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rAKA/src/model/fluid_diffusion/fluid_diffusion_model.cc
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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);
}
/* -------------------------------------------------------------------------- */
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) {
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^t*D*B");
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)) const 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
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