Identify subdomains tool.

Applications/Utils/MeshGeoTools/CMakeLists.txt

@@ -15,3 +15,11 @@ target_link_libraries(constructMeshesFromGeometry
     ApplicationsFileIO
     ${OGS_VTK_REQUIRED_LIBS}
 )
+
+add_executable(identifySubdomains IdentifySubdomains.cpp )
+set_target_properties(identifySubdomains PROPERTIES FOLDER Utilities)
+target_link_libraries(identifySubdomains
+    MeshGeoToolsLib
+    ApplicationsFileIO
+    ${OGS_VTK_REQUIRED_LIBS}
+)

Applications/Utils/MeshGeoTools/IdentifySubdomains.cpp

@@ -0,0 +1,139 @@
+/**
+ * \copyright
+ * Copyright (c) 2012-2018, OpenGeoSys Community (http://www.opengeosys.org)
+ *            Distributed under a Modified BSD License.
+ *              See accompanying file LICENSE.txt or
+ *              http://www.opengeosys.org/project/license
+ *
+ */
+
+#include <tclap/CmdLine.h>
+
+#include "Applications/ApplicationsLib/LogogSetup.h"
+#include "BaseLib/BuildInfo.h"
+#include "MeshGeoToolsLib/IdentifySubdomainMesh.h"
+#include "MeshGeoToolsLib/MeshNodeSearcher.h"
+#include "MeshGeoToolsLib/SearchLength.h"
+#include "MeshLib/IO/readMeshFromFile.h"
+#include "MeshLib/IO/writeMeshToFile.h"
+#include "MeshLib/Mesh.h"
+
+std::vector<std::unique_ptr<MeshLib::Mesh>> readMeshes(
+    std::vector<std::string> const& filenames)
+{
+    std::vector<std::unique_ptr<MeshLib::Mesh>> meshes;
+    meshes.reserve(filenames.size());
+
+    for (auto const& filename : filenames)
+    {
+        meshes.emplace_back(MeshLib::IO::readMeshFromFile(filename));
+    }
+    if (meshes.empty())
+    {
+        OGS_FATAL("No subdomain meshes were read.");
+    }
+    return meshes;
+}
+
+int main(int argc, char* argv[])
+{
+    ApplicationsLib::LogogSetup logog_setup;
+
+    TCLAP::CmdLine cmd(
+        "Checks if the subdomain meshes are part of the bulk mesh and writes "
+        "the 'bulk_node_ids' and the 'bulk_element_ids' in each of them.\n\n"
+        "OpenGeoSys-6 software, version " +
+            BaseLib::BuildInfo::git_describe +
+            ".\n"
+            "Copyright (c) 2012-2018, OpenGeoSys Community "
+            "(http://www.opengeosys.org)",
+        ' ', BaseLib::BuildInfo::git_describe);
+
+    TCLAP::ValueArg<bool> force_overwrite_arg(
+        "f",
+        "force",
+        "Overwrites the existing subdomain meshes. (default: do not "
+        "overwrite.)",
+        false,
+        false,
+        "true/false");
+    cmd.add(force_overwrite_arg);
+
+    TCLAP::ValueArg<std::string> output_prefix_arg(
+        "o",
+        "output_prefix",
+        "Prefix the subdomain meshes' filenames with the output prefix/path.",
+        false,
+        "",
+        "path");
+    cmd.add(output_prefix_arg);
+
+    TCLAP::ValueArg<double> search_length_arg(
+        "s",
+        "searchlength",
+        "search length determining radius for the node search algorithm. "
+        "Non-negative floating point number (default 1e-16) ",
+        false,
+        1e-16,
+        "float");
+    cmd.add(search_length_arg);
+
+    TCLAP::ValueArg<std::string> bulk_mesh_arg(
+        "m", "mesh", "the file name of the bulk mesh", true, "", "mesh file");
+    cmd.add(bulk_mesh_arg);
+
+    // All the remaining arguments are used as file names for boundary/subdomain
+    // meshes.
+    TCLAP::UnlabeledMultiArg<std::string> subdomain_meshes_filenames_arg(
+        "subdomain_meshes_filenames", "mesh file names.", true,
+        "subdomain mesh file");
+    cmd.add(subdomain_meshes_filenames_arg);
+    cmd.parse(argc, argv);
+
+    //
+    // The bulk mesh.
+    //
+    std::unique_ptr<MeshLib::Mesh> bulk_mesh{
+        MeshLib::IO::readMeshFromFile(bulk_mesh_arg.getValue())};
+
+    //
+    // Read the subdomain meshes.
+    //
+    auto const subdomain_meshes =
+        readMeshes(subdomain_meshes_filenames_arg.getValue());
+
+    //
+    // Bulk mesh node searcher.
+    //
+    auto const& mesh_node_searcher =
+        MeshGeoToolsLib::MeshNodeSearcher::getMeshNodeSearcher(
+            *bulk_mesh,
+            std::make_unique<MeshGeoToolsLib::SearchLength>(
+                search_length_arg.getValue()));
+
+    //
+    // Identify the subdomains in the bulk mesh.
+    //
+    for (auto& mesh_ptr : subdomain_meshes)
+    {
+        // If force overwrite is set or the output is to different mesh than
+        // the input mesh.
+        bool const overwrite_property_vectors =
+            force_overwrite_arg.getValue() ||
+            !output_prefix_arg.getValue().empty();
+        identifySubdomainMesh(*mesh_ptr, *bulk_mesh, mesh_node_searcher,
+                              overwrite_property_vectors);
+    }
+
+    //
+    // Output after the successful subdomain mesh identification.
+    //
+    for (auto const& mesh_ptr : subdomain_meshes)
+    {
+        MeshLib::IO::writeMeshToFile(
+            *mesh_ptr,
+            output_prefix_arg.getValue() + mesh_ptr->getName() + ".vtu");
+    }
+
+    return EXIT_SUCCESS;
+}

Applications/Utils/Tests.cmake

@@ -40,6 +40,34 @@ AddTest(
     expected_post_single_joint_pcs_0_ts_1_t_1.000000.vtu post_single_joint_pcs_0_ts_1_t_1.000000.vtu u u 1e-14 1e-14
 )
 
+AddTest(
+    NAME identifySubdomains_2D_Create
+    PATH MeshGeoToolsLib/IdentifySubdomains
+    EXECUTABLE identifySubdomains
+    EXECUTABLE_ARGS -m 2D_mesh.vtu -o ${Data_BINARY_DIR}/MeshGeoToolsLib/IdentifySubdomains/new_ -- 2D_mesh_top_boundary.vtu 2D_mesh_bottom_boundary.vtu
+    REQUIREMENTS NOT OGS_USE_MPI
+    TESTER vtkdiff
+    DIFF_DATA
+    2D_mesh_top.vtu new_2D_mesh_top_boundary.vtu bulk_node_ids bulk_node_ids 0 0
+    2D_mesh_top.vtu new_2D_mesh_top_boundary.vtu bulk_element_ids bulk_element_ids 0 0
+    2D_mesh_bottom.vtu new_2D_mesh_bottom_boundary.vtu bulk_node_ids bulk_node_ids 0 0
+    2D_mesh_bottom.vtu new_2D_mesh_bottom_boundary.vtu bulk_element_ids bulk_element_ids 0 0
+)
+
+AddTest(
+    NAME identifySubdomains_2D_Check
+    PATH MeshGeoToolsLib/IdentifySubdomains
+    EXECUTABLE identifySubdomains
+    EXECUTABLE_ARGS -m 2D_mesh.vtu -o ${Data_BINARY_DIR}/MeshGeoToolsLib/IdentifySubdomains/check_ -- 2D_mesh_top.vtu 2D_mesh_bottom.vtu
+    REQUIREMENTS NOT OGS_USE_MPI
+    TESTER vtkdiff
+    DIFF_DATA
+    2D_mesh_top.vtu check_2D_mesh_top.vtu bulk_node_ids bulk_node_ids 0 0
+    2D_mesh_top.vtu check_2D_mesh_top.vtu bulk_element_ids bulk_element_ids 0 0
+    2D_mesh_bottom.vtu check_2D_mesh_bottom.vtu bulk_node_ids bulk_node_ids 0 0
+    2D_mesh_bottom.vtu check_2D_mesh_bottom.vtu bulk_element_ids bulk_element_ids 0 0
+)
+
 # Mac is producing slightly different partitioning, so the results are not
 # comparable.
 AddTest(

Jenkinsfile

@@ -99,7 +99,7 @@ pipeline {
               //       .*potential recursive class relation.*
               recordIssues tools: [[pattern: 'build/DoxygenWarnings.log',
                 tool: [$class: 'Doxygen']]],
-                unstableTotalAll: 23
+                unstableTotalAll: 24
               dir('build/docs') { stash(name: 'doxygen') }
               publishHTML(target: [allowMissing: false, alwaysLinkToLastBuild: true,
                   keepAll: true, reportDir: 'build/docs', reportFiles: 'index.html',