ProcessLib::ComponentTransport Namespace Reference

Classes
class	ComponentTransportLocalAssemblerInterface
class	ComponentTransportProcess
struct	ComponentTransportProcessData
struct	Field
struct	IntegrationPointData
struct	InterpolationPoint
class	LocalAssemblerData
struct	LookupTable

Functions
void	checkMPLProperties (MeshLib::Mesh const &mesh, MaterialPropertyLib::MaterialSpatialDistributionMap const &media_map)
std::unique_ptr< Process >	createComponentTransportProcess (std::string const &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)
std::unique_ptr< LookupTable >	createLookupTable (std::optional< std::string > const tabular_file, std::filesystem::path const &project_directory, std::vector< std::vector< std::reference_wrapper< ProcessVariable > > > const &process_variables)
static void	intersection (std::vector< std::size_t > &vec1, std::vector< std::size_t > const &vec2)

Function Documentation

checkMPLProperties()

void ProcessLib::ComponentTransport::checkMPLProperties	(	MeshLib::Mesh const &	mesh,
		MaterialPropertyLib::MaterialSpatialDistributionMap const &	media_map )

Definition at line 24 of file CreateComponentTransportProcess.cpp.

{
    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_id : mesh.getElements() | MeshLib::views::ids)
    {
        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);
        }
    }
}

References MaterialPropertyLib::decay_rate, MaterialPropertyLib::density, MeshLib::Mesh::getElements(), MaterialPropertyLib::MaterialSpatialDistributionMap::getMedium(), MeshLib::views::ids, MaterialPropertyLib::longitudinal_dispersivity, OGS_FATAL, MaterialPropertyLib::permeability, MaterialPropertyLib::pore_diffusion, MaterialPropertyLib::porosity, MaterialPropertyLib::retardation_factor, MaterialPropertyLib::transversal_dispersivity, and MaterialPropertyLib::viscosity.

Referenced by createComponentTransportProcess().

createComponentTransportProcess()

std::unique_ptr< Process > ProcessLib::ComponentTransport::createComponentTransportProcess	(	std::string const &	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 )

Input File Parameter

prj__processes__process__type

Input File Parameter

prj__processes__process__ComponentTransport__coupling_scheme

Process Variables

Input File Parameter

prj__processes__process__ComponentTransport__process_variables

Primary process variables as they appear in the global component vector.

Input File Parameter

prj__processes__process__ComponentTransport__process_variables__pressure

Input File Parameter

prj__processes__process__ComponentTransport__process_variables__concentration

Temperature is optional.

Input File Parameter

prj__processes__process__ComponentTransport__process_variables__temperature

Process Parameters

Input File Parameter

prj__processes__process__ComponentTransport__specific_body_force

Input File Parameter

prj__processes__process__ComponentTransport__non_advective_form

Input File Parameter

prj__processes__process__ComponentTransport__chemically_induced_porosity_change

Input File Parameter

prj__processes__process__ComponentTransport__temperature_field

Input File Parameter

prj__processes__process__ComponentTransport__tabular_file

Input File Parameter

prj__processes__process__ComponentTransport__aperture_size

Input File Parameter

prj__processes__process__ComponentTransport__aperture_size__parameter

Input File Parameter

prj__processes__process__linear

Input File Parameter

prj__processes__process__ComponentTransport__linear_solver_compute_only_upon_timestep_change

Input File Parameter

prj__processes__process__calculatesurfaceflux

Definition at line 71 of file CreateComponentTransportProcess.cpp.

{
    config.checkConfigParameter("type", "ComponentTransport");
 
    DBUG("Create ComponentTransportProcess.");
 
    auto const coupling_scheme =
        config.getConfigParameter<std::string>("coupling_scheme",
                                               "monolithic_scheme");
    const bool use_monolithic_scheme = (coupling_scheme != "staggered");


    auto const pv_config = config.getConfigSubtree("process_variables");
 
    std::vector<std::vector<std::reference_wrapper<ProcessVariable>>>
        process_variables;

    std::vector collected_process_variables = findProcessVariables(
        variables, pv_config,
        {
         "pressure",
         "concentration"});

    std::vector const temperature_variable = findProcessVariables(
        variables, pv_config,
        "temperature", true /*temperature is optional*/);
    bool const isothermal = temperature_variable.empty();
    if (!isothermal)
    {
        assert(temperature_variable.size() == 1);
        collected_process_variables.insert(
            ++collected_process_variables.begin(), temperature_variable[0]);
    }
 
    // 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());
    }
 
    // Allocate the collected process variables into a two-dimensional vector,
    // depending on what scheme is adopted
    if (use_monolithic_scheme)  // monolithic scheme.
    {
        if (!isothermal)
        {
            OGS_FATAL(
                "Currently, non-isothermal component transport process can "
                "only be simulated in staggered 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));
            // temperature
            if (!isothermal)
            {
                per_process_variable.emplace_back(
                    collected_process_variables[1]);
                process_variables.push_back(std::move(per_process_variable));
            }
            // concentration
            assert(components.size() + (isothermal ? 1 : 2) ==
                   collected_process_variables.size());
            std::transform(components.begin(), components.end(),
                           std::back_inserter(process_variables),
                           sort_by_component);
        }
    }

    std::vector<double> const b =
        config.getConfigParameter<std::vector<double>>("specific_body_force");
    assert(!b.empty() && b.size() < 4);
    // Specific body force parameter.
    Eigen::VectorXd specific_body_force(b.size());
    int const mesh_space_dimension =
        MeshLib::getSpaceDimension(mesh.getNodes());
    if (static_cast<int>(b.size()) != mesh_space_dimension)
    {
        OGS_FATAL(
            "specific body force (gravity vector) has {:d} components, mesh "
            "dimension is {:d}",
            b.size(), mesh_space_dimension);
    }
    bool const has_gravity = MathLib::toVector(b).norm() > 0;
    if (has_gravity)
    {
        std::copy_n(b.data(), b.size(), specific_body_force.data());
    }
 
    bool const non_advective_form =
        config.getConfigParameter<bool>("non_advective_form", false);
 
    bool chemically_induced_porosity_change =
        config.getConfigParameter<bool>("chemically_induced_porosity_change",
                                        false);
 
    auto const temperature_field = ParameterLib::findOptionalTagParameter<
        double>(
        config, "temperature_field", parameters, 1, &mesh);
    if (!isothermal && temperature_field != nullptr)
    {
        OGS_FATAL("Temperature field is set for non-isothermal setup.")
    }
 
    auto media_map =
        MaterialPropertyLib::createMaterialSpatialDistributionMap(media, mesh);
 
    auto lookup_table = ComponentTransport::createLookupTable(
        config.getConfigParameterOptional<std::string>("tabular_file"),
        config.projectDirectory(),
        process_variables);
 
    DBUG("Check the media properties of ComponentTransport process ...");
    checkMPLProperties(mesh, media_map);
    DBUG("Media properties verified.");
 
    auto stabilizer = NumLib::createNumericalStabilization(mesh, config);
 
    auto const* aperture_size_parameter = &ParameterLib::findParameter<double>(
        ProcessLib::Process::constant_one_parameter_name, parameters, 1);
    auto const aperture_config =
        config.getConfigSubtreeOptional("aperture_size");
    if (aperture_config)
    {
        aperture_size_parameter = &ParameterLib::findParameter<double>(
            *aperture_config, "parameter", parameters, 1);
    }
 
    auto const is_linear =
        config.getConfigParameter("linear", false);
 
    auto const ls_compute_only_upon_timestep_change =
        config.getConfigParameter(
            "linear_solver_compute_only_upon_timestep_change", false);
 
    auto const rotation_matrices = MeshLib::getElementRotationMatrices(
        mesh_space_dimension, mesh.getDimension(), mesh.getElements());
    std::vector<Eigen::VectorXd> projected_specific_body_force_vectors;
    projected_specific_body_force_vectors.reserve(rotation_matrices.size());
 
    std::transform(rotation_matrices.begin(), rotation_matrices.end(),
                   std::back_inserter(projected_specific_body_force_vectors),
                   [&specific_body_force](const auto& R)
                   { return R * R.transpose() * specific_body_force; });
 
    ComponentTransportProcessData process_data{
        std::move(media_map),
        has_gravity,
        non_advective_form,
        temperature_field,
        chemically_induced_porosity_change,
        chemical_solver_interface.get(),
        std::move(lookup_table),
        std::move(stabilizer),
        projected_specific_body_force_vectors,
        mesh_space_dimension,
        *aperture_size_parameter,
        isothermal,
        NumLib::ShapeMatrixCache{integration_order}};
 
    SecondaryVariableCollection secondary_variables;
 
    ProcessLib::createSecondaryVariables(config, secondary_variables);
 
    std::unique_ptr<ProcessLib::SurfaceFluxData> surfaceflux;
    auto surfaceflux_config =
        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), is_linear,
        ls_compute_only_upon_timestep_change);
}

References BaseLib::ConfigTree::checkConfigParameter(), checkMPLProperties(), ProcessLib::Process::constant_one_parameter_name, createLookupTable(), MaterialPropertyLib::createMaterialSpatialDistributionMap(), NumLib::createNumericalStabilization(), ProcessLib::createSecondaryVariables(), ProcessLib::SurfaceFluxData::createSurfaceFluxData(), DBUG(), ParameterLib::findOptionalTagParameter(), ParameterLib::findParameter(), ProcessLib::findProcessVariables(), BaseLib::ConfigTree::getConfigParameter(), BaseLib::ConfigTree::getConfigParameterOptional(), BaseLib::ConfigTree::getConfigSubtree(), BaseLib::ConfigTree::getConfigSubtreeOptional(), MeshLib::Mesh::getDimension(), MeshLib::getElementRotationMatrices(), MeshLib::Mesh::getElements(), MeshLib::Mesh::getNodes(), MeshLib::getSpaceDimension(), OGS_FATAL, BaseLib::ConfigTree::projectDirectory(), and MathLib::toVector().

Referenced by ProjectData::parseProcesses().

createLookupTable()

std::unique_ptr< LookupTable > ProcessLib::ComponentTransport::createLookupTable	(	std::optional< std::string > const	tabular_file,
		std::filesystem::path const &	project_directory,
		std::vector< std::vector< std::reference_wrapper< ProcessVariable > > > const &	process_variables )

Definition at line 48 of file CreateLookupTable.cpp.

{
    if (!tabular_file)
    {
        return nullptr;
    }
 
    auto const path_to_tabular_file =
        BaseLib::joinPaths(project_directory.string(), *tabular_file);
 
    if (!BaseLib::IsFileExisting(path_to_tabular_file))
    {
        OGS_FATAL(
            "Not found the tabular file with the specified file path: {:s}",
            path_to_tabular_file);
    }
 
    INFO("Found the tabular file: {:s}", path_to_tabular_file);
 
    std::ifstream in(path_to_tabular_file);
    if (!in)
    {
        OGS_FATAL("Couldn't open the tabular file: {:s}.",
                  path_to_tabular_file);
    }
 
    // read field names
    std::string line;
    std::getline(in, line);
    std::vector<std::string> field_names;
    boost::split(field_names, line, boost::is_any_of("\t "));
 
    // categorize entry fields
    std::vector<std::string> input_field_names;
    std::copy_if(field_names.begin(), field_names.end(),
                 std::back_inserter(input_field_names),
                 [](auto const& field_name) -> bool
                 { return field_name.find("_new") == std::string::npos; });
 
    // read table entries
    std::map<std::string, std::vector<double>> tabular_data;
    while (std::getline(in, line))
    {
        std::vector<std::string> field_data;
        boost::split(field_data, line, boost::is_any_of("\t "));
 
        assert(field_data.size() == field_names.size());
        for (std::size_t field_id = 0; field_id < field_data.size(); ++field_id)
        {
            tabular_data[field_names[field_id]].push_back(
                std::stod(field_data[field_id]));
        }
    }
    in.close();
 
    std::vector<Field> input_fields;
    input_fields.reserve(input_field_names.size());
    for (auto const& field_name : input_field_names)
    {
        auto pv = std::find_if(process_variables.begin(),
                               process_variables.end(),
                               [&field_name](auto const& v) -> bool
                               {
                                   return v[0].get().getName() == field_name ||
                                          v[0].get().getName() + "_prev" ==
                                              field_name;
                               });
 
        if (pv == process_variables.end())
        {
            OGS_FATAL(
                "Not found field name {:s} in the group of process variables "
                "defined in the project file.",
                field_name);
        }
 
        auto const process_id =
            static_cast<int>(std::distance(process_variables.cbegin(), pv));
 
        auto seed_points = tabular_data[field_name];
        BaseLib::makeVectorUnique(seed_points);
 
        std::vector<std::vector<std::size_t>> point_id_groups;
        for (auto const seed_point : seed_points)
        {
            auto const point_id_group =
                getIndexVector(tabular_data[field_name], seed_point);
            point_id_groups.push_back(point_id_group);
        }
 
        input_fields.emplace_back(point_id_groups, seed_points, field_name,
                                  process_id);
    }
 
    return std::make_unique<LookupTable>(std::move(input_fields),
                                         std::move(tabular_data));
}

References INFO(), BaseLib::IsFileExisting(), BaseLib::joinPaths(), BaseLib::makeVectorUnique(), and OGS_FATAL.

Referenced by createComponentTransportProcess().

intersection()

void ProcessLib::ComponentTransport::intersection ( std::vector< std::size_t > & vec1, std::vector< std::size_t > const & vec2 )

static

Definition at line 14 of file LookupTable.cpp.

{
    std::unordered_set<std::size_t> set(vec1.begin(), vec1.end());
    vec1.clear();
    for (auto const a : vec2)
    {
        if (set.contains(a))
        {
            vec1.push_back(a);
            set.erase(a);
        }
    }
}

Referenced by ProcessLib::ComponentTransport::LookupTable::getTableEntryID().