CreateOutputConfig.cpp

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// SPDX-FileCopyrightText: Copyright (c) OpenGeoSys Community (opengeosys.org)
// SPDX-License-Identifier: BSD-3-Clause
 
#include "CreateOutputConfig.h"
 
#include <spdlog/fmt/ranges.h>
 
#include <map>
 
#include "BaseLib/Algorithm.h"
#include "BaseLib/ConfigTree.h"
#include "BaseLib/FileTools.h"  // required for reading output_times from binary file
#include "MaterialLib/Utils/MediaCreation.h"  // required for splitMaterialIDString
#include "MeshLib/Mesh.h"
#include "MeshLib/Utils/createMaterialIDsBasedSubMesh.h"
#include "MeshLib/Utils/transformMeshToNodePartitionedMesh.h"
#ifdef USE_PETSC
#include "MeshLib/NodePartitionedMesh.h"
#endif  // USE_PETSC
 
std::string createMeshOutputName(std::vector<int> const& material_ids,
                                 std::string const& mesh_name)
{
    if (material_ids.empty())
    {
        return mesh_name;
    }
    return mesh_name + "_" + fmt::format("{}", fmt::join(material_ids, "_"));
}
 
std::string parseOutputMeshConfig(
    BaseLib::ConfigTree const& output_mesh_config,
    std::vector<std::unique_ptr<MeshLib::Mesh>>& meshes)
{
    auto const mesh_name = output_mesh_config.getValue<std::string>();
    auto const& mesh = MeshLib::findMeshByName(meshes, mesh_name);
 
    auto material_id_string =
        output_mesh_config.getConfigAttributeOptional<std::string>(
            "material_ids");
 
    if (!material_id_string)
    {
        return mesh_name;
    }
 
    auto const material_ids_for_output =
        MaterialLib::splitMaterialIdString(*material_id_string);
#ifdef USE_PETSC
    // this mesh isn't yet a NodePartitionedMesh
    auto subdomain_mesh = MeshLib::createMaterialIDsBasedSubMesh(
        mesh, material_ids_for_output,
        createMeshOutputName(material_ids_for_output, mesh_name));
    auto const* bulk_mesh =
        dynamic_cast<MeshLib::NodePartitionedMesh const*>(&mesh);
    meshes.push_back(MeshLib::transformMeshToNodePartitionedMesh(
        bulk_mesh, subdomain_mesh.get()));
#else
    meshes.push_back(MeshLib::createMaterialIDsBasedSubMesh(
        mesh, material_ids_for_output,
        createMeshOutputName(material_ids_for_output, mesh_name)));
#endif
 
    return meshes.back()->getName();
}
 
namespace ProcessLib
{
OutputConfig createOutputConfig(
    const BaseLib::ConfigTree& config,
    std::vector<std::unique_ptr<MeshLib::Mesh>>& meshes)
{
    OutputConfig output_config;
 
    output_config.output_type = [](auto output_type)
    {
        try
        {
            const std::map<std::string, OutputType> outputType_to_enum = {
                {"VTK", OutputType::vtk},
                {"XDMF", OutputType::xdmf}};
            auto type = outputType_to_enum.at(output_type);
 
            return type;
        }
        catch (std::out_of_range&)
        {
            OGS_FATAL(
                "No supported file type provided. Read `{:s}' from <output><type> \
                in prj File. Supported: VTK, XDMF.",
                output_type);
        }
    }(config.getConfigParameter<std::string>("type"));
 
    output_config.prefix =
        config.getConfigParameter<std::string>("prefix", "{:meshname}");
 
    output_config.suffix =
        config.getConfigParameter<std::string>("suffix",
                                               "_ts_{:timestep}_t_{:time}");
 
    output_config.compress_output =
        config.getConfigParameter("compress_output", true);
 
    auto const hdf =
        config.getConfigSubtreeOptional("hdf");
 
    output_config.number_of_files = [&hdf]() -> unsigned int
    {
        if (hdf)
        {
            return hdf->getConfigParameter<unsigned int>("number_of_files");
        }
        return 1;
    }();
    output_config.chunk_size_bytes = [&hdf]() -> unsigned int
    {
        if (hdf)
        {
            return hdf->getConfigParameter<unsigned int>("chunk_size_bytes");
        }
        return 1048576;  // default chunk size in bytes according to
                         // https://www.hdfgroup.org/2022/10/improve-hdf5-performance-using-caching/
    }();
    output_config.store_static_data_separately = [&hdf]() -> bool
    {
        if (hdf)
        {
            return hdf
                ->getConfigParameterOptional<bool>(
                    "store_static_data_separately")
                .value_or(false);
        }
        return false;  // default store_static_data_separately == false
    }();
 
    output_config.data_mode =
        config.getConfigParameter<std::string>("data_mode", "Appended");
 
    //
    // Construction of output times
    //
 
    output_config.fixed_output_times =
        config.getConfigParameter<std::vector<double>>("fixed_output_times",
                                                       {});
    if (output_config.fixed_output_times.empty())
    {
        std::string filename = config.getConfigParameter<std::string>(
            "fixed_output_times_from_file", "no_file");
 
        if (filename != "no_file")
        {
            output_config.fixed_output_times =
                BaseLib::readDoublesFromBinaryFile(
                    filename, config.projectDirectory().string());
        }
    }
    // Remove possible duplicated elements and sort.
    BaseLib::makeVectorUnique(output_config.fixed_output_times);
 
    auto& repeats_each_steps = output_config.repeats_each_steps;

    if (auto const timesteps = config.getConfigSubtreeOptional("timesteps"))
    {
        for (auto pair : timesteps->getConfigSubtreeList("pair"))
        {
            auto repeat = pair.getConfigParameter<unsigned>("repeat");
            auto each_steps = pair.getConfigParameter<unsigned>("each_steps");
 
            assert(repeat != 0 && each_steps != 0);
            repeats_each_steps.emplace_back(repeat, each_steps);
        }
 
        if (repeats_each_steps.empty())
        {
            OGS_FATAL(
                "You have not given any pair (<repeat/>, <each_steps/>) that "
                "defines at which timesteps output shall be written. "
                "Aborting.");
        }
    }
    // In case nothing was specified, i.e. no explicit time steps or fixed
    // output times, every time step will be written.
    if (output_config.fixed_output_times.empty() &&
        output_config.repeats_each_steps.empty())
    {
        repeats_each_steps.emplace_back(1, 1);
    }

    auto const out_vars = config.getConfigSubtree("variables");
 
    auto& output_variables = output_config.output_variables;
    for (auto out_var :
         out_vars.getConfigParameterList<std::string>("variable"))
    {
        if (output_variables.find(out_var) != output_variables.cend())
        {
            OGS_FATAL("output variable `{:s}' specified more than once.",
                      out_var);
        }
 
        DBUG("adding output variable `{:s}'", out_var);
        output_variables.insert(out_var);
    }
 
    // XDMF specific settings
    auto const xdmf_config =
        config.getConfigSubtreeOptional("xdmf_config");
 
    // Optional list of output variables that are written once instead of per
    // time step, i.e. as static attributes.
    if (auto const static_vars =
            xdmf_config
                ?  
                xdmf_config->getConfigSubtreeOptional("static_variables")
                : std::optional<BaseLib::ConfigTree>{})
    {
        auto& static_output_variables = output_config.static_output_variables;
        for (
            auto const& var :
            static_vars->getConfigParameterList<std::string>("variable"))
        {
            // static variable has to be in output_variables
            if (!output_variables.empty() &&
                output_variables.find(var) == output_variables.cend())
            {
                OGS_FATAL(
                    "static output `{:s}' is not in output variables list.",
                    var);
            }
            if (!static_output_variables.insert(var).second)
            {
                OGS_FATAL(
                    "static output variable `{:s}' specified more than once.",
                    var);
            }
            DBUG("adding static output variable `{:s}'", var);
        }
    }
 
    output_config.output_extrapolation_residuals =
        config.getConfigParameter<bool>("output_extrapolation_residuals",
                                        false);
 
    auto& mesh_names_for_output = output_config.mesh_names_for_output;
    if (auto const meshes_config = config.getConfigSubtreeOptional("meshes"))
    {
        if (output_config.prefix.find("{:meshname}") == std::string::npos)
        {
            OGS_FATAL(
                "There are multiple meshes defined in the output section of "
                "the project file, but the prefix doesn't contain "
                "'{{:meshname}}'. Thus the names for the files, the simulation "
                "results should be written to, would not be distinguishable "
                "for different meshes.");
        }
        for (auto mesh_config : meshes_config->getConfigParameterList("mesh"))
        {
            mesh_names_for_output.push_back(
                parseOutputMeshConfig(mesh_config, meshes));
            INFO("Configure mesh '{:s}' for output.",
                 mesh_names_for_output.back());
        }
    }
 
    if (auto const geometrical_sets_config =
        config.getConfigSubtreeOptional("geometrical_sets"))
    {
        for (
            auto geometrical_set_config :
            geometrical_sets_config->getConfigSubtreeList("geometrical_set"))
        {
            auto const geometrical_set_name =
                geometrical_set_config.getConfigParameter<std::string>("name",
                                                                       "");
            auto const geometry_name =
                geometrical_set_config.getConfigParameter<std::string>(
                    "geometry");
            mesh_names_for_output.push_back(geometrical_set_name + "_" +
                                            geometry_name);
        }
    }
 
    output_config.output_iteration_results =
        config.getConfigParameter<bool>("output_iteration_results", false);
 
    return output_config;
}
}  // namespace ProcessLib