraview.hh"
			#endif

			/* -------------------------------------------------------------------------- */
			namespace akantu {

			namespace heat_transfer {
			namespace details {
			class ComputeRhoFunctor {
			public:
			ComputeRhoFunctor(const HeatTransferModel & model) : model(model){};

			void operator()(Matrix<Real> & rho, const Element &) const {
			rho.set(model.getCapacity()*model.getDensity());
			}

			private:
			const HeatTransferModel & model;
			};
			}
			}

			/* -------------------------------------------------------------------------- */
			HeatTransferModel::HeatTransferModel(Mesh & mesh, UInt dim, const ID & id,
			const MemoryID & memory_id)
			: Model(mesh, ModelType::_heat_transfer_model, dim, id, memory_id),
			temperature_gradient("temperature_gradient", id),
			temperature_on_qpoints("temperature_on_qpoints", id),
			conductivity_on_qpoints("conductivity_on_qpoints", id),
			k_gradt_on_qpoints("k_gradt_on_qpoints", id) {
			AKANTU_DEBUG_IN();

			conductivity = Matrix<Real>(this->spatial_dimension, this->spatial_dimension);

			this->initDOFManager();

			this->registerDataAccessor(*this);

			if (this->mesh.isDistributed()) {
			auto & synchronizer = this->mesh.getElementSynchronizer();
			this->registerSynchronizer(synchronizer, _gst_htm_temperature);
			this->registerSynchronizer(synchronizer, _gst_htm_gradient_temperature);
			}

			registerFEEngineObject<FEEngineType>(id + ":fem", mesh, spatial_dimension);

			#ifdef AKANTU_USE_IOHELPER
			this->mesh.registerDumper<DumperParaview>("heat_transfer", id, true);
			this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_regular);
			#endif

			this->registerParam("conductivity", conductivity, _pat_parsmod);
			this->registerParam("conductivity_variation", conductivity_variation, 0.,
			_pat_parsmod);
			this->registerParam("temperature_reference", T_ref, 0., _pat_parsmod);
			this->registerParam("capacity", capacity, _pat_parsmod);
			this->registerParam("density", density, _pat_parsmod);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::initModel() {
			auto & fem = this->getFEEngine();
			fem.initShapeFunctions(_not_ghost);
			fem.initShapeFunctions(_ghost);

			temperature_on_qpoints.initialize(fem, _nb_component = 1);
			temperature_gradient.initialize(fem, _nb_component = spatial_dimension);
			conductivity_on_qpoints.initialize(
			fem, _nb_component = spatial_dimension * spatial_dimension);
			k_gradt_on_qpoints.initialize(fem, _nb_component = spatial_dimension);
			}

			/* -------------------------------------------------------------------------- */
			FEEngine & HeatTransferModel::getFEEngineBoundary(const ID & name) {
			return dynamic_cast<FEEngine &>(getFEEngineClassBoundary<FEEngineType>(name));
			}

			/* -------------------------------------------------------------------------- */
			template <typename T>
			void HeatTransferModel::allocNodalField(Array<T> *& array, const ID & name) {
			if (array == nullptr) {
			UInt nb_nodes = mesh.getNbNodes();
			std::stringstream sstr_disp;
			sstr_disp << id << ":" << name;

			array = &(alloc<T>(sstr_disp.str(), nb_nodes, 1, T()));
			}
			}

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

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::assembleCapacityLumped(const GhostType & ghost_type) {
			AKANTU_DEBUG_IN();

			auto & fem = getFEEngineClass<FEEngineType>();
			heat_transfer::details::ComputeRhoFunctor compute_rho(*this);

			for (auto & type : mesh.elementTypes(spatial_dimension, ghost_type)) {
			fem.assembleFieldLumped(compute_rho, "M", "temperature",
			this->getDOFManager(), type, ghost_type);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			MatrixType HeatTransferModel::getMatrixType(const ID & matrix_id) {
			if (matrix_id == "K" or matrix_id == "M") {
			return _symmetric;
			}

			return _mt_not_defined;
			}

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::assembleMatrix(const ID & matrix_id) {
			if (matrix_id == "K") {
			this->assembleConductivityMatrix();
			} else if (matrix_id == "M" and need_to_reassemble_capacity) {
			this->assembleCapacity();
			}
			}

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::assembleLumpedMatrix(const ID & matrix_id) {
			if (matrix_id == "M" and need_to_reassemble_capacity) {
			this->assembleCapacityLumped();
			}
			}

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::assembleResidual() {
			AKANTU_DEBUG_IN();

			this->assembleInternalHeatRate();

			this->getDOFManager().assembleToResidual("temperature",
			*this->external_heat_rate, 1);
			this->getDOFManager().assembleToResidual("temperature",
			*this->internal_heat_rate, 1);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::predictor() { ++temperature_release; }

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::assembleCapacityLumped() {
			AKANTU_DEBUG_IN();

			if (!this->getDOFManager().hasLumpedMatrix("M")) {
			this->getDOFManager().getNewLumpedMatrix("M");
			}

			this->getDOFManager().clearLumpedMatrix("M");

			assembleCapacityLumped(_not_ghost);
			assembleCapacityLumped(_ghost);

			need_to_reassemble_capacity_lumped = false;

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::initSolver(TimeStepSolverType time_step_solver_type,
			NonLinearSolverType) {
			DOFManager & dof_manager = this->getDOFManager();

			this->allocNodalField(this->temperature, "temperature");
			this->allocNodalField(this->external_heat_rate, "external_heat_rate");
			this->allocNodalField(this->internal_heat_rate, "internal_heat_rate");
			this->allocNodalField(this->blocked_dofs, "blocked_dofs");

			if (!dof_manager.hasDOFs("temperature")) {
			dof_manager.registerDOFs("temperature", *this->temperature, _dst_nodal);
			dof_manager.registerBlockedDOFs("temperature", *this->blocked_dofs);
			}

			if (time_step_solver_type == TimeStepSolverType::_dynamic \|\|
			time_step_solver_type == TimeStepSolverType::_dynamic_lumped) {
			this->allocNodalField(this->temperature_rate, "temperature_rate");

			if (!dof_manager.hasDOFsDerivatives("temperature", 1)) {
			dof_manager.registerDOFsDerivative("temperature", 1,
			*this->temperature_rate);
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			std::tuple<ID, TimeStepSolverType>
			HeatTransferModel::getDefaultSolverID(const AnalysisMethod & method) {
			switch (method) {
			case _explicit_lumped_mass: {
			return std::make_tuple("explicit_lumped", TimeStepSolverType::_dynamic_lumped);
			}
			case _static: {
			return std::make_tuple("static", TimeStepSolverType::_static);
			}
			case _implicit_dynamic: {
			return std::make_tuple("implicit", TimeStepSolverType::_dynamic);
			}
			default:
			return std::make_tuple("unknown", TimeStepSolverType::_not_defined);
			}
			}

			/* -------------------------------------------------------------------------- */
			ModelSolverOptions HeatTransferModel::getDefaultSolverOptions(
			const TimeStepSolverType & type) const {
			ModelSolverOptions options;

			switch (type) {
			case TimeStepSolverType::_dynamic_lumped: {
			options.non_linear_solver_type = NonLinearSolverType::_lumped;
			options.integration_scheme_type["temperature"] = IntegrationSchemeType::_forward_euler;
			options.solution_type["temperature"] = IntegrationScheme::_temperature_rate;
			break;
			}
			case TimeStepSolverType::_static: {
			options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
			options.integration_scheme_type["temperature"] = IntegrationSchemeType::_pseudo_time;
			options.solution_type["temperature"] = IntegrationScheme::_not_defined;
			break;
			}
			case TimeStepSolverType::_dynamic: {
			if (this->method == _explicit_consistent_mass) {
			options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
			options.integration_scheme_type["temperature"] = IntegrationSchemeType::_forward_euler;
			options.solution_type["temperature"] =
			IntegrationScheme::_temperature_rate;
			} else {
			options.non_linear_solver_type = _nls_newton_raphson;
			options.integration_scheme_type["temperature"] = _ist_backward_euler;
			options.solution_type["temperature"] = IntegrationScheme::_temperature;
			}
			break;
			}
			default:
			AKANTU_EXCEPTION(type << " is not a valid time step solver type");
			}

			return options;
			}

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::assembleConductivityMatrix() {
			AKANTU_DEBUG_IN();

			this->computeConductivityOnQuadPoints(_not_ghost);
			if (conductivity_release[_not_ghost] == conductivity_matrix_release)
			return;

			if (!this->getDOFManager().hasMatrix("K")) {
			this->getDOFManager().getNewMatrix("K", getMatrixType("K"));
			}
			this->getDOFManager().clearMatrix("K");

			switch (mesh.getSpatialDimension()) {
			case 1:
			this->assembleConductivityMatrix<1>(_not_ghost);
			break;
			case 2:
			this->assembleConductivityMatrix<2>(_not_ghost);
			break;
			case 3:
			this->assembleConductivityMatrix<3>(_not_ghost);
			break;
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			template <UInt dim>
			void HeatTransferModel::assembleConductivityMatrix(
			const GhostType & ghost_type) {
			AKANTU_DEBUG_IN();

			auto & fem = this->getFEEngine();

			for (auto && type : mesh.elementTypes(spatial_dimension, ghost_type)) {
			auto nb_element = mesh.getNbElement(type, ghost_type);
			auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
			auto nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);

			auto bt_d_b = std::make_unique<Array<Real>>(
			nb_element * nb_quadrature_points,
			nb_nodes_per_element * nb_nodes_per_element, "B^tDB");

			fem.computeBtDB(conductivity_on_qpoints(type, ghost_type), *bt_d_b, 2, type,
			ghost_type);

			/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
			auto K_e = std::make_unique<Array<Real>>(
			nb_element, nb_nodes_per_element * nb_nodes_per_element, "K_e");

			fem.integrate(bt_d_b, K_e, nb_nodes_per_element * nb_nodes_per_element,
			type, ghost_type);

			this->getDOFManager().assembleElementalMatricesToMatrix(
			"K", "temperature", *K_e, type, ghost_type, _symmetric);
			}

			conductivity_matrix_release = conductivity_release[ghost_type];

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::computeConductivityOnQuadPoints(
			const GhostType & ghost_type) {
			// if already computed once check if need to compute
			if (not initial_conductivity[ghost_type]) {
			// if temperature did not change, condictivity will not vary
			if (temperature_release == conductivity_release[ghost_type])
			return;

			// if conductivity_variation is 0 no need to recompute
			if (conductivity_variation == 0.)
			return;
			}

			for (auto & type : mesh.elementTypes(spatial_dimension, ghost_type)) {
			auto & temperature_interpolated = temperature_on_qpoints(type, ghost_type);

			// compute the temperature on quadrature points
			this->getFEEngine().interpolateOnIntegrationPoints(
			*temperature, temperature_interpolated, 1, type, ghost_type);

			auto & cond = conductivity_on_qpoints(type, ghost_type);
			for (auto && tuple :
			zip(make_view(cond, spatial_dimension, spatial_dimension),
			temperature_interpolated)) {
			auto & C = std::get<0>(tuple);
			auto & T = std::get<1>(tuple);
			C = conductivity;

			Matrix<Real> variation(spatial_dimension, spatial_dimension,
			conductivity_variation * (T - T_ref));
			// @TODO: Guillaume are you sure ? why due you compute variation then ?
			C += conductivity_variation;
			}
			}

			conductivity_release[ghost_type] = temperature_release;
			initial_conductivity[ghost_type] = false;

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::computeKgradT(const GhostType & ghost_type) {
			computeConductivityOnQuadPoints(ghost_type);

			for (auto & type : mesh.elementTypes(spatial_dimension, ghost_type)) {
			auto & gradient = temperature_gradient(type, ghost_type);
			this->getFEEngine().gradientOnIntegrationPoints(*temperature, gradient, 1,
			type, ghost_type);

			for (auto && values :
			zip(make_view(conductivity_on_qpoints(type, ghost_type),
			spatial_dimension, spatial_dimension),
			make_view(gradient, spatial_dimension),
			make_view(k_gradt_on_qpoints(type, ghost_type),
			spatial_dimension))) {
			const auto & C = std::get<0>(values);
			const auto & BT = std::get<1>(values);
			auto & k_BT = std::get<2>(values);

			k_BT.mul<false>(C, BT);
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::assembleInternalHeatRate() {
			AKANTU_DEBUG_IN();

			this->internal_heat_rate->clear();

			this->synchronize(_gst_htm_temperature);
			auto & fem = this->getFEEngine();

			for (auto ghost_type : ghost_types) {
			// compute k \grad T
			computeKgradT(ghost_type);

			for (auto type : mesh.elementTypes(spatial_dimension, ghost_type)) {
			UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);

			auto & k_gradt_on_qpoints_vect = k_gradt_on_qpoints(type, ghost_type);

			UInt nb_quad_points = k_gradt_on_qpoints_vect.size();
			Array<Real> bt_k_gT(nb_quad_points, nb_nodes_per_element);
			fem.computeBtD(k_gradt_on_qpoints_vect, bt_k_gT, type, ghost_type);

			UInt nb_elements = mesh.getNbElement(type, ghost_type);
			Array<Real> int_bt_k_gT(nb_elements, nb_nodes_per_element);

			fem.integrate(bt_k_gT, int_bt_k_gT, nb_nodes_per_element, type,
			ghost_type);

			this->getDOFManager().assembleElementalArrayLocalArray(
			int_bt_k_gT, *this->internal_heat_rate, type, ghost_type, -1);
			}
			}
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			Real HeatTransferModel::getStableTimeStep() {
			AKANTU_DEBUG_IN();

			Real el_size;
			Real min_el_size = std::numeric_limits<Real>::max();
			Real conductivitymax = conductivity(0, 0);

			// get the biggest parameter from k11 until k33//
			for (UInt i = 0; i < spatial_dimension; i++)
			for (UInt j = 0; j < spatial_dimension; j++)
			conductivitymax = std::max(conductivity(i, j), conductivitymax);

			for (auto & type : mesh.elementTypes(spatial_dimension, _not_ghost)) {

			UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);

			Array<Real> coord(0, nb_nodes_per_element * spatial_dimension);
			FEEngine::extractNodalToElementField(mesh, mesh.getNodes(), coord, type,
			_not_ghost);

			auto el_coord = coord.begin(spatial_dimension, nb_nodes_per_element);
			UInt nb_element = mesh.getNbElement(type);

			for (UInt el = 0; el < nb_element; ++el, ++el_coord) {
			el_size = getFEEngine().getElementInradius(*el_coord, type);
			min_el_size = std::min(min_el_size, el_size);
			}

			AKANTU_DEBUG_INFO("The minimum element size : "
			<< min_el_size
			<< " and the max conductivity is : " << conductivitymax);
			}

			Real min_dt =
			2. * min_el_size * min_el_size / 4. * density * capacity / conductivitymax;

			mesh.getCommunicator().allReduce(min_dt, SynchronizerOperation::_min);

			AKANTU_DEBUG_OUT();

			return min_dt;
			}
			/* -------------------------------------------------------------------------- */

			void HeatTransferModel::setTimeStep(Real time_step, const ID & solver_id) {
			Model::setTimeStep(time_step, solver_id);

			#if defined(AKANTU_USE_IOHELPER)
			this->mesh.getDumper("heat_transfer").setTimeStep(time_step);
			#endif
			}


			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::readMaterials() {
			auto sect = this->getParserSection();

			if (not std::get<1>(sect)) {
			const auto & section = std::get<0>(sect);
			this->parseSection(section);
			}

			conductivity_on_qpoints.set(conductivity);
			}

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

			readMaterials();
			}

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::assembleCapacity() {
			AKANTU_DEBUG_IN();
			auto ghost_type = _not_ghost;

			this->getDOFManager().clearMatrix("M");

			auto & fem = getFEEngineClass<FEEngineType>();

			heat_transfer::details::ComputeRhoFunctor rho_functor(*this);

			for (auto && type : mesh.elementTypes(spatial_dimension, ghost_type)) {
			fem.assembleFieldMatrix(rho_functor, "M", "temperature",
			this->getDOFManager(), type, ghost_type);
			}

			need_to_reassemble_capacity = false;

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::computeRho(Array<Real> & rho, ElementType type,
			GhostType ghost_type) {
			AKANTU_DEBUG_IN();

			FEEngine & fem = this->getFEEngine();
			UInt nb_element = mesh.getNbElement(type, ghost_type);
			UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);

			rho.resize(nb_element * nb_quadrature_points);
			rho.set(this->capacity);

			// Real * rho_1_val = rho.storage();
			// /// compute @f$ rho @f$ for each nodes of each element
			// for (UInt el = 0; el < nb_element; ++el) {
			// for (UInt n = 0; n < nb_quadrature_points; ++n) {
			// *rho_1_val++ = this->capacity;
			// }
			// }

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			Real HeatTransferModel::computeThermalEnergyByNode() {
			AKANTU_DEBUG_IN();

			Real ethermal = 0.;

			for (auto && pair : enumerate(make_view(
			*internal_heat_rate, internal_heat_rate->getNbComponent()))) {
			auto n = std::get<0>(pair);
			auto & heat_rate = std::get<1>(pair);

			Real heat = 0.;
			bool is_local_node = mesh.isLocalOrMasterNode(n);
			bool count_node = is_local_node;

			for (UInt i = 0; i < heat_rate.size(); ++i) {
			if (count_node)
			heat += heat_rate[i] * time_step;
			}
			ethermal += heat;
			}

			mesh.getCommunicator().allReduce(ethermal, SynchronizerOperation::_sum);

			AKANTU_DEBUG_OUT();
			return ethermal;
			}

			/* -------------------------------------------------------------------------- */
			template <class iterator>
			void HeatTransferModel::getThermalEnergy(
			iterator Eth, Array<Real>::const_iterator<Real> T_it,
			Array<Real>::const_iterator<Real> T_end) const {
			for (; T_it != T_end; ++T_it, ++Eth) {
			Eth = capacity density * *T_it;
			}
			}

			/* -------------------------------------------------------------------------- */
			Real HeatTransferModel::getThermalEnergy(const ElementType & type, UInt index) {
			AKANTU_DEBUG_IN();

			UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
			Vector<Real> Eth_on_quarature_points(nb_quadrature_points);

			auto T_it = this->temperature_on_qpoints(type).begin();
			T_it += index * nb_quadrature_points;

			auto T_end = T_it + nb_quadrature_points;

			getThermalEnergy(Eth_on_quarature_points.storage(), T_it, T_end);

			return getFEEngine().integrate(Eth_on_quarature_points, type, index);
			}

			/* -------------------------------------------------------------------------- */
			Real HeatTransferModel::getThermalEnergy() {
			Real Eth = 0;

			auto & fem = getFEEngine();

			for (auto && type : mesh.elementTypes(spatial_dimension)) {
			auto nb_element = mesh.getNbElement(type, _not_ghost);
			auto nb_quadrature_points = fem.getNbIntegrationPoints(type, _not_ghost);
			Array<Real> Eth_per_quad(nb_element * nb_quadrature_points, 1);

			auto & temperature_interpolated = temperature_on_qpoints(type);

			// compute the temperature on quadrature points
			this->getFEEngine().interpolateOnIntegrationPoints(
			*temperature, temperature_interpolated, 1, type);

			auto T_it = temperature_interpolated.begin();
			auto T_end = temperature_interpolated.end();
			getThermalEnergy(Eth_per_quad.begin(), T_it, T_end);

			Eth += fem.integrate(Eth_per_quad, type);
			}

			return Eth;
			}

			/* -------------------------------------------------------------------------- */
			Real HeatTransferModel::getEnergy(const std::string & id) {
			AKANTU_DEBUG_IN();
			Real energy = 0;

			if (id == "thermal")
			energy = getThermalEnergy();

			// reduction sum over all processors
			mesh.getCommunicator().allReduce(energy, SynchronizerOperation::_sum);

			AKANTU_DEBUG_OUT();
			return energy;
			}

			/* -------------------------------------------------------------------------- */
			Real HeatTransferModel::getEnergy(const std::string & id,
			const ElementType & type, UInt index) {
			AKANTU_DEBUG_IN();

			Real energy = 0.;

			if (id == "thermal")
			energy = getThermalEnergy(type, index);

			AKANTU_DEBUG_OUT();
			return energy;
			}

			/* -------------------------------------------------------------------------- */
			/* -------------------------------------------------------------------------- */
			#ifdef AKANTU_USE_IOHELPER

			dumper::Field * HeatTransferModel::createNodalFieldBool(
			const std::string & field_name, const std::string & group_name,
			__attribute__((unused)) bool padding_flag) {

			std::map<std::string, Array<bool> *> uint_nodal_fields;
			uint_nodal_fields["blocked_dofs"] = blocked_dofs;

			dumper::Field * field = nullptr;
			field = mesh.createNodalField(uint_nodal_fields[field_name], group_name);
			return field;
			}

			/* -------------------------------------------------------------------------- */
			dumper::Field * HeatTransferModel::createNodalFieldReal(
			const std::string & field_name, const std::string & group_name,
			__attribute__((unused)) bool padding_flag) {

			if (field_name == "capacity_lumped"){
			AKANTU_EXCEPTION("Capacity lumped is a nodal field now stored in the DOF manager."
			"Therefore it cannot be used by a dumper anymore");
			}

			std::map<std::string, Array<Real> *> real_nodal_fields;
			real_nodal_fields["temperature"] = temperature;
			real_nodal_fields["temperature_rate"] = temperature_rate;
			real_nodal_fields["external_heat_rate"] = external_heat_rate;
			real_nodal_fields["internal_heat_rate"] = internal_heat_rate;
			real_nodal_fields["increment"] = increment;

			dumper::Field * field =
			mesh.createNodalField(real_nodal_fields[field_name], group_name);

			return field;
			}

			/* -------------------------------------------------------------------------- */
			dumper::Field * HeatTransferModel::createElementalField(
			const std::string & field_name, const std::string & group_name,
			__attribute__((unused)) bool padding_flag,
			__attribute__((unused)) const UInt & spatial_dimension,
			const ElementKind & element_kind) {

			dumper::Field * field = nullptr;

			if (field_name == "partitions")
			field = mesh.createElementalField<UInt, dumper::ElementPartitionField>(
			mesh.getConnectivities(), group_name, this->spatial_dimension,
			element_kind);
			else if (field_name == "temperature_gradient") {
			ElementTypeMap<UInt> nb_data_per_elem =
			this->mesh.getNbDataPerElem(temperature_gradient, element_kind);

			field = mesh.createElementalField<Real, dumper::InternalMaterialField>(
			temperature_gradient, group_name, this->spatial_dimension, element_kind,
			nb_data_per_elem);
			} else if (field_name == "conductivity") {
			ElementTypeMap<UInt> nb_data_per_elem =
			this->mesh.getNbDataPerElem(conductivity_on_qpoints, element_kind);

			field = mesh.createElementalField<Real, dumper::InternalMaterialField>(
			conductivity_on_qpoints, group_name, this->spatial_dimension,
			element_kind, nb_data_per_elem);
			}

			return field;
			}

			/* -------------------------------------------------------------------------- */
			#else
			/* -------------------------------------------------------------------------- */
			dumper::Field * HeatTransferModel::createElementalField(
			__attribute__((unused)) const std::string & field_name,
			__attribute__((unused)) const std::string & group_name,
			__attribute__((unused)) bool padding_flag,
			__attribute__((unused)) const ElementKind & element_kind) {
			return nullptr;
			}

			/* -------------------------------------------------------------------------- */
			dumper::Field * HeatTransferModel::createNodalFieldBool(
			__attribute__((unused)) const std::string & field_name,
			__attribute__((unused)) const std::string & group_name,
			__attribute__((unused)) bool padding_flag) {
			return nullptr;
			}

			/* -------------------------------------------------------------------------- */
			dumper::Field * HeatTransferModel::createNodalFieldReal(
			__attribute__((unused)) const std::string & field_name,
			__attribute__((unused)) const std::string & group_name,
			__attribute__((unused)) bool padding_flag) {
			return nullptr;
			}
			#endif

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::dump(const std::string & dumper_name) {
			mesh.dump(dumper_name);
			}

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::dump(const std::string & dumper_name, UInt step) {
			mesh.dump(dumper_name, step);
			}

			/* ------------------------------------------------------------------------- */
			void HeatTransferModel::dump(const std::string & dumper_name, Real time,
			UInt step) {
			mesh.dump(dumper_name, time, step);
			}

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::dump() { mesh.dump(); }

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::dump(UInt step) { mesh.dump(step); }

			/* -------------------------------------------------------------------------- */
			void HeatTransferModel::dump(Real time, UInt step) { mesh.dump(time, step); }

			/* -------------------------------------------------------------------------- */
			inline UInt HeatTransferModel::getNbData(const Array<UInt> & indexes,
			const SynchronizationTag & tag) const {
			AKANTU_DEBUG_IN();

			UInt size = 0;
			UInt nb_nodes = indexes.size();

			switch (tag) {
			case _gst_htm_temperature: {
			size += nb_nodes * sizeof(Real);
			break;
			}
			default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
			}

			AKANTU_DEBUG_OUT();
			return size;
			}

			/* -------------------------------------------------------------------------- */
			inline void HeatTransferModel::packData(CommunicationBuffer & buffer,
			const Array<UInt> & indexes,
			const SynchronizationTag & tag) const {
			AKANTU_DEBUG_IN();

			for (auto index : indexes) {
			switch (tag) {
			case _gst_htm_temperature: {
			buffer << (*temperature)(index);
			break;
			}
			default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
			}
			}
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			inline void HeatTransferModel::unpackData(CommunicationBuffer & buffer,
			const Array<UInt> & indexes,
			const SynchronizationTag & tag) {
			AKANTU_DEBUG_IN();

			for (auto index : indexes) {
			switch (tag) {
			case _gst_htm_temperature: {
			buffer >> (*temperature)(index);
			break;
			}
			default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			inline UInt HeatTransferModel::getNbData(const Array<Element> & elements,
			const SynchronizationTag & tag) const {
			AKANTU_DEBUG_IN();

			UInt size = 0;
			UInt nb_nodes_per_element = 0;
			Array<Element>::const_iterator<Element> it = elements.begin();
			Array<Element>::const_iterator<Element> end = elements.end();
			for (; it != end; ++it) {
			const Element & el = *it;
			nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
			}

			switch (tag) {
			case _gst_htm_temperature: {
			size += nb_nodes_per_element * sizeof(Real); // temperature
			break;
			}
			case _gst_htm_gradient_temperature: {
			// temperature gradient
			size += getNbIntegrationPoints(elements) * spatial_dimension * sizeof(Real);
			size += nb_nodes_per_element * sizeof(Real); // nodal temperatures
			break;
			}
			default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
			}

			AKANTU_DEBUG_OUT();
			return size;
			}

			/* -------------------------------------------------------------------------- */
			inline void HeatTransferModel::packData(CommunicationBuffer & buffer,
			const Array<Element> & elements,
			const SynchronizationTag & tag) const {
			switch (tag) {
			case _gst_htm_temperature: {
			packNodalDataHelper(*temperature, buffer, elements, mesh);
			break;
			}
			case _gst_htm_gradient_temperature: {
			packElementalDataHelper(temperature_gradient, buffer, elements, true,
			getFEEngine());
			packNodalDataHelper(*temperature, buffer, elements, mesh);
			break;
			}
			default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
			}
			}

			/* -------------------------------------------------------------------------- */
			inline void HeatTransferModel::unpackData(CommunicationBuffer & buffer,
			const Array<Element> & elements,
			const SynchronizationTag & tag) {
			switch (tag) {
			case _gst_htm_temperature: {
			unpackNodalDataHelper(*temperature, buffer, elements, mesh);
			break;
			}
			case _gst_htm_gradient_temperature: {
			unpackElementalDataHelper(temperature_gradient, buffer, elements, true,
			getFEEngine());
			unpackNodalDataHelper(*temperature, buffer, elements, mesh);

			break;
			}
			default: { AKANTU_ERROR("Unknown ghost synchronization tag : " << tag); }
			}
			}

			/* -------------------------------------------------------------------------- */
			} // akantu

rAKA/src/model/heat_transfer/heat_transfer_model.cc08b1837389c4features/issue-template

heat_transfer_model.ccView Options

rAKA/src/model/heat_transfer/heat_transfer_model.cc
08b1837389c4features/issue-template

heat_transfer_model.cc
View Options