CreateComponentTransportProcess.cpp
/**
* \file
* \copyright
* Copyright (c) 2012-2021, OpenGeoSys Community (http://www.opengeosys.org)
* Distributed under a Modified BSD License.
* See accompanying file LICENSE.txt or
* http://www.opengeosys.org/project/license
*
*/
#include "CreateComponentTransportProcess.h"
#include "ChemistryLib/ChemicalSolverInterface.h"
#include "MaterialLib/MPL/CreateMaterialSpatialDistributionMap.h"
#include "MeshLib/IO/readMeshFromFile.h"
#include "ProcessLib/Output/CreateSecondaryVariables.h"
#include "ProcessLib/SurfaceFlux/SurfaceFluxData.h"
#include "ProcessLib/Utils/ProcessUtils.h"
#include "ComponentTransportProcess.h"
#include "ComponentTransportProcessData.h"
namespace ProcessLib
{
namespace ComponentTransport
{
void checkMPLProperties(
MeshLib::Mesh const& mesh,
MaterialPropertyLib::MaterialSpatialDistributionMap const& media_map)
{
std::array const required_properties_medium = {
MaterialPropertyLib::PropertyType::porosity,
MaterialPropertyLib::PropertyType::transversal_dispersivity,
MaterialPropertyLib::PropertyType::longitudinal_dispersivity,
MaterialPropertyLib::PropertyType::permeability};
std::array const required_properties_liquid_phase = {
MaterialPropertyLib::PropertyType::density,
MaterialPropertyLib::PropertyType::viscosity};
std::array const required_properties_components = {
MaterialPropertyLib::PropertyType::retardation_factor,
MaterialPropertyLib::PropertyType::decay_rate,
MaterialPropertyLib::PropertyType::pore_diffusion};
for (auto const& element : mesh.getElements())
{
auto const element_id = element->getID();
auto const& medium = *media_map.getMedium(element_id);
checkRequiredProperties(medium, required_properties_medium);
// check if liquid phase definition and the corresponding properties
// exist
auto const& liquid_phase = medium.phase("AqueousLiquid");
checkRequiredProperties(liquid_phase, required_properties_liquid_phase);
// check if components and the corresponding properties exist
auto const number_of_components = liquid_phase.numberOfComponents();
for (std::size_t component_id = 0; component_id < number_of_components;
++component_id)
{
if (!liquid_phase.hasComponent(component_id))
{
OGS_FATAL(
"The component {:d} in the AqueousLiquid phase isn't "
"specified.",
component_id);
}
auto const& component = liquid_phase.component(component_id);
checkRequiredProperties(component, required_properties_components);
}
}
}
std::unique_ptr<Process> createComponentTransportProcess(
std::string name,
MeshLib::Mesh& mesh,
std::unique_ptr<ProcessLib::AbstractJacobianAssembler>&& jacobian_assembler,
std::vector<ProcessVariable> const& variables,
std::vector<std::unique_ptr<ParameterLib::ParameterBase>> const& parameters,
unsigned const integration_order,
BaseLib::ConfigTree const& config,
std::vector<std::unique_ptr<MeshLib::Mesh>> const& meshes,
std::map<int, std::shared_ptr<MaterialPropertyLib::Medium>> const& media,
std::unique_ptr<ChemistryLib::ChemicalSolverInterface>&&
chemical_solver_interface)
{
//! \ogs_file_param{prj__processes__process__type}
config.checkConfigParameter("type", "ComponentTransport");
DBUG("Create ComponentTransportProcess.");
auto const coupling_scheme =
//! \ogs_file_param{prj__processes__process__ComponentTransport__coupling_scheme}
config.getConfigParameter<std::string>("coupling_scheme",
"monolithic_scheme");
const bool use_monolithic_scheme = (coupling_scheme != "staggered");
// Process variable.
//! \ogs_file_param{prj__processes__process__ComponentTransport__process_variables}
auto const pv_config = config.getConfigSubtree("process_variables");
std::vector<std::vector<std::reference_wrapper<ProcessVariable>>>
process_variables;
// Collect all process variables in a vector before allocation
// pressure first, concentration then
auto const collected_process_variables = findProcessVariables(
variables, pv_config,
{//! \ogs_file_param_special{prj__processes__process__ComponentTransport__process_variables__pressure}
"pressure",
//! \ogs_file_param_special{prj__processes__process__ComponentTransport__process_variables__concentration}
"concentration"});
// Check number of components for each process variable
auto it = std::find_if(
collected_process_variables.cbegin(),
collected_process_variables.cend(),
[](std::reference_wrapper<ProcessLib::ProcessVariable> const& pv) {
return pv.get().getNumberOfGlobalComponents() != 1;
});
if (it != collected_process_variables.end())
{
OGS_FATAL(
"Number of components for process variable '{:s}' should be 1 "
"rather "
"than {:d}.",
it->get().getName(),
it->get().getNumberOfGlobalComponents());
}
int const hydraulic_process_id = 0;
int const first_transport_process_id = use_monolithic_scheme ? 0 : 1;
// Allocate the collected process variables into a two-dimensional vector,
// depending on what scheme is adopted
if (use_monolithic_scheme) // monolithic scheme.
{
process_variables.push_back(std::move(collected_process_variables));
}
else // staggered scheme.
{
std::vector<std::reference_wrapper<ProcessLib::ProcessVariable>>
per_process_variable;
if (!chemical_solver_interface)
{
for (auto& pv : collected_process_variables)
{
per_process_variable.emplace_back(pv);
process_variables.push_back(std::move(per_process_variable));
}
}
else
{
auto sort_by_component = [&per_process_variable,
collected_process_variables](
auto const& c_name) {
auto pv = std::find_if(collected_process_variables.begin(),
collected_process_variables.end(),
[&c_name](auto const& v) -> bool {
return v.get().getName() == c_name;
});
if (pv == collected_process_variables.end())
{
OGS_FATAL(
"Component {:s} given in "
"<chemical_system>/<solution>/"
"<components> is not found in specified "
"coupled processes (see "
"<process>/<process_variables>/"
"<concentration>).",
c_name);
}
per_process_variable.emplace_back(*pv);
return std::move(per_process_variable);
};
auto const components =
chemical_solver_interface->getComponentList();
// pressure
per_process_variable.emplace_back(collected_process_variables[0]);
process_variables.push_back(std::move(per_process_variable));
// concentration
assert(components.size() + 1 == collected_process_variables.size());
std::transform(components.begin(), components.end(),
std::back_inserter(process_variables),
sort_by_component);
}
}
// Specific body force parameter.
Eigen::VectorXd specific_body_force;
std::vector<double> const b =
//! \ogs_file_param{prj__processes__process__ComponentTransport__specific_body_force}
config.getConfigParameter<std::vector<double>>("specific_body_force");
assert(!b.empty() && b.size() < 4);
if (b.size() < mesh.getDimension())
{
OGS_FATAL(
"specific body force (gravity vector) has {:d} components, mesh "
"dimension is {:d}",
b.size(), mesh.getDimension());
}
bool const has_gravity = MathLib::toVector(b).norm() > 0;
if (has_gravity)
{
specific_body_force.resize(b.size());
std::copy_n(b.data(), b.size(), specific_body_force.data());
}
bool const non_advective_form =
//! \ogs_file_param{prj__processes__process__ComponentTransport__non_advective_form}
config.getConfigParameter<bool>("non_advective_form", false);
auto media_map =
MaterialPropertyLib::createMaterialSpatialDistributionMap(media, mesh);
DBUG("Check the media properties of ComponentTransport process ...");
checkMPLProperties(mesh, *media_map);
DBUG("Media properties verified.");
ComponentTransportProcessData process_data{std::move(media_map),
specific_body_force,
has_gravity,
non_advective_form,
chemical_solver_interface.get(),
hydraulic_process_id,
first_transport_process_id};
SecondaryVariableCollection secondary_variables;
ProcessLib::createSecondaryVariables(config, secondary_variables);
std::unique_ptr<ProcessLib::SurfaceFluxData> surfaceflux;
auto surfaceflux_config =
//! \ogs_file_param{prj__processes__process__calculatesurfaceflux}
config.getConfigSubtreeOptional("calculatesurfaceflux");
if (surfaceflux_config)
{
surfaceflux = ProcessLib::SurfaceFluxData::createSurfaceFluxData(
*surfaceflux_config, meshes);
}
return std::make_unique<ComponentTransportProcess>(
std::move(name), mesh, std::move(jacobian_assembler), parameters,
integration_order, std::move(process_variables),
std::move(process_data), std::move(secondary_variables),
use_monolithic_scheme, std::move(surfaceflux),
std::move(chemical_solver_interface));
}
} // namespace ComponentTransport
} // namespace ProcessLib
