Classes
struct	IntegrationPointData

class	ComponentTransportLocalAssemblerInterface

class	LocalAssemblerData

class	ComponentTransportProcess

struct	ComponentTransportProcessData

struct	InterpolationPoint

struct	Field

struct	LookupTable

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

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)

std::unique_ptr< LookupTable >	createLookupTable (std::optional< std::string > const tabular_file, std::vector< std::vector< std::reference_wrapper< ProcessVariable >>> const &process_variables)

static std::vector< std::size_t >	intersection (std::vector< std::size_t > const &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 28 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 : 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);
         }
     }
 }

Referenced by createComponentTransportProcess().

◆ createComponentTransportProcess()

std::unique_ptr< Process > ProcessLib::ComponentTransport::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
	)

Input File Parameter:: prj__processes__process__type

Input File Parameter:: prj__processes__process__ComponentTransport__coupling_scheme

Input File Parameter:: prj__processes__process__ComponentTransport__process_variables

Input File Parameter:: prj__processes__process__ComponentTransport__process_variables__pressure

Input File Parameter:: prj__processes__process__ComponentTransport__process_variables__concentration

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__calculatesurfaceflux

Definition at line 77 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");
  
     // Process variable.
  
     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,
         {
          "pressure",
          "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 =
         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 =
         config.getConfigParameter<bool>("non_advective_form", false);
  
     bool chemically_induced_porosity_change =
         config.getConfigParameter<bool>("chemically_induced_porosity_change",
                                         false);
  
     auto const temperature = ParameterLib::findOptionalTagParameter<double>(
         config, "temperature_field", parameters, 1, &mesh);
  
     auto media_map =
         MaterialPropertyLib::createMaterialSpatialDistributionMap(media, mesh);
  
     auto lookup_table = ComponentTransport::createLookupTable(
         config.getConfigParameterOptional<std::string>("tabular_file"),
         process_variables);
  
     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,
         temperature,
         chemically_induced_porosity_change,
         chemical_solver_interface.get(),
         std::move(lookup_table),
         hydraulic_process_id,
         first_transport_process_id};
  
     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));
 }

References BaseLib::ConfigTree::checkConfigParameter(), checkMPLProperties(), createLookupTable(), MaterialPropertyLib::createMaterialSpatialDistributionMap(), ProcessLib::createSecondaryVariables(), ProcessLib::SurfaceFluxData::createSurfaceFluxData(), DBUG(), ProcessLib::findProcessVariables(), BaseLib::ConfigTree::getConfigParameter(), BaseLib::ConfigTree::getConfigParameterOptional(), BaseLib::ConfigTree::getConfigSubtree(), BaseLib::ConfigTree::getConfigSubtreeOptional(), MeshLib::Mesh::getDimension(), MaterialPropertyLib::name, OGS_FATAL, and MathLib::toVector().

Referenced by ProjectData::parseProcesses().

◆ createLookupTable()

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

Definition at line 55 of file CreateLookupTable.cpp.

 {
     if (!tabular_file)
     {
         return nullptr;
     }
  
     auto const path_to_tabular_file =
         BaseLib::joinPaths(BaseLib::getProjectDirectory(), *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 anonymous_namespace{CreateLookupTable.cpp}::getIndexVector(), BaseLib::getProjectDirectory(), INFO(), BaseLib::IsFileExisting(), BaseLib::joinPaths(), BaseLib::makeVectorUnique(), and OGS_FATAL.

Referenced by createComponentTransportProcess().

◆ intersection()

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

static

Definition at line 21 of file LookupTable.cpp.

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

References MathLib::LinAlg::set().

Referenced by MeshGeoToolsLib::GeoMapper::getMeshElevation(), and ProcessLib::ComponentTransport::LookupTable::getTableEntryID().

Classes

Functions

Function Documentation

◆ checkMPLProperties()

◆ createComponentTransportProcess()

◆ createLookupTable()

◆ intersection()