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hydro_mechanic…

fluid_diffusion_model.cc
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			/**
			* @file fluid_diffusion_model.hh
			*
			* @author Emil Gallyamov <emil.gallyamov@epfl.ch>
			*
			* @date creation: Aug 2019
			*
			* @brief Implementation of Transient fluid diffusion model
			*
			* @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 "fluid_diffusion_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.hh"
			#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 fluid_diffusion {
			namespace details {
			class ComputeRhoFunctor {
			public:
			ComputeRhoFunctor(const FluidDiffusionModel & model) : model(model){};

			void operator()(Matrix<Real> & rho, const Element & element) const {
			const auto & type = element.type;
			const auto & gt = element.ghost_type;
			const auto & aperture = model.getApertureOnQpoints(type, gt);
			auto nb_quad_points = aperture.getNbComponent();
			Real aperture_av = 0.;
			for (auto q : arange(nb_quad_points)) {
			aperture_av += aperture(element.element, q);
			}
			aperture_av /= nb_quad_points;
			if (model.isModelVelocityDependent()) {
			rho.set(model.getCompressibility() * aperture_av);
			} else {
			rho.set((model.getCompressibility() + model.getPushability()) *
			aperture_av);
			}
			}

			private:
			const FluidDiffusionModel & model;
			};
			} // namespace details
			} // namespace fluid_diffusion

			/* -------------------------------------------------------------------------- */
			FluidDiffusionModel::FluidDiffusionModel(Mesh & mesh, UInt dim, const ID & id)
			: Model(mesh, ModelType::_fluid_diffusion_model, dim, id),
			pressure_gradient("pressure_gradient", id),
			pressure_on_qpoints("pressure_on_qpoints", id),
			delta_pres_on_qpoints("delta_pres_on_qpoints", id),
			permeability_on_qpoints("permeability_on_qpoints", id),
			aperture_on_qpoints("aperture_on_qpoints", id),
			prev_aperture_on_qpoints("prev_aperture_on_qpoints", id),
			k_gradp_on_qpoints("k_gradp_on_qpoints", id) {
			AKANTU_DEBUG_IN();

			// mesh.registerEventHandler(*this, akantu::_ehp_lowest);

			this->spatial_dimension = std::max(1, int(mesh.getSpatialDimension()) - 1);

			this->initDOFManager();

			this->registerDataAccessor(*this);

			if (this->mesh.isDistributed()) {
			auto & synchronizer = this->mesh.getElementSynchronizer();
			this->registerSynchronizer(synchronizer, SynchronizationTag::_fdm_pressure);
			this->registerSynchronizer(synchronizer,
			SynchronizationTag::_fdm_gradient_pressure);
			}

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

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

			this->registerParam("viscosity", viscosity, 1., _pat_parsmod);
			this->registerParam("compressibility", compressibility, 1., _pat_parsmod);
			this->registerParam("default_aperture", default_aperture, 1.e-5,
			_pat_parsmod);
			this->registerParam("use_aperture_speed", use_aperture_speed, _pat_parsmod);
			this->registerParam("pushability", pushability, 1., _pat_parsmod);
			this->registerParam("insertion_damage", insertion_damage, 0., _pat_parsmod);

			AKANTU_DEBUG_OUT();
			}

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

			pressure_on_qpoints.initialize(fem, _nb_component = 1);
			delta_pres_on_qpoints.initialize(fem, _nb_component = 1);
			pressure_gradient.initialize(fem, _nb_component = 1);
			permeability_on_qpoints.initialize(fem, _nb_component = 1);
			aperture_on_qpoints.initialize(fem, _nb_component = 1);
			if (use_aperture_speed) {
			prev_aperture_on_qpoints.initialize(fem, _nb_component = 1);
			}
			k_gradp_on_qpoints.initialize(fem, _nb_component = 1);

			this->initBC(this, pressure, *external_flux);
			}

			/* -------------------------------------------------------------------------- */
			FEEngine & FluidDiffusionModel::getFEEngineBoundary(const ID & name) {
			return aka::as_type<FEEngine>(getFEEngineClassBoundary<FEEngineType>(name));
			}
			/* -------------------------------------------------------------------------- */
			FluidDiffusionModel::~FluidDiffusionModel() = default;

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

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

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

			AKANTU_DEBUG_OUT();
			}

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

			return _mt_not_defined;
			}

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

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

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

			this->assembleInternalFlux();

			this->getDOFManager().assembleToResidual("pressure", *this->external_flux, 1);
			this->getDOFManager().assembleToResidual("pressure", *this->internal_flux, 1);

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::predictor() { ++pressure_release; }

			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::afterSolveStep(bool converged) {
			AKANTU_DEBUG_IN();

			if (not converged) {
			return;
			}

			++solution_release;
			need_to_reassemble_capacity_lumped = true;
			need_to_reassemble_capacity = true;

			/// interpolating pressures on integration points for further use by BC
			const GhostType gt = _not_ghost;
			for (auto && type : mesh.elementTypes(spatial_dimension, gt, _ek_regular)) {
			Array<Real> tmp(pressure_on_qpoints(type, gt));
			this->getFEEngine().interpolateOnIntegrationPoints(
			*pressure, pressure_on_qpoints(type, gt), 1, type, gt);
			delta_pres_on_qpoints(type, gt) = pressure_on_qpoints(type, gt);
			delta_pres_on_qpoints(type, gt) -= tmp;
			}
			AKANTU_DEBUG_OUT();
			}
			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::assembleCapacityLumped() {
			AKANTU_DEBUG_IN();

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

			this->getDOFManager().getLumpedMatrix("M").zero();

			assembleCapacityLumped(_not_ghost);
			assembleCapacityLumped(_ghost);

			need_to_reassemble_capacity_lumped = false;

			AKANTU_DEBUG_OUT();
			}

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

			this->allocNodalField(this->pressure, 1, "pressure");
			this->allocNodalField(this->external_flux, 1, "external_flux");
			this->allocNodalField(this->internal_flux, 1, "internal_flux");
			this->allocNodalField(this->blocked_dofs, 1, "blocked_dofs");
			// this->allocNodalField(this->aperture, "aperture");

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

			if (time_step_solver_type == TimeStepSolverType::_dynamic \|\|
			time_step_solver_type == TimeStepSolverType::_dynamic_lumped) {
			this->allocNodalField(this->pressure_rate, 1, "pressure_rate");

			if (!dof_manager.hasDOFsDerivatives("pressure", 1)) {
			dof_manager.registerDOFsDerivative("pressure", 1, *this->pressure_rate);
			}
			}
			}
			/* -------------------------------------------------------------------------- */
			std::tuple<ID, TimeStepSolverType>
			FluidDiffusionModel::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 FluidDiffusionModel::getDefaultSolverOptions(
			const TimeStepSolverType & type) const {
			ModelSolverOptions options;

			switch (type) {
			case TimeStepSolverType::_dynamic_lumped: {
			options.non_linear_solver_type = NonLinearSolverType::_lumped;
			options.integration_scheme_type["pressure"] =
			IntegrationSchemeType::_forward_euler;
			options.solution_type["pressure"] = IntegrationScheme::_pressure_rate;
			break;
			}
			case TimeStepSolverType::_static: {
			options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
			options.integration_scheme_type["pressure"] =
			IntegrationSchemeType::_pseudo_time;
			options.solution_type["pressure"] = 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["pressure"] =
			IntegrationSchemeType::_forward_euler;
			options.solution_type["pressure"] = IntegrationScheme::_pressure_rate;
			} else {
			options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
			options.integration_scheme_type["pressure"] =
			IntegrationSchemeType::_backward_euler;
			options.solution_type["pressure"] = IntegrationScheme::_pressure;
			}
			break;
			}
			default:
			AKANTU_EXCEPTION(type << " is not a valid time step solver type");
			}

			return options;
			}

			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::assemblePermeabilityMatrix() {
			AKANTU_DEBUG_IN();

			this->computePermeabilityOnQuadPoints(_not_ghost);
			if (permeability_release[_not_ghost] == permeability_matrix_release) {
			return;
			}

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

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

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::assemblePermeabilityMatrix(
			const GhostType & ghost_type) {
			AKANTU_DEBUG_IN();

			auto & fem = this->getFEEngine();

			for (auto && type :
			mesh.elementTypes(spatial_dimension, ghost_type, _ek_regular)) {
			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(permeability_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", "pressure", *K_e, type, ghost_type, _symmetric);
			}

			permeability_matrix_release = permeability_release[ghost_type];

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::computePermeabilityOnQuadPoints(
			const GhostType & ghost_type) {

			// if already computed once check if need to compute
			if (not initial_permeability[ghost_type]) {
			// if aperture did not change, permeability will not vary
			if (solution_release == permeability_release[ghost_type]) {
			return;
			}
			}

			for (const auto & type :
			mesh.elementTypes(spatial_dimension, ghost_type, _ek_regular)) {

			// auto nb_nodes_per_element = mesh.getNbNodesPerElement(type);
			// auto nb_element = mesh.getNbElement(type);
			// Array<Real> aperture_interpolated(nb_element * nb_nodes_per_element,
			// 1);

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

			auto & perm = permeability_on_qpoints(type, ghost_type);
			auto & aperture = aperture_on_qpoints(type, ghost_type);
			for (auto && tuple : zip(perm, aperture)) {
			auto & k = std::get<0>(tuple);
			auto & aper = std::get<1>(tuple);
			k = aper * aper * aper / (12 * this->viscosity);
			}
			}

			permeability_release[ghost_type] = solution_release;
			initial_permeability[ghost_type] = false;

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::computeKgradP(const GhostType & ghost_type) {
			computePermeabilityOnQuadPoints(ghost_type);

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

			for (auto && values : zip(permeability_on_qpoints(type, ghost_type),
			gradient, k_gradp_on_qpoints(type, ghost_type))) {
			const auto & k = std::get<0>(values);
			const auto & BP = std::get<1>(values);
			auto & k_BP = std::get<2>(values);

			k_BP = k * BP;
			}
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::assembleInternalFlux() {
			AKANTU_DEBUG_IN();

			this->internal_flux->clear();

			this->synchronize(SynchronizationTag::_fdm_pressure);
			auto & fem = this->getFEEngine();

			for (auto ghost_type : ghost_types) {
			// compute k \grad P
			computeKgradP(ghost_type);

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

			auto & k_gradp_on_qpoints_vect = k_gradp_on_qpoints(type, ghost_type);

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

			if (this->use_aperture_speed) {
			auto aper_speed = aperture_on_qpoints(type, ghost_type);
			aper_speed -= prev_aperture_on_qpoints(type, ghost_type);
			aper_speed *= 1 / this->time_step;
			Array<Real> aper_speed_by_shapes(nb_quad_points, nb_nodes_per_element);

			fem.computeNtb(aper_speed, aper_speed_by_shapes, type, ghost_type);
			bt_k_gP += aper_speed_by_shapes;
			}
			UInt nb_elements = mesh.getNbElement(type, ghost_type);
			Array<Real> int_bt_k_gP(nb_elements, nb_nodes_per_element);

			fem.integrate(bt_k_gP, int_bt_k_gP, nb_nodes_per_element, type,
			ghost_type);

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

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

			Real el_size;
			Real min_el_size = std::numeric_limits<Real>::max();
			Real max_aper_on_qpoint = std::numeric_limits<Real>::min();

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

			auto nb_nodes_per_element = mesh.getNbNodesPerElement(type);
			auto & aper = aperture_on_qpoints(type, _not_ghost);
			auto nb_quad_per_element = aper.getNbComponent();
			auto mesh_dim = this->mesh.getSpatialDimension();
			Array<Real> coord(0, nb_nodes_per_element * mesh_dim);
			FEEngine::extractNodalToElementField(mesh, mesh.getNodes(), coord, type,
			_not_ghost);

			for (auto && data : zip(make_view(coord, mesh_dim, nb_nodes_per_element),
			make_view(aper, nb_quad_per_element))) {
			Matrix<Real> & el_coord = std::get<0>(data);
			Vector<Real> & el_aper = std::get<1>(data);
			el_size = getFEEngine().getElementInradius(el_coord, type);
			min_el_size = std::min(min_el_size, el_size);
			max_aper_on_qpoint = std::max(max_aper_on_qpoint, el_aper.norm<L_inf>());
			}

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

			Real min_dt = 2. * min_el_size * min_el_size / 4 * this->compressibility /
			max_aper_on_qpoint / max_aper_on_qpoint;

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

			AKANTU_DEBUG_OUT();

			return min_dt;
			}

			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::setTimeStep(Real dt, const ID & solver_id) {
			Model::setTimeStep(time_step, solver_id);
			this->time_step = dt;
			#if defined(AKANTU_USE_IOHELPER)
			// this->mesh.getDumper("fluid_diffusion").setTimeStep(time_step);
			#endif
			}

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

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

			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::initFullImpl(const ModelOptions & options) {
			readMaterials();
			Model::initFullImpl(options);
			}

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

			this->getDOFManager().getMatrix("M").zero();

			auto & fem = getFEEngineClass<FEEngineType>();

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

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

			need_to_reassemble_capacity = false;

			AKANTU_DEBUG_OUT();
			}

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

			rho.copy(aperture_on_qpoints(type, ghost_type));
			if (this->use_aperture_speed) {
			rho *= this->compressibility;
			} else {
			rho *= (this->compressibility + this->pushability);
			}

			AKANTU_DEBUG_OUT();
			} // namespace akantu

			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::onElementsAdded(const Array<Element> & element_list,
			const NewElementsEvent & /event/) {
			AKANTU_DEBUG_IN();
			if (element_list.empty()) {
			return;
			}
			/// TODO had to do this ugly way because the meeting is in 3 days
			// removing it will make the assemble mass matrix fail. jacobians are not
			// updated
			auto & fem = this->getFEEngine();
			fem.initShapeFunctions(_not_ghost);
			fem.initShapeFunctions(_ghost);

			this->resizeFields();

			auto type_fluid =
			*mesh.elementTypes(spatial_dimension, _not_ghost, _ek_regular).begin();
			const auto nb_quad_elem =
			getFEEngine().getNbIntegrationPoints(type_fluid, _not_ghost);
			auto aperture_it =
			make_view(getApertureOnQpoints(type_fluid), nb_quad_elem).begin();

			/// assign default aperture to newly added nodes
			for (auto && element : element_list) {
			auto elem_id = element.element;
			for (auto ip : arange(nb_quad_elem)) {
			aperture_it[elem_id](ip) = this->default_aperture;
			}
			}
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::resizeFields() {

			AKANTU_DEBUG_IN();

			/// elemental fields
			auto & fem = this->getFEEngine();
			pressure_on_qpoints.initialize(fem, _nb_component = 1);
			delta_pres_on_qpoints.initialize(fem, _nb_component = 1);
			pressure_gradient.initialize(fem, _nb_component = 1);
			permeability_on_qpoints.initialize(fem, _nb_component = 1);
			aperture_on_qpoints.initialize(fem, _nb_component = 1);
			if (use_aperture_speed) {
			prev_aperture_on_qpoints.initialize(fem, _nb_component = 1);
			}
			k_gradp_on_qpoints.initialize(fem, _nb_component = 1);

			/// nodal fields
			UInt nb_nodes = mesh.getNbNodes();

			if (pressure != nullptr) {
			pressure->resize(nb_nodes, 0.);
			++solution_release;
			}
			if (external_flux != nullptr) {
			external_flux->resize(nb_nodes, 0.);
			}
			if (internal_flux != nullptr) {
			internal_flux->resize(nb_nodes, 0.);
			}
			if (blocked_dofs != nullptr) {
			blocked_dofs->resize(nb_nodes, false);
			}
			if (pressure_rate != nullptr) {
			pressure_rate->resize(nb_nodes, 0.);
			}
			need_to_reassemble_capacity_lumped = true;
			need_to_reassemble_capacity = true;

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			#if defined(AKANTU_COHESIVE_ELEMENT)
			void FluidDiffusionModel::getApertureOnQpointsFromCohesive(
			const SolidMechanicsModelCohesive & coh_model, bool first_time) {
			AKANTU_DEBUG_IN();

			// get element types
			auto & coh_mesh = coh_model.getMesh();
			const auto dim = coh_mesh.getSpatialDimension();
			const GhostType gt = _not_ghost;
			auto type = *coh_mesh.elementTypes(dim, gt, _ek_regular).begin();
			const ElementType type_facets = Mesh::getFacetType(type);
			const ElementType typecoh = FEEngine::getCohesiveElementType(type_facets);
			// const auto nb_coh_elem = coh_mesh.getNbElement(typecoh);
			const auto nb_quad_coh_elem = coh_model.getFEEngine("CohesiveFEEngine")
			.getNbIntegrationPoints(typecoh, gt);

			auto type_fluid =
			*mesh.elementTypes(spatial_dimension, gt, _ek_regular).begin();
			const auto nb_fluid_elem = mesh.getNbElement(type_fluid);
			const auto nb_quad_elem =
			getFEEngine().getNbIntegrationPoints(type_fluid, gt);
			// AKANTU_DEBUG_ASSERT(nb_quad_coh_elem == nb_quad_elem,
			// "Different number of integration points per cohesive "
			// "and fluid elements");

			// save previous aperture
			if (not first_time and use_aperture_speed) {
			prev_aperture_on_qpoints.copy(aperture_on_qpoints);
			}

			// AKANTU_DEBUG_ASSERT(nb_coh_elem == nb_fluid_elem,
			// "Different number of cohesive and fluid elements");

			auto aperture_it =
			make_view(getApertureOnQpoints(type_fluid), nb_quad_elem).begin();

			/// loop on each segment element
			for (auto && element_nb : arange(nb_fluid_elem)) {
			Element element{type_fluid, element_nb, gt};
			auto global_coh_elem =
			mesh.getElementalData<akantu::Element>("cohesive_elements")(element);
			auto ge = global_coh_elem.element;
			auto le = coh_model.getMaterialLocalNumbering(
			global_coh_elem.type, global_coh_elem.ghost_type)(ge);
			auto model_mat_index = coh_model.getMaterialByElement(
			global_coh_elem.type, global_coh_elem.ghost_type)(ge);
			const auto & material = coh_model.getMaterial(model_mat_index);

			// /// access cohesive material
			// const auto & mat = dynamic_cast<const MaterialCohesive &>(material);
			// const auto & normal_open_norm = mat.getNormalOpeningNorm(typecoh, gt);
			const auto normal_open_norm_it =
			make_view(material.getArray<Real>("normal_opening_norm", typecoh),
			nb_quad_coh_elem)
			.begin();
			if (nb_quad_elem == 1) {
			/// coh el quad points are averaged to assign single opening to flow el
			Real aperture_av = 0.;
			for (UInt ip : arange(nb_quad_coh_elem)) {
			auto normal_open_norm_ip = normal_open_norm_it[le](ip);
			aperture_av += normal_open_norm_ip;
			}
			aperture_av /= nb_quad_coh_elem;
			auto & aperture_ip = aperture_it[ge](0);
			if (aperture_av < this->default_aperture) {
			aperture_ip = this->default_aperture;
			} else {
			aperture_ip = aperture_av;
			}
			} else {
			/// each flow el quad point gets aperture from corresponding coh el qp
			for (UInt ip : arange(nb_quad_coh_elem)) {
			auto normal_open_norm_ip = normal_open_norm_it[le](ip);
			auto & aperture_ip = aperture_it[ge](ip);
			if (normal_open_norm_ip < this->default_aperture) {
			aperture_ip = this->default_aperture;
			} else {
			aperture_ip = normal_open_norm_ip;
			}
			}
			}
			}

			// save previous aperture
			if (first_time && use_aperture_speed) {
			prev_aperture_on_qpoints.copy(aperture_on_qpoints);
			}

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::updateFluidElementsFromCohesive(
			const SolidMechanicsModelCohesive & coh_model) {
			AKANTU_DEBUG_IN();

			// get element types
			auto & coh_mesh = coh_model.getMesh();
			const auto dim = coh_mesh.getSpatialDimension();
			const GhostType gt = _not_ghost;
			auto type = *coh_mesh.elementTypes(dim, gt, _ek_regular).begin();
			const ElementType type_facets = Mesh::getFacetType(type);
			const ElementType typecoh = FEEngine::getCohesiveElementType(type_facets);
			const auto nb_coh_elem = coh_mesh.getNbElement(typecoh);
			const auto nb_quad_coh_elem = coh_model.getFEEngine("CohesiveFEEngine")
			.getNbIntegrationPoints(typecoh, gt);

			auto type_fluid =
			*mesh.elementTypes(spatial_dimension, gt, _ek_regular).begin();
			const auto nb_fluid_elem = mesh.getNbElement(type_fluid);

			// check if there is need to add more fluid elements
			if (nb_coh_elem == nb_fluid_elem) {
			return;
			}

			NewElementsEvent new_facets;
			NewNodesEvent new_nodes;
			NewElementsEvent new_fluid_facets;

			/// loop on each cohesive element and check its damage
			for (auto && coh_el : arange(nb_coh_elem)) {

			// check if this cohesive element is present in fluid mesh
			auto & existing_coh_elements =
			mesh.getData<Element>("cohesive_elements", type_facets, gt);
			Element coh_element = {typecoh, coh_el, gt};
			auto it = existing_coh_elements.find(coh_element);
			if (it != UInt(-1)) {
			continue;
			}

			// check damage at the cohesive element
			// Element element{type_fluid, element_nb, gt};
			auto le = coh_model.getMaterialLocalNumbering(typecoh, gt)(coh_el);
			auto model_mat_index = coh_model.getMaterialByElement(typecoh, gt)(coh_el);
			const auto & material = coh_model.getMaterial(model_mat_index);
			const auto damage_it =
			make_view(material.getArray<Real>("damage", typecoh), nb_quad_coh_elem)
			.begin();
			Real damage_av = 0.;
			for (auto ip : arange(nb_quad_coh_elem)) {
			auto damage_ip = damage_it[le](ip);
			damage_av += damage_ip;
			}
			damage_av /= nb_quad_coh_elem;

			if (damage_av < this->insertion_damage) {
			continue;
			}

			// add fluid element to connectivity and corresponding nodes
			Array<UInt> & nodes_added = new_nodes.getList();
			auto & crack_facets = coh_mesh.getElementGroup("crack_facets");
			auto & nodes = mesh.getNodes();
			auto && coh_nodes = coh_mesh.getNodes();
			auto && coh_conn = coh_mesh.getConnectivity(typecoh, gt);
			Vector<UInt> conn(coh_conn.getNbComponent() / 2);
			auto coh_facet_conn_it = make_view(coh_mesh.getConnectivity(typecoh, gt),
			coh_conn.getNbComponent() / 2)
			.begin();
			auto cohesive_nodes_first_half = coh_facet_conn_it[2 * coh_el];
			for (auto c : akantu::arange(conn.size())) {
			auto coh_node = cohesive_nodes_first_half(c);
			Vector<Real> pos(mesh.getSpatialDimension());
			for (auto && data : enumerate(pos)) {
			std::get<1>(data) = coh_nodes(coh_node, std::get<0>(data));
			}
			auto idx = nodes.find(pos);
			if (idx == UInt(-1)) {
			nodes.push_back(pos);
			conn(c) = nodes.size() - 1;
			nodes_added.push_back(nodes.size() - 1);
			} else {
			conn(c) = idx;
			}
			}
			mesh.getData<Element>("cohesive_elements", type_facets, gt)
			.push_back(coh_element);
			mesh.getConnectivity(type_facets, gt).push_back(conn);
			Element fluid_facet{type_facets,
			mesh.getConnectivity(type_facets, gt).size() - 1, gt};
			new_fluid_facets.getList().push_back(fluid_facet);

			// instantiate connectivity type for this facet type if not yet done
			if (not coh_mesh.getConnectivities().exists(type_facets, gt)) {
			coh_mesh.addConnectivityType(type_facets, gt);
			}

			// add two facets per cohesive element into cohesive mesh
			auto & facet_conn_mesh = coh_mesh.getConnectivity(type_facets, gt);
			for (auto f : akantu::arange(2)) {
			Vector<UInt> coh_nodes_one_side = coh_facet_conn_it[2 * coh_el + f];
			facet_conn_mesh.push_back(coh_nodes_one_side);
			Element new_facet{type_facets, facet_conn_mesh.size() - 1, gt};
			crack_facets.add(new_facet);
			new_facets.getList().push_back(new_facet);
			}
			}
			mesh.sendEvent(new_nodes);
			mesh.sendEvent(new_fluid_facets);
			MeshUtils::fillElementToSubElementsData(coh_mesh);
			coh_mesh.sendEvent(new_facets);

			AKANTU_DEBUG_OUT();
			}

			#endif

			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::applyExternalFluxAtElementGroup(
			const Real & rate, const ElementGroup & source_facets,
			GhostType ghost_type) {
			AKANTU_DEBUG_IN();

			for (auto && type :
			source_facets.elementTypes(spatial_dimension, ghost_type)) {
			const auto & element_ids = source_facets.getElements(type, ghost_type);

			const auto nb_fluid_elem = mesh.getNbElement(type);
			const auto type_size = element_ids.size();
			AKANTU_DEBUG_ASSERT(type_size <= nb_fluid_elem,
			"Number of provided source facets exceeds total number "
			"of flow elements");
			const auto fluid_conn_it =
			make_view(mesh.getConnectivity(type, ghost_type),
			mesh.getConnectivity(type, ghost_type).getNbComponent())
			.begin();
			auto & source = getExternalFlux();
			source.clear();

			/// loop on each element of the group
			for (auto el : element_ids) {
			AKANTU_DEBUG_ASSERT(el <= nb_fluid_elem,
			"Element number in the source facets group exceeds "
			"maximum number of flow elements");

			const Vector<UInt> fluid_conn = fluid_conn_it[el];
			for (const auto & node : fluid_conn) {
			source(node) += rate / (fluid_conn.size() * element_ids.size());
			}
			}
			}
			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			Array<Real> FluidDiffusionModel::getQpointsCoord() {
			AKANTU_DEBUG_IN();

			const auto & nodes_coords = mesh.getNodes();
			const GhostType gt = _not_ghost;
			auto type_fluid =
			*mesh.elementTypes(spatial_dimension, gt, _ek_regular).begin();
			const auto nb_fluid_elem = mesh.getNbElement(type_fluid);
			auto & fem = this->getFEEngine();
			const auto nb_quad_points = fem.getNbIntegrationPoints(type_fluid, gt);

			Array<Real> quad_coords(nb_fluid_elem * nb_quad_points,
			spatial_dimension + 1);
			fem.interpolateOnIntegrationPoints(nodes_coords, quad_coords,
			spatial_dimension + 1, type_fluid, gt);
			AKANTU_DEBUG_OUT();
			return quad_coords;
			}

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

			std::shared_ptr<dumpers::Field> FluidDiffusionModel::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.get();

			auto field = mesh.createNodalField(uint_nodal_fields[field_name], group_name);
			return field;
			}

			/* -------------------------------------------------------------------------- */
			std::shared_ptr<dumpers::Field> FluidDiffusionModel::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["pressure"] = pressure.get();
			real_nodal_fields["pressure_rate"] = pressure_rate.get();
			real_nodal_fields["external_flux"] = external_flux.get();
			real_nodal_fields["internal_flux"] = internal_flux.get();
			// real_nodal_fields["increment"] = increment.get();

			std::shared_ptr<dumpers::Field> field =
			mesh.createNodalField(real_nodal_fields[field_name], group_name);

			return field;
			}

			/* -------------------------------------------------------------------------- */
			std::shared_ptr<dumpers::Field> FluidDiffusionModel::createElementalField(
			const std::string & field_name, const std::string & group_name,
			bool /padding_flag/, UInt /spatial_dimension/,
			ElementKind element_kind) {

			std::shared_ptr<dumpers::Field> field;

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

			field = mesh.createElementalField<Real, dumpers::InternalMaterialField>(
			pressure_gradient, group_name, this->spatial_dimension, element_kind,
			nb_data_per_elem);
			} else if (field_name == "permeability") {
			ElementTypeMap<UInt> nb_data_per_elem =
			this->mesh.getNbDataPerElem(permeability_on_qpoints);

			field = mesh.createElementalField<Real, dumpers::InternalMaterialField>(
			permeability_on_qpoints, group_name, this->spatial_dimension,
			element_kind, nb_data_per_elem);
			} else if (field_name == "aperture") {
			ElementTypeMap<UInt> nb_data_per_elem =
			this->mesh.getNbDataPerElem(aperture_on_qpoints);

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

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

			return field;
			}

			/* -------------------------------------------------------------------------- */
			#else
			/* -------------------------------------------------------------------------- */
			std::shared_ptr<dumpers::Field> FluidDiffusionModel::createElementalField(
			__attribute__((unused)) const std::string & field_name,
			__attribute__((unused)) const std::string & group_name,
			__attribute__((unused)) bool padding_flag,
			__attribute__((unused)) UInt spatial_dimension,
			__attribute__((unused)) ElementKind element_kind) {
			return nullptr;
			}

			/* -------------------------------------------------------------------------- */
			std::shared_ptr<dumpers::Field> FluidDiffusionModel::createNodalFieldBool(
			__attribute__((unused)) const std::string & field_name,
			__attribute__((unused)) const std::string & group_name,
			__attribute__((unused)) bool padding_flag) {
			return nullptr;
			}

			/* -------------------------------------------------------------------------- */
			std::shared_ptr<dumpers::Field> FluidDiffusionModel::createNodalFieldReal(
			__attribute__((unused)) const std::string & field_name,
			__attribute__((unused)) const std::string & group_name,
			__attribute__((unused)) bool padding_flag) {
			return nullptr;
			}
			#endif

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

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

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

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

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

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

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

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

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

			AKANTU_DEBUG_OUT();
			return size;
			}

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

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

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

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

			AKANTU_DEBUG_OUT();
			}

			/* -------------------------------------------------------------------------- */
			inline UInt
			FluidDiffusionModel::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 SynchronizationTag::_fdm_pressure: {
			size += nb_nodes_per_element * sizeof(Real); // pressure
			break;
			}
			case SynchronizationTag::_fdm_gradient_pressure: {
			// pressure gradient
			size += getNbIntegrationPoints(elements) * sizeof(Real);
			size += nb_nodes_per_element * sizeof(Real); // nodal pressures
			break;
			}
			default: {
			AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
			}
			}

			AKANTU_DEBUG_OUT();
			return size;
			}

			/* -------------------------------------------------------------------------- */
			inline void
			FluidDiffusionModel::packData(CommunicationBuffer & buffer,
			const Array<Element> & elements,
			const SynchronizationTag & tag) const {
			switch (tag) {
			case SynchronizationTag::_fdm_pressure: {
			packNodalDataHelper(*pressure, buffer, elements, mesh);
			break;
			}
			case SynchronizationTag::_fdm_gradient_pressure: {
			packElementalDataHelper(pressure_gradient, buffer, elements, true,
			getFEEngine());
			packNodalDataHelper(*pressure, buffer, elements, mesh);
			break;
			}
			default: {
			AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
			}
			}
			}

			/* -------------------------------------------------------------------------- */
			inline void FluidDiffusionModel::unpackData(CommunicationBuffer & buffer,
			const Array<Element> & elements,
			const SynchronizationTag & tag) {
			switch (tag) {
			case SynchronizationTag::_fdm_pressure: {
			unpackNodalDataHelper(*pressure, buffer, elements, mesh);
			break;
			}
			case SynchronizationTag::_fdm_gradient_pressure: {
			unpackElementalDataHelper(pressure_gradient, buffer, elements, true,
			getFEEngine());
			unpackNodalDataHelper(*pressure, buffer, elements, mesh);

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

			/* -------------------------------------------------------------------------- */
			void FluidDiffusionModel::injectIntoFacetsByCoord(const Vector<Real> & position,
			const Real & injection_rate) {
			AKANTU_DEBUG_IN();

			auto dim = mesh.getSpatialDimension();
			const auto gt = _not_ghost;
			const auto & pos = mesh.getNodes();
			const auto pos_it = make_view(pos, dim).begin();
			auto & source = *external_flux;

			Vector<Real> bary_facet(dim);

			Real min_dist = std::numeric_limits<Real>::max();
			Element inj_facet;
			for_each_element(
			mesh,
			[&](auto && facet) {
			mesh.getBarycenter(facet, bary_facet);
			auto dist = std::abs(bary_facet.distance(position));
			if (dist < min_dist) {
			min_dist = dist;
			inj_facet = facet;
			}
			},
			_spatial_dimension = dim - 1);

			auto & facet_conn = mesh.getConnectivity(inj_facet.type, gt);
			auto nb_nodes_per_elem = facet_conn.getNbComponent();
			for (auto node : arange(nb_nodes_per_elem)) {
			source(facet_conn(inj_facet.element, node)) =
			injection_rate / nb_nodes_per_elem;
			}
			AKANTU_DEBUG_OUT();
			}

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

rAKA/src/model/fluid_diffusion/fluid_diffusion_model.cc8770148297befeatures/hydro_mechanic…

fluid_diffusion_model.ccView Options

rAKA/src/model/fluid_diffusion/fluid_diffusion_model.cc
8770148297befeatures/hydro_mechanic…

fluid_diffusion_model.cc
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