PVTU2VTU.cpp

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// SPDX-FileCopyrightText: Copyright (c) OpenGeoSys Community (opengeosys.org)
// SPDX-License-Identifier: BSD-3-Clause
 
#include <tclap/CmdLine.h>
 
#include <algorithm>
#include <boost/property_tree/ptree.hpp>
#include <boost/property_tree/xml_parser.hpp>
#include <filesystem>
#include <fstream>
#include <memory>
#include <numeric>
#include <range/v3/algorithm/copy.hpp>
#include <range/v3/algorithm/transform.hpp>
#include <range/v3/numeric/accumulate.hpp>
#include <range/v3/range/conversion.hpp>
#include <range/v3/view/filter.hpp>
#include <string>
#include <unordered_set>
#include <vector>
 
#include "BaseLib/DemangleTypeInfo.h"
#include "BaseLib/FileTools.h"
#include "BaseLib/Logging.h"
#include "BaseLib/MPI.h"
#include "BaseLib/RunTime.h"
#include "BaseLib/TCLAPArguments.h"
#include "GeoLib/AABB.h"
#include "GeoLib/OctTree.h"
#include "InfoLib/GitInfo.h"
#include "MathLib/Point3d.h"
#include "MeshLib/Elements/Element.h"
#include "MeshLib/IO/VtkIO/VtuInterface.h"
#include "MeshLib/Mesh.h"
#include "MeshLib/Node.h"
#include "MeshLib/Properties.h"
#include "MeshLib/Utils/IntegrationPointWriter.h"
#include "MeshLib/Utils/getOrCreateMeshProperty.h"
#include "MeshToolsLib/IntegrationPointDataTools.h"
 
struct MeshEntityMapInfo
{
    std::size_t partition_id;
    std::size_t original_id;
};
 
template <typename T>
bool createPropertyVector(
    MeshLib::Mesh& merged_mesh,
    std::vector<std::unique_ptr<MeshLib::Mesh>> const& partitioned_meshes,
    MeshLib::PropertyVector<T> const* const pv,
    MeshLib::Properties const& properties,
    std::vector<MeshEntityMapInfo> const& merged_node_map,
    std::vector<MeshEntityMapInfo> const& merged_element_map)
{
    if (pv == nullptr)
    {
        return false;
    }
 
    if (pv->getPropertyName() == "vtkGhostType")
    {
        // Do nothing
        return true;
    }
 
    auto const item_type = pv->getMeshItemType();
 
    auto const pv_name = pv->getPropertyName();
 
    auto const pv_num_components = pv->getNumberOfGlobalComponents();
 
    if (pv_name == "OGS_VERSION" || pv_name == "IntegrationPointMetaData")
    {
        auto new_pv = MeshLib::getOrCreateMeshProperty<T>(
            merged_mesh, pv_name, item_type, pv_num_components);
        new_pv->assign(*pv);
 
        return true;
    }
 
    std::vector<MeshLib::PropertyVector<T>*> partition_property_vectors;
    partition_property_vectors.reserve(partitioned_meshes.size());
    for (auto const& mesh : partitioned_meshes)
    {
        partition_property_vectors.emplace_back(
            mesh->getProperties().getPropertyVector<T>(pv_name, item_type,
                                                       pv_num_components));
    }
 
    auto createNewCellOrNodePropertyVector =
        [&](std::vector<MeshEntityMapInfo> const& mesh_entity_map)
    {
        auto new_pv = MeshLib::getOrCreateMeshProperty<T>(
            merged_mesh, pv_name, item_type, pv_num_components);
        std::size_t counter = 0;
        for (auto const& entity_info : mesh_entity_map)
        {
            auto const& partition_pv =
                partition_property_vectors[entity_info.partition_id];
            for (int i_com = 0; i_com < pv_num_components; i_com++)
            {
                (*new_pv)[counter * pv_num_components + i_com] =
                    (*partition_pv)[entity_info.original_id *
                                        pv_num_components +
                                    i_com];
            }
            counter++;
        }
    };
 
    if (item_type == MeshLib::MeshItemType::Node)
    {
        createNewCellOrNodePropertyVector(merged_node_map);
        return true;
    }
 
    if (item_type == MeshLib::MeshItemType::Cell)
    {
        createNewCellOrNodePropertyVector(merged_element_map);
        return true;
    }
 
    if (item_type == MeshLib::MeshItemType::IntegrationPoint)
    {
        std::vector<std::vector<std::size_t>> partition_element_offsets;
        partition_element_offsets.reserve(partitioned_meshes.size());
        for (auto const& mesh : partitioned_meshes)
        {
            partition_element_offsets.emplace_back(
                MeshToolsLib::getIntegrationPointDataOffsetsOfMeshElements(
                    mesh->getElements(), *pv, properties));
        }
 
        auto new_pv = MeshLib::getOrCreateMeshProperty<T>(
            merged_mesh, pv_name, item_type, pv_num_components);
 
        // Count the integration points
        auto const ip_meta_data =
            MeshLib::getIntegrationPointMetaDataSingleField(
                MeshLib::getIntegrationPointMetaData(properties), pv_name);
 
        auto number_of_integration_points = [&](auto const* element)
        {
            return MeshToolsLib::getNumberOfElementIntegrationPoints(
                ip_meta_data, *element);
        };
 
        std::size_t const counter = ranges::accumulate(
            merged_mesh.getElements() |
                ranges::views::transform(number_of_integration_points),
            std::size_t{0});
        new_pv->resize(counter * pv_num_components);
 
        auto const global_ip_offsets =
            MeshToolsLib::getIntegrationPointDataOffsetsOfMeshElements(
                merged_mesh.getElements(), *pv, properties);
 
        std::size_t element_counter = 0;
        for (auto const& element_info : merged_element_map)
        {
            MeshLib::PropertyVector<T> const& partition_pv =
                *(partition_property_vectors[element_info.partition_id]);
 
            auto const& offsets =
                partition_element_offsets[element_info.partition_id];
 
            int const begin_pos = offsets[element_info.original_id];
            int const end_pos = offsets[element_info.original_id + 1];
 
            std::copy(partition_pv.begin() + begin_pos,
                      partition_pv.begin() + end_pos,
                      new_pv->begin() + global_ip_offsets[element_counter]);
 
            element_counter++;
        }
    }
 
    return true;
}
 
std::vector<std::string> readVtuFileNames(std::string const& pvtu_file_name)
{
    std::ifstream ins(pvtu_file_name);
 
    if (!ins)
    {
        OGS_FATAL("Could not open pvtu file {:s}.", pvtu_file_name);
    }
 
    using boost::property_tree::ptree;
    ptree pt;
    read_xml(ins, pt);
 
    auto root = pt.get_child("VTKFile");
 
    std::vector<std::string> vtu_file_names;
 
    std::string file_path = BaseLib::extractPath(pvtu_file_name);
 
    for (ptree::value_type const& v : root.get_child("PUnstructuredGrid"))
    {
        if (v.first == "Piece")
        {
            vtu_file_names.push_back(BaseLib::joinPaths(
                file_path,
                // only gets the vtu file name:
                std::filesystem::path(v.second.get("<xmlattr>.Source", ""))
                    .filename()
                    .string()));
        }
    }
 
    if (vtu_file_names.empty())
    {
        OGS_FATAL("PVTU file {:s} does not contain any vtu piece",
                  pvtu_file_name);
    }
 
    return vtu_file_names;
}
 
// all nodes (also 'ghost' nodes) of all meshes sorted by partition
std::tuple<std::vector<MeshLib::Node*>, std::vector<std::size_t>>
getMergedNodesVector(std::vector<std::unique_ptr<MeshLib::Mesh>> const& meshes)
{
    std::vector<std::size_t> number_of_nodes_per_partition;
    ranges::transform(meshes, std::back_inserter(number_of_nodes_per_partition),
                      [](auto const& mesh)
                      { return mesh->getNumberOfNodes(); });
    std::vector<std::size_t> const offsets =
        BaseLib::sizesToOffsets(number_of_nodes_per_partition);
 
    std::vector<MeshLib::Node*> all_nodes;
    all_nodes.reserve(offsets.back());
    for (auto const& mesh : meshes)
    {
        ranges::copy(mesh->getNodes(), std::back_inserter(all_nodes));
    }
    return {all_nodes, offsets};
}
 
std::tuple<std::vector<MeshLib::Element*>, std::vector<MeshEntityMapInfo>>
getRegularElements(std::vector<std::unique_ptr<MeshLib::Mesh>> const& meshes)
{
    std::vector<MeshLib::Element*> regular_elements;
 
    std::size_t partition_counter = 0;
    std::vector<MeshEntityMapInfo> merged_element_map;
    for (auto const& mesh : meshes)
    {
        MeshLib::Properties const& properties = mesh->getProperties();
 
        auto const* const ghost_id_vector =
            properties.getPropertyVector<unsigned char>("vtkGhostType");
        assert(ghost_id_vector);
 
        auto const& mesh_elements = mesh->getElements();
 
        auto const last_element_id_of_previous_partition =
            regular_elements.size();
 
        auto is_regular_element = [&](MeshLib::Element const* element)
        { return (*ghost_id_vector)[element->getID()] == 0; };
 
        auto regular_mesh_elements =
            mesh_elements | ranges::views::filter(is_regular_element);
        regular_elements.insert(regular_elements.end(),
                                regular_mesh_elements.begin(),
                                regular_mesh_elements.end());
 
        for (auto element_id = last_element_id_of_previous_partition;
             element_id < regular_elements.size();
             element_id++)
        {
            merged_element_map.push_back(
                {partition_counter, regular_elements[element_id]->getID()});
        }
 
        partition_counter++;
    }
 
    return {regular_elements, merged_element_map};
}
 
MeshLib::Node* getExistingNodeFromOctTree(
    GeoLib::OctTree<MeshLib::Node, 16>& oct_tree, Eigen::Vector3d const& extent,
    MeshLib::Node const& node, std::size_t const element_id)
{
    std::vector<MeshLib::Node*> query_nodes;
    auto const eps =
        std::numeric_limits<double>::epsilon() * extent.squaredNorm();
    Eigen::Vector3d const min = node.asEigenVector3d().array() - eps;
    auto constexpr dir = std::numeric_limits<double>::max();
    Eigen::Vector3d const max = {std::nextafter(node[0] + eps, dir),
                                 std::nextafter(node[1] + eps, dir),
                                 std::nextafter(node[2] + eps, dir)};
    oct_tree.getPointsInRange(min, max, query_nodes);
 
    if (query_nodes.empty())
    {
        OGS_FATAL(
            "query_nodes for node [{}], ({}, {}, {}) of element "
            "[{}] are empty, eps is {}",
            node.getID(), node[0], node[1], node[2], element_id, eps);
    }
    auto const it =
        std::find_if(query_nodes.begin(), query_nodes.end(),
                     [&node, eps](auto const* p)
                     {
                         return (p->asEigenVector3d() - node.asEigenVector3d())
                                    .squaredNorm() < eps;
                     });
    if (it == query_nodes.end())
    {
        OGS_FATAL(
            "did not find node: [{}] ({}, {}, {}) of element [{}] in "
            "query_nodes",
            node.getID(), node[0], node[1], node[2], element_id);
    }
    return *it;
}
 
void resetNodesInRegularElements(
    std::vector<MeshLib::Element*> const& regular_elements,
    GeoLib::OctTree<MeshLib::Node, 16>& oct_tree,
    Eigen::Vector3d const& extent)
{
    for (auto& e : regular_elements)
    {
        for (unsigned i = 0; i < e->getNumberOfNodes(); i++)
        {
            auto* const node = e->getNode(i);
            MeshLib::Node* node_ptr = nullptr;
            if (!oct_tree.addPoint(node, node_ptr))
            {
                auto const node_ptr = getExistingNodeFromOctTree(
                    oct_tree, extent, *node, e->getID());
                e->setNode(i, node_ptr);
            }
        }
    }
}
 
std::pair<std::vector<MeshLib::Node*>, std::vector<MeshEntityMapInfo>>
makeNodesUnique(std::vector<MeshLib::Node*> const& all_merged_nodes_tmp,
                std::vector<std::size_t> const& partition_offsets,
                GeoLib::OctTree<MeshLib::Node, 16>& oct_tree)
{
    std::vector<MeshLib::Node*> unique_merged_nodes;
    unique_merged_nodes.reserve(all_merged_nodes_tmp.size());
 
    std::vector<MeshEntityMapInfo> merged_node_map;
    merged_node_map.reserve(all_merged_nodes_tmp.size());
 
    for (std::size_t i = 0; i < partition_offsets.size() - 1; ++i)
    {
        for (std::size_t pos = partition_offsets[i];
             pos < partition_offsets[i + 1];
             ++pos)
        {
            auto* node = all_merged_nodes_tmp[pos];
            MeshLib::Node* node_ptr = nullptr;
            if (oct_tree.addPoint(node, node_ptr))
            {
                unique_merged_nodes.push_back(node);
                merged_node_map.push_back({i, pos - partition_offsets[i]});
            }
        }
    }
    return {unique_merged_nodes, merged_node_map};
}
 
std::unique_ptr<MeshLib::Mesh> mergeSubdomainMeshes(
    std::vector<std::unique_ptr<MeshLib::Mesh>> const& meshes)
{
    BaseLib::RunTime merged_element_timer;
    merged_element_timer.start();
    // If structured binding is used for the returned tuple, Mac compiler gives
    // an error in reference to local binding in calling applyToPropertyVectors.
    auto [regular_elements, merged_element_map] = getRegularElements(meshes);
    INFO(
        "Collection of {} regular elements and computing element map took {} s",
        regular_elements.size(), merged_element_timer.elapsed());
 
    // alternative implementation of getNodesOfRegularElements
    BaseLib::RunTime collect_nodes_timer;
    collect_nodes_timer.start();
    auto [all_merged_nodes_tmp, partition_offsets] =
        getMergedNodesVector(meshes);
    INFO("Collection of {} nodes and computing offsets took {} s",
         all_merged_nodes_tmp.size(), collect_nodes_timer.elapsed());
 
    BaseLib::RunTime merged_nodes_timer;
    merged_nodes_timer.start();
    GeoLib::AABB aabb(all_merged_nodes_tmp.begin(), all_merged_nodes_tmp.end());
    auto oct_tree = std::unique_ptr<GeoLib::OctTree<MeshLib::Node, 16>>(
        GeoLib::OctTree<MeshLib::Node, 16>::createOctTree(
            aabb.getMinPoint(), aabb.getMaxPoint(), 1e-16));
 
    auto [unique_merged_nodes, merged_node_map] =
        makeNodesUnique(all_merged_nodes_tmp, partition_offsets, *oct_tree);
    INFO("Make nodes unique ({} unique nodes) / computing map took {} s",
         unique_merged_nodes.size(), merged_nodes_timer.elapsed());
 
    BaseLib::RunTime reset_nodes_in_elements_timer;
    reset_nodes_in_elements_timer.start();
    auto const extent = aabb.getMaxPoint() - aabb.getMinPoint();
    resetNodesInRegularElements(regular_elements, *oct_tree, extent);
    INFO("Reset nodes in regular elements took {} s",
         reset_nodes_in_elements_timer.elapsed());
 
    BaseLib::RunTime mesh_creation_timer;
    mesh_creation_timer.start();
    // The Node pointers of 'merged_nodes' and Element pointers of
    // 'regular_elements' are shared with 'meshes', the partitioned meshes.
    auto merged_mesh = std::make_unique<MeshLib::Mesh>(
        "pvtu_merged_mesh", unique_merged_nodes, regular_elements,
        false /* compute_element_neighbors */);
    INFO("creation of merged mesh took {} s", mesh_creation_timer.elapsed());
 
    auto const& properties = meshes[0]->getProperties();
 
    BaseLib::RunTime property_timer;
    property_timer.start();
    applyToPropertyVectors(
        properties,
        [&, &merged_node_map = merged_node_map,
         &merged_element_map = merged_element_map](auto type,
                                                   auto const& property)
        {
            return createPropertyVector<decltype(type)>(
                *merged_mesh, meshes,
                dynamic_cast<MeshLib::PropertyVector<decltype(type)> const*>(
                    property),
                properties, merged_node_map, merged_element_map);
        });
    INFO("merge properties into merged mesh took {} s",
         property_timer.elapsed());
    return merged_mesh;
}
 
template <typename T>
bool transfer(MeshLib::Properties const& subdomain_properties,
              MeshLib::Mesh& original_mesh,
              MeshLib::PropertyVector<std::size_t> const& global_ids,
              std::string_view const property_name,
              MeshLib::MeshItemType const mesh_item_type)
{
    if (!subdomain_properties.existsPropertyVector<T>(property_name))
    {
        INFO("Skipping property '{}' since it is not from type '{}'.",
             property_name, BaseLib::typeToString<T>());
        return false;
    }
    auto const* subdomain_pv =
        subdomain_properties.getPropertyVector<T>(property_name);
    auto const number_of_components =
        subdomain_pv->getNumberOfGlobalComponents();
 
    auto* original_pv = MeshLib::getOrCreateMeshProperty<T>(
        original_mesh, std::string(property_name), mesh_item_type,
        number_of_components);
 
    for (std::size_t i = 0; i < global_ids.size(); ++i)
    {
        auto const& global_id = global_ids[i];
        for (std::remove_cvref_t<decltype(number_of_components)>
                 component_number = 0;
             component_number < number_of_components;
             ++component_number)
        {
            original_pv->getComponent(global_id, component_number) =
                subdomain_pv->getComponent(i, component_number);
        }
    }
    INFO("Data array {} from data type '{}' transferred.", property_name,
         BaseLib::typeToString<T>());
    return true;
}
 
void transferPropertiesFromPartitionedMeshToUnpartitionedMesh(
    MeshLib::Mesh const& subdomain_mesh, MeshLib::Mesh& original_mesh,
    MeshLib::MeshItemType const mesh_item_type)
{
    auto const& subdomain_properties = subdomain_mesh.getProperties();
    if (!subdomain_properties.existsPropertyVector<std::size_t>(
            MeshLib::globalIDString(mesh_item_type), mesh_item_type, 1))
    {
        OGS_FATAL(
            "The data array '{}' is required for the transfer of data from "
            "subdomain mesh to the global mesh. But it doesn't exist in "
            "subdomain mesh '{}'.",
            MeshLib::globalIDString(mesh_item_type), subdomain_mesh.getName());
    }
    auto const* global_ids =
        subdomain_properties.getPropertyVector<std::size_t>(
            MeshLib::globalIDString(mesh_item_type), mesh_item_type, 1);
    if (global_ids == nullptr)
    {
        OGS_FATAL("The data array '{}' is not available but required.",
                  MeshLib::globalIDString(mesh_item_type));
    }
 
    auto const& property_names =
        subdomain_properties.getPropertyVectorNames(mesh_item_type);
 
    for (auto const& property_name : property_names)
    {
        if (property_name == MeshLib::globalIDString(mesh_item_type))
        {
            continue;
        }
        if (property_name == MeshLib::getBulkIDString(mesh_item_type))
        {
            INFO(
                "Skipping property '{}' since it is adjusted locally in "
                "NodeWiseMeshPartitioner::renumberBulkNodeIdsProperty().",
                MeshLib::getBulkIDString(mesh_item_type));
            continue;
        }
        if (property_name == "vtkGhostType")
        {
            INFO(
                "Skipping property 'vtkGhostType' since it is only required "
                "for parallel execution.");
            continue;
        }
        if (transfer<double>(subdomain_properties, original_mesh, *global_ids,
                             property_name, mesh_item_type) ||
            transfer<float>(subdomain_properties, original_mesh, *global_ids,
                            property_name, mesh_item_type) ||
            transfer<unsigned>(subdomain_properties, original_mesh, *global_ids,
                               property_name, mesh_item_type) ||
            transfer<unsigned long>(subdomain_properties, original_mesh,
                                    *global_ids, property_name,
                                    mesh_item_type) ||
            transfer<std::size_t>(subdomain_properties, original_mesh,
                                  *global_ids, property_name, mesh_item_type) ||
            transfer<int>(subdomain_properties, original_mesh, *global_ids,
                          property_name, mesh_item_type) ||
            transfer<long>(subdomain_properties, original_mesh, *global_ids,
                           property_name, mesh_item_type))
        {
            INFO("Data array {} transferred from '{}' to'{}'", property_name,
                 subdomain_mesh.getName(), original_mesh.getName());
        }
    }
}
 
void transferPropertiesFromPartitionedMeshToUnpartitionedMesh(
    MeshLib::Mesh const& subdomain_mesh, MeshLib::Mesh& original_mesh)
{
    transferPropertiesFromPartitionedMeshToUnpartitionedMesh(
        subdomain_mesh, original_mesh, MeshLib::MeshItemType::Node);
 
    transferPropertiesFromPartitionedMeshToUnpartitionedMesh(
        subdomain_mesh, original_mesh, MeshLib::MeshItemType::Cell);
}
 
int main(int argc, char* argv[])
{
    TCLAP::CmdLine cmd(
        "This tool merges VTU files of PVTU into one single VTU file. Apart "
        "from the mesh data, all property data are merged as well"
        "\n\nOpenGeoSys-6 software, version " +
            GitInfoLib::GitInfo::ogs_version +
            ".\n"
            "Copyright (c) 2012-2026, OpenGeoSys Community "
            "(http://www.opengeosys.org)",
        ' ', GitInfoLib::GitInfo::ogs_version);
 
    TCLAP::ValueArg<std::string> output_arg(
        "o", "output", "Output (.vtu). The output mesh file (format = *.vtu)",
        true, "", "OUTPUT_FILE");
    cmd.add(output_arg);
 
    TCLAP::ValueArg<std::string> input_arg(
        "i", "input", "Input (.pvtu). The partitioned input mesh file", true,
        "", "INPUT_FILE");
    cmd.add(input_arg);
 
    TCLAP::ValueArg<std::string> original_mesh_input_arg(
        "m", "original_mesh",
        "optional, the original unpartitioned input mesh (*.vtu)", false, "",
        "");
    cmd.add(original_mesh_input_arg);
 
    auto log_level_arg = BaseLib::makeLogLevelArg();
 
    cmd.add(log_level_arg);
    cmd.parse(argc, argv);
 
    BaseLib::MPI::Setup mpi_setup(argc, argv);
    BaseLib::initOGSLogger(log_level_arg.getValue());
 
    if (BaseLib::getFileExtension(input_arg.getValue()) != ".pvtu")
    {
        OGS_FATAL("The extension of input file name {:s} is not \"pvtu\"",
                  input_arg.getValue());
    }
    if (BaseLib::getFileExtension(output_arg.getValue()) != ".vtu")
    {
        OGS_FATAL("The extension of output file name {:s} is not \"vtu\"",
                  output_arg.getValue());
    }
 
    auto const vtu_file_names = readVtuFileNames(input_arg.getValue());
 
    std::vector<std::unique_ptr<MeshLib::Mesh>> meshes;
    meshes.reserve(vtu_file_names.size());
 
    BaseLib::RunTime io_timer;
    io_timer.start();
    for (auto const& file_name : vtu_file_names)
    {
        auto mesh = std::unique_ptr<MeshLib::Mesh>(
            MeshLib::IO::VtuInterface::readVTUFile(file_name));
 
        MeshLib::Properties const& properties = mesh->getProperties();
 
        if (!properties.existsPropertyVector<unsigned char>("vtkGhostType"))
        {
            OGS_FATAL(
                "Property vector vtkGhostType does not exist in mesh {:s}.",
                file_name);
        }
 
        meshes.emplace_back(std::move(mesh));
    }
    INFO("Reading meshes took {} s", io_timer.elapsed());
 
    std::unique_ptr<MeshLib::Mesh> merged_mesh;
    if (original_mesh_input_arg.getValue().empty())
    {
        // use old, slow method that generates node and element orderings not
        // consistent with the original mesh
        merged_mesh = mergeSubdomainMeshes(meshes);
    }
    else
    {
        BaseLib::RunTime io_timer;
        io_timer.start();
        merged_mesh = std::unique_ptr<MeshLib::Mesh>(
            MeshLib::IO::VtuInterface::readVTUFile(
                original_mesh_input_arg.getValue()));
        INFO("Reading original unpartitioned mesh took {} s",
             io_timer.elapsed());
        for (auto const& subdomain_mesh : meshes)
        {
            transferPropertiesFromPartitionedMeshToUnpartitionedMesh(
                *(subdomain_mesh.get()), *merged_mesh);
        }
    }
 
    MeshLib::IO::VtuInterface writer(merged_mesh.get());
 
    BaseLib::RunTime writing_timer;
    writing_timer.start();
    auto const result = writer.writeToFile(output_arg.getValue());
    if (!result)
    {
        ERR("Could not write mesh to '{:s}'.", output_arg.getValue());
        return EXIT_FAILURE;
    }
    INFO("writing mesh took {} s", writing_timer.elapsed());
 
    // Since the Node pointers of 'merged_nodes' and Element pointers of
    // 'regular_elements' are held by 'meshes', the partitioned meshes, the
    // memory by these pointers are released by 'meshes' automatically.
    // Therefore, only node vector and element vector of merged_mesh should be
    // cleaned.
    merged_mesh->shallowClean();
 
    return EXIT_SUCCESS;
}