ProjectData.cpp

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#include "ProjectData.h"
 
#include <pybind11/eval.h>
 
#include <algorithm>
#include <boost/algorithm/string/predicate.hpp>
#include <cctype>
#include <range/v3/action/sort.hpp>
#include <range/v3/action/unique.hpp>
#include <range/v3/algorithm/contains.hpp>
#include <range/v3/range/conversion.hpp>
#include <range/v3/view/adjacent_remove_if.hpp>
#include <set>
 
#include "BaseLib/Algorithm.h"
#include "BaseLib/ConfigTree.h"
#include "BaseLib/FileTools.h"
#include "BaseLib/Logging.h"
#include "BaseLib/StringTools.h"
#include "GeoLib/GEOObjects.h"
#include "GeoLib/IO/AsciiRasterInterface.h"
#include "GeoLib/IO/NetCDFRasterReader.h"
#include "GeoLib/Raster.h"
#include "InfoLib/CMakeInfo.h"
#include "MaterialLib/MPL/CreateMedium.h"
#include "MaterialLib/Utils/MediaCreation.h"
#include "MathLib/Curve/CreatePiecewiseLinearCurve.h"
#if defined(USE_LIS)
#include "MathLib/LinAlg/EigenLis/LinearSolverOptionsParser.h"
#elif defined(USE_PETSC)
#include "MathLib/LinAlg/PETSc/LinearSolverOptionsParser.h"
#else
#include "MathLib/LinAlg/Eigen/LinearSolverOptionsParser.h"
#endif
#include "MeshGeoToolsLib/ConstructMeshesFromGeometries.h"
#include "MeshGeoToolsLib/CreateSearchLength.h"
#include "MeshGeoToolsLib/SearchLength.h"
#include "MeshLib/Mesh.h"
#include "MeshLib/Utils/SetMeshSpaceDimension.h"
#include "MeshToolsLib/ZeroMeshFieldDataByMaterialIDs.h"
#include "NumLib/ODESolver/ConvergenceCriterion.h"
#include "ProcessLib/CreateJacobianAssembler.h"
#include "ProcessLib/DeactivatedSubdomain.h"
 
// FileIO
#include "GeoLib/IO/XmlIO/Boost/BoostXmlGmlInterface.h"
#include "MeshLib/IO/readMeshFromFile.h"
#include "ParameterLib/ConstantParameter.h"
#include "ParameterLib/CreateCoordinateSystem.h"
#include "ParameterLib/Utils.h"
#include "ProcessLib/CreateTimeLoop.h"
#include "ProcessLib/TimeLoop.h"
 
#ifdef OGS_EMBED_PYTHON_INTERPRETER
#include "Applications/CLI/ogs_embedded_python.h"
#endif
 
#ifdef OGS_BUILD_PROCESS_COMPONENTTRANSPORT
#include "ChemistryLib/CreateChemicalSolverInterface.h"
#include "ProcessLib/ComponentTransport/CreateComponentTransportProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_STEADYSTATEDIFFUSION
#include "ProcessLib/SteadyStateDiffusion/CreateSteadyStateDiffusion.h"
#endif
#ifdef OGS_BUILD_PROCESS_HT
#include "ProcessLib/HT/CreateHTProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_HEATCONDUCTION
#include "ProcessLib/HeatConduction/CreateHeatConductionProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_HEATTRANSPORTBHE
#include "ProcessLib/HeatTransportBHE/CreateHeatTransportBHEProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_WELLBORESIMULATOR
#include "ProcessLib/WellboreSimulator/CreateWellboreSimulatorProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_HYDROMECHANICS
#include "ProcessLib/HydroMechanics/CreateHydroMechanicsProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_LARGEDEFORMATION
#include "ProcessLib/LargeDeformation/CreateLargeDeformationProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_LIE_M
#include "ProcessLib/LIE/SmallDeformation/CreateSmallDeformationProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_LIE_HM
#include "ProcessLib/LIE/HydroMechanics/CreateHydroMechanicsProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_LIQUIDFLOW
#include "ProcessLib/LiquidFlow/CreateLiquidFlowProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_STOKESFLOW
#include "ProcessLib/StokesFlow/CreateStokesFlowProcess.h"
#endif
 
#ifdef OGS_BUILD_PROCESS_THERMORICHARDSMECHANICS
#include "ProcessLib/ThermoRichardsMechanics/CreateThermoRichardsMechanicsProcess.h"
#endif
 
#ifdef OGS_BUILD_PROCESS_PHASEFIELD
#include "ProcessLib/PhaseField/CreatePhaseFieldProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_RICHARDSCOMPONENTTRANSPORT
#include "ProcessLib/RichardsComponentTransport/CreateRichardsComponentTransportProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_RICHARDSFLOW
#include "ProcessLib/RichardsFlow/CreateRichardsFlowProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_RICHARDSMECHANICS
#include "ProcessLib/RichardsMechanics/CreateRichardsMechanicsProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_SMALLDEFORMATION
#include "ProcessLib/SmallDeformation/CreateSmallDeformationProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_SMALLDEFORMATIONNONLOCAL
#include "ProcessLib/SmallDeformationNonlocal/CreateSmallDeformationNonlocalProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_TES
#include "ProcessLib/TES/CreateTESProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_TH2M
#include "ProcessLib/TH2M/CreateTH2MProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_THERMALTWOPHASEFLOWWITHPP
#include "ProcessLib/ThermalTwoPhaseFlowWithPP/CreateThermalTwoPhaseFlowWithPPProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_THERMOHYDROMECHANICS
#include "ProcessLib/ThermoHydroMechanics/CreateThermoHydroMechanicsProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_THERMOMECHANICALPHASEFIELD
#include "ProcessLib/ThermoMechanicalPhaseField/CreateThermoMechanicalPhaseFieldProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_THERMOMECHANICS
#include "ProcessLib/ThermoMechanics/CreateThermoMechanicsProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_THERMORICHARDSFLOW
#include "ProcessLib/ThermoRichardsFlow/CreateThermoRichardsFlowProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_TWOPHASEFLOWWITHPP
#include "ProcessLib/TwoPhaseFlowWithPP/CreateTwoPhaseFlowWithPPProcess.h"
#endif
#ifdef OGS_BUILD_PROCESS_TWOPHASEFLOWWITHPRHO
#include "ProcessLib/TwoPhaseFlowWithPrho/CreateTwoPhaseFlowWithPrhoProcess.h"
#endif
 
namespace
{
void readGeometry(std::string const& fname, GeoLib::GEOObjects& geo_objects,
                  std::string const& dir_first, std::string const& dir_second)
{
    DBUG("Reading geometry file '{:s}'.", fname);
    GeoLib::IO::BoostXmlGmlInterface gml_reader(geo_objects);
    std::string geometry_file = BaseLib::joinPaths(dir_first, fname);
    if (!BaseLib::IsFileExisting(geometry_file))
    {
        // Fallback to reading gml from prj-file directory
        geometry_file = BaseLib::joinPaths(dir_second, fname);
        WARN("File {:s} not found in {:s}! Trying reading from {:s}.", fname,
             dir_first, dir_second);
        if (!BaseLib::IsFileExisting(geometry_file))
        {
            OGS_FATAL("Could not read geometry file {:s} in {:s}.", fname,
                      dir_second);
        }
    }
    gml_reader.readFile(geometry_file);
}
 
std::unique_ptr<MeshLib::Mesh> readSingleMesh(
    BaseLib::ConfigTree const& mesh_config_parameter,
    std::string const& directory)
{
    std::string const mesh_file = BaseLib::joinPaths(
        directory, mesh_config_parameter.getValue<std::string>());
    DBUG("Reading mesh file '{:s}'.", mesh_file);
 
    auto mesh = std::unique_ptr<MeshLib::Mesh>(MeshLib::IO::readMeshFromFile(
        mesh_file, true /* compute_element_neighbors */));
    if (!mesh)
    {
        std::filesystem::path abspath{mesh_file};
        try
        {
            abspath = std::filesystem::absolute(mesh_file);
        }
        catch (std::filesystem::filesystem_error const& e)
        {
            ERR("Determining the absolute path of '{}' failed: {}", mesh_file,
                e.what());
        }
 
        OGS_FATAL("Could not read mesh from '{:s}' file. No mesh added.",
                  abspath.string());
    }
 
#ifdef DOXYGEN_DOCU_ONLY
    mesh_config_parameter.getConfigAttributeOptional<bool>("axially_symmetric");
#endif  // DOXYGEN_DOCU_ONLY
 
    if (auto const axially_symmetric =
        mesh_config_parameter.getConfigAttributeOptional<bool>(
            "axially_symmetric"))
    {
        mesh->setAxiallySymmetric(*axially_symmetric);
        if (mesh->getDimension() == 3 && mesh->isAxiallySymmetric())
        {
            OGS_FATAL("3D mesh cannot be axially symmetric.");
        }
    }
 
    return mesh;
}
 
std::vector<std::unique_ptr<MeshLib::Mesh>> readMeshes(
    BaseLib::ConfigTree const& config, std::string const& directory,
    std::string const& project_directory)
{
    std::vector<std::unique_ptr<MeshLib::Mesh>> meshes;
 
    GeoLib::GEOObjects geoObjects;
 
    auto optional_meshes = config.getConfigSubtreeOptional("meshes");
    if (optional_meshes)
    {
        DBUG("Reading multiple meshes.");
        auto const configs = optional_meshes->getConfigParameterList("mesh");
        std::transform(configs.begin(), configs.end(),
                       std::back_inserter(meshes),
                       [&directory](auto const& mesh_config)
                       { return readSingleMesh(mesh_config, directory); });
        if (auto const geometry_file_name =
            config.getConfigParameterOptional<std::string>("geometry"))
        {
            readGeometry(*geometry_file_name, geoObjects, directory,
                         project_directory);
        }
    }
    else
    {  // Read single mesh with geometry.
        meshes.push_back(
            readSingleMesh(config.getConfigParameter("mesh"), directory));
 
        auto const geometry_file_name =
            config.getConfigParameter<std::string>("geometry");
        readGeometry(geometry_file_name, geoObjects, directory,
                     project_directory);
    }
 
    {  // generate meshes from geometries
        std::unique_ptr<MeshGeoToolsLib::SearchLength> search_length_algorithm =
            MeshGeoToolsLib::createSearchLengthAlgorithm(config, *meshes[0]);
        bool const multiple_nodes_allowed = false;
        auto additional_meshes =
            MeshGeoToolsLib::constructAdditionalMeshesFromGeoObjects(
                geoObjects, *meshes[0], std::move(search_length_algorithm),
                multiple_nodes_allowed);
 
        std::move(begin(additional_meshes), end(additional_meshes),
                  std::back_inserter(meshes));
    }
 
    auto mesh_names = MeshLib::views::names | ranges::to<std::vector>() |
                      ranges::actions::sort;
    auto const sorted_names = meshes | mesh_names;
    auto const unique_names = meshes | mesh_names | ranges::actions::unique;
    if (unique_names.size() < sorted_names.size())
    {
        WARN(
            "Mesh names aren't unique. From project file read mesh names are:");
        for (auto const& name : meshes | MeshLib::views::names)
        {
            INFO("- {}", name);
        }
    }
 
    auto const zero_mesh_field_data_by_material_ids =
        config.getConfigParameterOptional<std::vector<int>>(
            "zero_mesh_field_data_by_material_ids");
    if (zero_mesh_field_data_by_material_ids)
    {
        WARN(
            "Tag 'zero_mesh_field_data_by_material_ids` is experimental. Its "
            "name may be changed, or it may be removed due to its "
            "corresponding feature becomes a single tool. Please use it with "
            "care!");
        MeshToolsLib::zeroMeshFieldDataByMaterialIDs(
            *meshes[0], *zero_mesh_field_data_by_material_ids);
    }
 
    MeshLib::setMeshSpaceDimension(meshes);
 
    return meshes;
}
 
std::vector<GeoLib::NamedRaster> readRasters(
    BaseLib::ConfigTree const& config, std::string const& raster_directory,
    GeoLib::MinMaxPoints const& min_max_points)
{
    INFO("readRasters ...");
    std::vector<GeoLib::NamedRaster> named_rasters;
 
    auto optional_rasters = config.getConfigSubtreeOptional("rasters");
    if (optional_rasters)
    {
        auto const configs = optional_rasters->getConfigSubtreeList("raster");
        std::transform(
            configs.begin(), configs.end(), std::back_inserter(named_rasters),
            [&raster_directory, &min_max_points](auto const& raster_config)
            {
                return GeoLib::IO::readRaster(raster_config, raster_directory,
                                              min_max_points);
            });
    }
    INFO("readRasters done");
    return named_rasters;
}
 
// for debugging raster reading implementation
// void writeRasters(std::vector<GeoLib::NamedRaster> const& named_rasters,
//                  std::string const& output_directory)
//{
//    for (auto const& named_raster : named_rasters)
//    {
// #if defined(USE_PETSC)
//        int my_mpi_rank;
//        MPI_Comm_rank(MPI_COMM_WORLD, &my_mpi_rank);
// #endif
//        FileIO::AsciiRasterInterface::writeRasterAsASC(
//            named_raster.raster, output_directory + "/" +
//                                     named_raster.raster_name +
// #if defined(USE_PETSC)
//                                     "_" + std::to_string(my_mpi_rank) +
// #endif
//                                     ".asc");
//    }
//}
 
}  // namespace
 
ProjectData::ProjectData() = default;
 
ProjectData::ProjectData(BaseLib::ConfigTree const& project_config,
                         std::string const& project_directory,
                         std::string const& output_directory,
                         std::string const& mesh_directory,
                         [[maybe_unused]] std::string const& script_directory)
    : _mesh_vec(readMeshes(project_config, mesh_directory, project_directory)),
      _named_rasters(readRasters(project_config, project_directory,
                                 GeoLib::AABB(_mesh_vec[0]->getNodes().begin(),
                                              _mesh_vec[0]->getNodes().end())
                                     .getMinMaxPoints()))
{
    // for debugging raster reading implementation
    // writeRasters(_named_rasters, output_directory);
    if (auto const python_script =
        project_config.getConfigParameterOptional<std::string>("python_script"))
    {
        namespace py = pybind11;
 
#ifdef OGS_EMBED_PYTHON_INTERPRETER
        _py_scoped_interpreter.emplace(ApplicationsLib::setupEmbeddedPython());
#endif
 
        // Append to python's module search path
        auto py_path = py::module::import("sys").attr("path");
        py_path.attr("append")(script_directory);  // .prj or -s directory
 
        auto const script_path =
            BaseLib::joinPaths(script_directory, *python_script);
 
        // Evaluate in scope of main module
        py::object scope = py::module::import("__main__").attr("__dict__");
        // add (global) variables
        auto globals = py::dict(scope);
        globals["ogs_prj_directory"] = project_directory;
        globals["ogs_mesh_directory"] = mesh_directory;
        globals["ogs_script_directory"] = script_directory;
        try
        {
            py::eval_file(script_path, scope);
        }
        catch (py::error_already_set const& e)
        {
            OGS_FATAL("Error evaluating python script {}: {}", script_path,
                      e.what());
        }
    }
 
    parseCurves(project_config.getConfigSubtreeOptional("curves"));
 
    auto parameter_names_for_transformation =
        parseParameters(project_config.getConfigSubtree("parameters"));
 
    _local_coordinate_system = ParameterLib::createCoordinateSystem(
        project_config.getConfigSubtreeOptional("local_coordinate_system"),
        _parameters);
 
    for (auto& parameter : _parameters)
    {
        if (std::find(begin(parameter_names_for_transformation),
                      end(parameter_names_for_transformation),
                      parameter->name) !=
            end(parameter_names_for_transformation))
        {
            if (!_local_coordinate_system)
            {
                OGS_FATAL(
                    "The parameter '{:s}' is using the local coordinate system "
                    "but no local coordinate system was provided.",
                    parameter->name);
            }
            parameter->setCoordinateSystem(*_local_coordinate_system);
        }
 
        parameter->initialize(_parameters);
    }
 
    parseProcessVariables(project_config.getConfigSubtree("process_variables"));
 
    parseMedia(project_config.getConfigSubtreeOptional("media"));
 
    parseLinearSolvers(project_config.getConfigSubtree("linear_solvers"));
 
    auto chemical_solver_interface = parseChemicalSolverInterface(
        project_config.getConfigSubtreeOptional("chemical_system"),
        output_directory);
 
    parseProcesses(project_config.getConfigSubtree("processes"),
                   project_directory, output_directory,
                   std::move(chemical_solver_interface));
 
    parseNonlinearSolvers(project_config.getConfigSubtree("nonlinear_solvers"));
 
    parseTimeLoop(project_config.getConfigSubtree("time_loop"),
                  output_directory);
}
 
void ProjectData::parseProcessVariables(
    BaseLib::ConfigTree const& process_variables_config)
{
    DBUG("Parse process variables:");
 
    std::set<std::string> names;
 
    for (auto var_config
         : process_variables_config.getConfigSubtreeList("process_variable"))
    {
        // Either the mesh name is given, or the first mesh's name will be
        // taken. Taking the first mesh's value is deprecated.
        auto const mesh_name =
            var_config.getConfigParameter<std::string>("mesh",
                                                       _mesh_vec[0]->getName());
 
        auto& mesh = MeshLib::findMeshByName(_mesh_vec, mesh_name);
 
        auto pv = ProcessLib::ProcessVariable{var_config, mesh, _mesh_vec,
                                              _parameters, _curves};
        if (!names.insert(pv.getName()).second)
        {
            OGS_FATAL("A process variable with name `{:s}' already exists.",
                      pv.getName());
        }
 
        _process_variables.push_back(std::move(pv));
    }
}
 
std::vector<std::string> ProjectData::parseParameters(
    BaseLib::ConfigTree const& parameters_config)
{
    using namespace ProcessLib;
 
    std::set<std::string> names;
    std::vector<std::string> parameter_names_for_transformation;
 
    DBUG("Reading parameters:");
    for (auto parameter_config :
         parameters_config.getConfigSubtreeList("parameter"))
    {
        auto p = ParameterLib::createParameter(parameter_config, _mesh_vec,
                                               _named_rasters, _curves);
        if (!names.insert(p->name).second)
        {
            OGS_FATAL("A parameter with name `{:s}' already exists.", p->name);
        }
 
        auto const use_local_coordinate_system =
            parameter_config.getConfigParameterOptional<bool>(
                "use_local_coordinate_system");
        if (!!use_local_coordinate_system && *use_local_coordinate_system)
        {
            parameter_names_for_transformation.push_back(p->name);
        }
 
        _parameters.push_back(std::move(p));
    }
 
    _parameters.push_back(
        std::make_unique<ParameterLib::ConstantParameter<double>>(
            ProcessLib::DeactivatedSubdomain::zero_parameter_name, 0.0));
    _parameters.push_back(
        std::make_unique<ParameterLib::ConstantParameter<double>>(
            ProcessLib::Process::constant_one_parameter_name, 1.0));
 
    return parameter_names_for_transformation;
}
 
void ProjectData::parseMedia(
    std::optional<BaseLib::ConfigTree> const& media_config)
{
    if (!media_config)
    {
        return;
    }
 
    DBUG("Reading media:");
 
    if (_mesh_vec.empty() || _mesh_vec[0] == nullptr)
    {
        ERR("A mesh is required to define medium materials.");
        return;
    }
 
    for (auto const& medium_config :
         media_config->getConfigSubtreeList("medium"))
    {
        auto create_medium = [dim = _mesh_vec[0]->getDimension(),
                              &medium_config, this](int const id)
        {
            return MaterialPropertyLib::createMedium(
                id, _mesh_vec[0]->getDimension(), medium_config, _parameters,
                _local_coordinate_system ? &*_local_coordinate_system : nullptr,
                _curves);
        };
 
        auto const material_id_string =
            medium_config.getConfigAttribute<std::string>("id", "0");
 
        std::vector<int> const material_ids_of_this_medium =
            MaterialLib::parseMaterialIdString(material_id_string,
                                               materialIDs(*_mesh_vec[0]));
 
        for (auto const& id : material_ids_of_this_medium)
        {
            MaterialLib::createMediumForId(
                id, _media, material_ids_of_this_medium, create_medium);
        }
    }
 
    if (_media.empty())
    {
        OGS_FATAL("No entity is found inside <media>.");
    }
}
 
std::unique_ptr<ChemistryLib::ChemicalSolverInterface>
ProjectData::parseChemicalSolverInterface(
    std::optional<BaseLib::ConfigTree> const& config,
    std::string const& output_directory)
{
    if (!config)
    {
        return nullptr;
    }
 
    std::unique_ptr<ChemistryLib::ChemicalSolverInterface>
        chemical_solver_interface;
#ifdef OGS_BUILD_PROCESS_COMPONENTTRANSPORT
    INFO(
        "Ready for initializing interface to a chemical solver for water "
        "chemistry calculation.");
 
    auto const chemical_solver =
        config->getConfigAttribute<std::string>("chemical_solver");
 
    if (boost::iequals(chemical_solver, "Phreeqc"))
    {
        INFO(
            "Configuring phreeqc interface for water chemistry calculation "
            "using file-based approach.");
 
        chemical_solver_interface = ChemistryLib::createChemicalSolverInterface<
            ChemistryLib::ChemicalSolver::Phreeqc>(_mesh_vec, _linear_solvers,
                                                   *config, output_directory);
    }
    else if (boost::iequals(chemical_solver, "PhreeqcKernel"))
    {
        OGS_FATAL(
            "The chemical solver option of PhreeqcKernel is not accessible for "
            "the time being. Please set 'Phreeqc'' as the chemical solver for "
            "reactive transport modeling.");
    }
    else if (boost::iequals(chemical_solver, "SelfContained"))
    {
        INFO(
            "Use self-contained chemical solver for water chemistry "
            "calculation.");
 
        chemical_solver_interface = ChemistryLib::createChemicalSolverInterface<
            ChemistryLib::ChemicalSolver::SelfContained>(
            _mesh_vec, _linear_solvers, *config, output_directory);
    }
    else
    {
        OGS_FATAL(
            "Unknown chemical solver. Please specify either Phreeqc or "
            "PhreeqcKernel as the solver for water chemistry calculation "
            "instead.");
    }
#else
    (void)output_directory;
 
    OGS_FATAL(
        "Found the type of the process to be solved is not component transport "
        "process. Please specify the process type to ComponentTransport. At "
        "the present, water chemistry calculation is only available for "
        "component transport process.");
#endif
    return chemical_solver_interface;
}
 
void ProjectData::parseProcesses(
    BaseLib::ConfigTree const& processes_config,
    std::string const& project_directory,
    std::string const& output_directory,
    [[maybe_unused]] std::unique_ptr<ChemistryLib::ChemicalSolverInterface>&&
        chemical_solver_interface)
{
    (void)project_directory;  // to avoid compilation warning
    (void)output_directory;   // to avoid compilation warning
 
    DBUG("Reading processes:");
    for (auto process_config : processes_config.getConfigSubtreeList("process"))
    {
        auto const type =
            process_config.peekConfigParameter<std::string>("type");
 
        auto const name =
            process_config.getConfigParameter<std::string>("name");
 
        [[maybe_unused]] auto const integration_order =
            process_config.getConfigParameter<int>("integration_order");
 
        std::unique_ptr<ProcessLib::Process> process;
 
        auto jacobian_assembler = ProcessLib::createJacobianAssembler(
            process_config.getConfigSubtreeOptional("jacobian_assembler"));
 
#ifdef OGS_BUILD_PROCESS_STEADYSTATEDIFFUSION
        if (type == "STEADY_STATE_DIFFUSION")
        {
            // The existence check of the in the configuration referenced
            // process variables is checked in the physical process.
            // TODO at the moment we have only one mesh, later there can be
            // several meshes. Then we have to assign the referenced mesh
            // here.
            process =
                ProcessLib::SteadyStateDiffusion::createSteadyStateDiffusion(
                    name, *_mesh_vec[0], std::move(jacobian_assembler),
                    _process_variables, _parameters, integration_order,
                    process_config, _mesh_vec, _media);
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_LIQUIDFLOW
            if (type == "LIQUID_FLOW")
        {
            process = ProcessLib::LiquidFlow::createLiquidFlowProcess(
                name, *_mesh_vec[0], std::move(jacobian_assembler),
                _process_variables, _parameters, integration_order,
                process_config, _mesh_vec, _media);
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_STOKESFLOW
            if (type == "StokesFlow")
        {
            WARN(
                "The StokesFlow process is deprecated and will be removed in "
                "OGS-6.5.5.");
            switch (_mesh_vec[0]->getDimension())
            {
                case 2:
                    process =
                        ProcessLib::StokesFlow::createStokesFlowProcess<2>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters, integration_order,
                            process_config, _media);
                    break;
                default:
                    OGS_FATAL(
                        "StokesFlow process does not support given "
                        "dimension {:d}",
                        _mesh_vec[0]->getDimension());
            }
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_TES
            if (type == "TES")
        {
            WARN(
                "The TES process is deprecated and will be removed in "
                "OGS-6.5.5.");
            process = ProcessLib::TES::createTESProcess(
                name, *_mesh_vec[0], std::move(jacobian_assembler),
                _process_variables, _parameters, integration_order,
                process_config);
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_TH2M
            if (type == "TH2M")
        {
            switch (_mesh_vec[0]->getDimension())
            {
                case 2:
                    process = ProcessLib::TH2M::createTH2MProcess<2>(
                        name, *_mesh_vec[0], std::move(jacobian_assembler),
                        _process_variables, _parameters,
                        _local_coordinate_system, integration_order,
                        process_config, _media);
                    break;
                case 3:
                    process = ProcessLib::TH2M::createTH2MProcess<3>(
                        name, *_mesh_vec[0], std::move(jacobian_assembler),
                        _process_variables, _parameters,
                        _local_coordinate_system, integration_order,
                        process_config, _media);
                    break;
                default:
                    OGS_FATAL("TH2M process does not support given dimension");
            }
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_HEATCONDUCTION
            if (type == "HEAT_CONDUCTION")
        {
            process = ProcessLib::HeatConduction::createHeatConductionProcess(
                name, *_mesh_vec[0], std::move(jacobian_assembler),
                _process_variables, _parameters, integration_order,
                process_config, _media);
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_HEATTRANSPORTBHE
            if (type == "HEAT_TRANSPORT_BHE")
        {
            if (_mesh_vec[0]->getDimension() != 3)
            {
                OGS_FATAL(
                    "HEAT_TRANSPORT_BHE can only work with a 3-dimensional "
                    "mesh! ");
            }
 
            process =
                ProcessLib::HeatTransportBHE::createHeatTransportBHEProcess(
                    name, *_mesh_vec[0], std::move(jacobian_assembler),
                    _process_variables, _parameters, integration_order,
                    process_config, _curves, _media);
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_WELLBORESIMULATOR
            if (type == "WELLBORE_SIMULATOR")
        {
            if (_mesh_vec[0]->getDimension() != 1)
            {
                OGS_FATAL(
                    "WELLBORE_SIMULATOR can only work with a 1-dimensional "
                    "mesh!");
            }
 
            process =
                ProcessLib::WellboreSimulator::createWellboreSimulatorProcess(
                    name, *_mesh_vec[0], std::move(jacobian_assembler),
                    _process_variables, _parameters, integration_order,
                    process_config, _media);
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_HYDROMECHANICS
            if (type == "HYDRO_MECHANICS")
        {
            if (  
                process_config.getConfigParameterOptional<int>("dimension"))
            {
                OGS_FATAL(
                    "The 'dimension' tag has been removed in the merge-request "
                    "!4766."
                    "The dimension is now taken from the main mesh and the tag "
                    "must be"
                    "removed. There is a python script in the merge-request "
                    "description"
                    "for automatic conversion.");
            }
            switch (_mesh_vec[0]->getDimension())
            {
                case 2:
                    process =
                        ProcessLib::HydroMechanics::createHydroMechanicsProcess<
                            2>(name, *_mesh_vec[0],
                               std::move(jacobian_assembler),
                               _process_variables, _parameters,
                               _local_coordinate_system, integration_order,
                               process_config, _media);
                    break;
                case 3:
                    process =
                        ProcessLib::HydroMechanics::createHydroMechanicsProcess<
                            3>(name, *_mesh_vec[0],
                               std::move(jacobian_assembler),
                               _process_variables, _parameters,
                               _local_coordinate_system, integration_order,
                               process_config, _media);
                    break;
                default:
                    OGS_FATAL(
                        "HYDRO_MECHANICS process does not support given "
                        "dimension");
            }
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_LARGEDEFORMATION
            if (type == "LARGE_DEFORMATION")
        {
            switch (_mesh_vec[0]->getDimension())
            {
                case 2:
                    process = ProcessLib::LargeDeformation::
                        createLargeDeformationProcess<2>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config, _media);
                    break;
                case 3:
                    process = ProcessLib::LargeDeformation::
                        createLargeDeformationProcess<3>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config, _media);
                    break;
                default:
                    OGS_FATAL(
                        "LARGE_DEFORMATION process does not support given "
                        "dimension");
            }
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_LIE_HM
            if (type == "HYDRO_MECHANICS_WITH_LIE")
        {
            if (  
                process_config.getConfigParameterOptional<int>("dimension"))
            {
                OGS_FATAL(
                    "The 'dimension' tag has been removed in the merge-request "
                    "!4766."
                    "The dimension is now taken from the main mesh and the tag "
                    "must be"
                    "removed. There is a python script in the merge-request "
                    "description"
                    "for automatic conversion.");
            }
            switch (_mesh_vec[0]->getDimension())
            {
                case 2:
                    process = ProcessLib::LIE::HydroMechanics::
                        createHydroMechanicsProcess<2>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config, _media);
                    break;
                case 3:
                    process = ProcessLib::LIE::HydroMechanics::
                        createHydroMechanicsProcess<3>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config, _media);
                    break;
                default:
                    OGS_FATAL(
                        "HYDRO_MECHANICS_WITH_LIE process does not support "
                        "given dimension");
            }
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_HT
            if (type == "HT")
        {
            process = ProcessLib::HT::createHTProcess(
                name, *_mesh_vec[0], std::move(jacobian_assembler),
                _process_variables, _parameters, integration_order,
                process_config, _mesh_vec, _media);
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_COMPONENTTRANSPORT
            if (type == "ComponentTransport")
        {
            process =
                ProcessLib::ComponentTransport::createComponentTransportProcess(
                    name, *_mesh_vec[0], std::move(jacobian_assembler),
                    _process_variables, _parameters, integration_order,
                    process_config, _mesh_vec, _media,
                    std::move(chemical_solver_interface));
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_PHASEFIELD
            if (type == "PHASE_FIELD")
        {
            switch (_mesh_vec[0]->getDimension())
            {
                case 2:
                    process =
                        ProcessLib::PhaseField::createPhaseFieldProcess<2>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config);
                    break;
                case 3:
                    process =
                        ProcessLib::PhaseField::createPhaseFieldProcess<3>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config);
                    break;
            }
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_RICHARDSCOMPONENTTRANSPORT
            if (type == "RichardsComponentTransport")
        {
            process = ProcessLib::RichardsComponentTransport::
                createRichardsComponentTransportProcess(
                    name, *_mesh_vec[0], std::move(jacobian_assembler),
                    _process_variables, _parameters, integration_order,
                    process_config, _media);
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_SMALLDEFORMATION
            if (type == "SMALL_DEFORMATION")
        {
            switch (_mesh_vec[0]->getDimension())
            {
                case 2:
                    process = ProcessLib::SmallDeformation::
                        createSmallDeformationProcess<2>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config, _media);
                    break;
                case 3:
                    process = ProcessLib::SmallDeformation::
                        createSmallDeformationProcess<3>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config, _media);
                    break;
                default:
                    OGS_FATAL(
                        "SMALL_DEFORMATION process does not support given "
                        "dimension");
            }
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_SMALLDEFORMATIONNONLOCAL
            if (type == "SMALL_DEFORMATION_NONLOCAL")
        {
            WARN(
                "The SMALL_DEFORMATION_NONLOCAL process is deprecated and will "
                "be removed in OGS-6.5.5.");
            switch (_mesh_vec[0]->getDimension())
            {
                case 2:
                    process = ProcessLib::SmallDeformationNonlocal::
                        createSmallDeformationNonlocalProcess<2>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config);
                    break;
                case 3:
                    process = ProcessLib::SmallDeformationNonlocal::
                        createSmallDeformationNonlocalProcess<3>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config);
                    break;
                default:
                    OGS_FATAL(
                        "SMALL_DEFORMATION_NONLOCAL process does not support "
                        "given dimension {:d}",
                        _mesh_vec[0]->getDimension());
            }
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_LIE_M
            if (type == "SMALL_DEFORMATION_WITH_LIE")
        {
            if (  
                process_config.getConfigParameterOptional<int>("dimension"))
            {
                OGS_FATAL(
                    "The 'dimension' tag has been removed in the merge-request "
                    "!4766."
                    "The dimension is now taken from the main mesh and the tag "
                    "must be"
                    "removed. There is a python script in the merge-request "
                    "description"
                    "for automatic conversion.");
            }
            switch (_mesh_vec[0]->getDimension())
            {
                case 2:
                    process = ProcessLib::LIE::SmallDeformation::
                        createSmallDeformationProcess<2>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config);
                    break;
                case 3:
                    process = ProcessLib::LIE::SmallDeformation::
                        createSmallDeformationProcess<3>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config);
                    break;
                default:
                    OGS_FATAL(
                        "SMALL_DEFORMATION_WITH_LIE process does not support "
                        "given dimension");
            }
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_THERMOHYDROMECHANICS
            if (type == "THERMO_HYDRO_MECHANICS")
        {
            if (  
                process_config.getConfigParameterOptional<int>("dimension"))
            {
                OGS_FATAL(
                    "The 'dimension' tag has been removed in the merge-request "
                    "!4766."
                    "The dimension is now taken from the main mesh and the tag "
                    "must be"
                    "removed. There is a python script in the merge-request "
                    "description"
                    "for automatic conversion.");
            }
            switch (_mesh_vec[0]->getDimension())
            {
                case 2:
                    process = ProcessLib::ThermoHydroMechanics::
                        createThermoHydroMechanicsProcess<2>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config, _media);
                    break;
                case 3:
                    process = ProcessLib::ThermoHydroMechanics::
                        createThermoHydroMechanicsProcess<3>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config, _media);
                    break;
                default:
                    OGS_FATAL(
                        "THERMO_HYDRO_MECHANICS process does not support given "
                        "dimension");
            }
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_THERMOMECHANICALPHASEFIELD
            if (type == "THERMO_MECHANICAL_PHASE_FIELD")
        {
            WARN(
                "The THERMO_MECHANICAL_PHASE_FIELD process is deprecated and "
                "will be removed in OGS-6.5.5.");
            switch (_mesh_vec[0]->getDimension())
            {
                case 2:
                    process = ProcessLib::ThermoMechanicalPhaseField::
                        createThermoMechanicalPhaseFieldProcess<2>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config);
                    break;
                case 3:
                    process = ProcessLib::ThermoMechanicalPhaseField::
                        createThermoMechanicalPhaseFieldProcess<3>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config);
                    break;
            }
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_THERMOMECHANICS
            if (type == "THERMO_MECHANICS")
        {
            switch (_mesh_vec[0]->getDimension())
            {
                case 2:
                    process = ProcessLib::ThermoMechanics::
                        createThermoMechanicsProcess<2>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config, _media);
                    break;
                case 3:
                    process = ProcessLib::ThermoMechanics::
                        createThermoMechanicsProcess<3>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config, _media);
                    break;
            }
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_RICHARDSFLOW
            if (type == "RICHARDS_FLOW")
        {
            process = ProcessLib::RichardsFlow::createRichardsFlowProcess(
                name, *_mesh_vec[0], std::move(jacobian_assembler),
                _process_variables, _parameters, integration_order,
                process_config, _media);
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_RICHARDSMECHANICS
            if (type == "RICHARDS_MECHANICS")
        {
            if (  
                process_config.getConfigParameterOptional<int>("dimension"))
            {
                OGS_FATAL(
                    "The 'dimension' tag has been removed in the merge-request "
                    "!4766."
                    "The dimension is now taken from the main mesh and the tag "
                    "must be"
                    "removed. There is a python script in the merge-request "
                    "description"
                    "for automatic conversion.");
            }
            switch (_mesh_vec[0]->getDimension())
            {
                case 2:
                    process = ProcessLib::RichardsMechanics::
                        createRichardsMechanicsProcess<2>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config, _media);
                    break;
                case 3:
                    process = ProcessLib::RichardsMechanics::
                        createRichardsMechanicsProcess<3>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config, _media);
                    break;
            }
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_THERMORICHARDSFLOW
            if (type == "THERMO_RICHARDS_FLOW")
        {
            process =
                ProcessLib::ThermoRichardsFlow::createThermoRichardsFlowProcess(
                    name, *_mesh_vec[0], std::move(jacobian_assembler),
                    _process_variables, _parameters, integration_order,
                    process_config, _media);
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_THERMORICHARDSMECHANICS
            if (type == "THERMO_RICHARDS_MECHANICS")
        {
            switch (_mesh_vec[0]->getDimension())
            {
                case 2:
                    process = ProcessLib::ThermoRichardsMechanics::
                        createThermoRichardsMechanicsProcess<2>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config, _media);
                    break;
                case 3:
                    process = ProcessLib::ThermoRichardsMechanics::
                        createThermoRichardsMechanicsProcess<3>(
                            name, *_mesh_vec[0], std::move(jacobian_assembler),
                            _process_variables, _parameters,
                            _local_coordinate_system, integration_order,
                            process_config, _media);
                    break;
            }
        }
        else
#endif
 
#ifdef OGS_BUILD_PROCESS_TWOPHASEFLOWWITHPP
            if (type == "TWOPHASE_FLOW_PP")
        {
            process =
                ProcessLib::TwoPhaseFlowWithPP::createTwoPhaseFlowWithPPProcess(
                    name, *_mesh_vec[0], std::move(jacobian_assembler),
                    _process_variables, _parameters, integration_order,
                    process_config, _media);
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_TWOPHASEFLOWWITHPRHO
            if (type == "TWOPHASE_FLOW_PRHO")
        {
            WARN(
                "The TWOPHASE_FLOW_PRHO process is deprecated and will be "
                "removed in OGS-6.5.5.");
            process = ProcessLib::TwoPhaseFlowWithPrho::
                createTwoPhaseFlowWithPrhoProcess(
                    name, *_mesh_vec[0], std::move(jacobian_assembler),
                    _process_variables, _parameters, integration_order,
                    process_config, _media);
        }
        else
#endif
#ifdef OGS_BUILD_PROCESS_THERMALTWOPHASEFLOWWITHPP
            if (type == "THERMAL_TWOPHASE_WITH_PP")
        {
            process = ProcessLib::ThermalTwoPhaseFlowWithPP::
                createThermalTwoPhaseFlowWithPPProcess(
                    name, *_mesh_vec[0], std::move(jacobian_assembler),
                    _process_variables, _parameters, integration_order,
                    process_config, _media);
        }
        else
#endif
        {
            OGS_FATAL("Unknown process type: {:s}", type);
        }
 
        if (ranges::contains(_processes, name,
                             [](std::unique_ptr<ProcessLib::Process> const& p)
                             { return p->name; }))
        {
            OGS_FATAL("The process name '{:s}' is not unique.", name);
        }
        _processes.push_back(std::move(process));
    }
}
 
void ProjectData::parseTimeLoop(BaseLib::ConfigTree const& config,
                                std::string const& output_directory)
{
    DBUG("Reading time loop configuration.");
 
    bool const compensate_non_equilibrium_initial_residuum = std::any_of(
        std::begin(_process_variables),
        std::end(_process_variables),
        [](auto const& process_variable)
        { return process_variable.compensateNonEquilibriumInitialResiduum(); });
 
    _time_loop = ProcessLib::createTimeLoop(
        config, output_directory, _processes, _nonlinear_solvers, _mesh_vec,
        compensate_non_equilibrium_initial_residuum);
 
    if (!_time_loop)
    {
        OGS_FATAL("Initialization of time loop failed.");
    }
}
 
void ProjectData::parseLinearSolvers(BaseLib::ConfigTree const& config)
{
    DBUG("Reading linear solver configuration.");
 
    for (auto conf : config.getConfigSubtreeList("linear_solver"))
    {
        auto const name = conf.getConfigParameter<std::string>("name");
        auto const linear_solver_parser =
            MathLib::LinearSolverOptionsParser<GlobalLinearSolver>{};
        auto const solver_options =
            linear_solver_parser.parseNameAndOptions("", &conf);
 
        BaseLib::insertIfKeyUniqueElseError(
            _linear_solvers,
            name,
            std::make_unique<GlobalLinearSolver>(std::get<0>(solver_options),
                                                 std::get<1>(solver_options)),
            "The linear solver name is not unique");
    }
}
 
void ProjectData::parseNonlinearSolvers(BaseLib::ConfigTree const& config)
{
    DBUG("Reading non-linear solver configuration.");
 
    for (auto conf : config.getConfigSubtreeList("nonlinear_solver"))
    {
        auto const ls_name =
            conf.getConfigParameter<std::string>("linear_solver");
        auto const& linear_solver = BaseLib::getOrError(
            _linear_solvers, ls_name,
            "A linear solver with the given name does not exist.");
 
        auto const name = conf.getConfigParameter<std::string>("name");
        BaseLib::insertIfKeyUniqueElseError(
            _nonlinear_solvers,
            name,
            NumLib::createNonlinearSolver(*linear_solver, conf).first,
            "The nonlinear solver name is not unique");
    }
}
 
void ProjectData::parseCurves(std::optional<BaseLib::ConfigTree> const& config)
{
    if (!config)
    {
        return;
    }
 
    DBUG("Reading curves configuration.");
 
    for (auto conf : config->getConfigSubtreeList("curve"))
    {
        auto const name = conf.getConfigParameter<std::string>("name");
        BaseLib::insertIfKeyUniqueElseError(
            _curves,
            name,
            MathLib::createPiecewiseLinearCurve<
                MathLib::PiecewiseLinearInterpolation>(conf),
            "The curve name is not unique.");
    }
}
 
MeshLib::Mesh& ProjectData::getMesh(std::string const& mesh_name) const
{
    return MeshLib::findMeshByName(_mesh_vec, mesh_name);
}