Refactor part mesh tool

Applications/Utils/ModelPreparation/CMakeLists.txt

@@ -19,6 +19,4 @@ target_link_libraries(createNeumannBc
     ${OGS_VTK_REQUIRED_LIBS}
 )
 
-if(OGS_BUILD_METIS)
-    add_subdirectory(PartitionMesh)
-endif()
+add_subdirectory(PartitionMesh)

Applications/Utils/ModelPreparation/PartitionMesh/CMakeLists.txt

@@ -1,6 +1,8 @@
-add_executable(partmesh PartitionMesh.cpp NodeWiseMeshPartitioner.h NodeWiseMeshPartitioner.cpp)
+add_executable(partmesh PartitionMesh.cpp Metis.cpp NodeWiseMeshPartitioner.cpp)
+
 set_target_properties(partmesh PROPERTIES FOLDER Utilities)
 target_link_libraries(partmesh MeshLib)
+add_dependencies(partmesh mpmetis)
 
 ####################
 ### Installation ###

Applications/Utils/ModelPreparation/PartitionMesh/Metis.cpp

@@ -0,0 +1,99 @@
+/**
+ * \file
+ *
+ * \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 <iostream>
+
+#include "BaseLib/Error.h"
+#include "MeshLib/Elements/Element.h"
+
+namespace ApplicationUtils
+{
+void writeMETIS(std::vector<MeshLib::Element*> const& elements,
+                const std::string& file_name)
+{
+    std::ofstream os(file_name, std::ios::trunc);
+    if (!os.is_open())
+    {
+        OGS_FATAL("Error: cannot open file %s.", file_name.data());
+    }
+
+    if (!os.good())
+    {
+        OGS_FATAL("Error: Cannot write in file %s.", file_name.data());
+    }
+
+    os << elements.size() << " \n";
+    for (const auto* elem : elements)
+    {
+        os << elem->getNodeIndex(0) + 1;
+        for (unsigned j = 1; j < elem->getNumberOfNodes(); j++)
+        {
+            os << " " << elem->getNodeIndex(j) + 1;
+        }
+        os << "\n";
+    }
+}
+
+std::vector<std::size_t> readMetisData(const std::string& file_name_base,
+                                       long const number_of_partitions,
+                                       std::size_t const number_of_nodes)
+{
+    const std::string npartitions_str = std::to_string(number_of_partitions);
+
+    // Read partitioned mesh data from METIS
+    const std::string fname_parts =
+        file_name_base + ".mesh.npart." + npartitions_str;
+
+    std::ifstream npart_in(fname_parts);
+    if (!npart_in.is_open())
+    {
+        OGS_FATAL(
+            "Error: cannot open file %s. It may not exist!\n"
+            "Run mpmetis beforehand or use option -m",
+            fname_parts.data());
+    }
+
+    std::vector<std::size_t> partition_ids(number_of_nodes);
+
+
+    std::size_t counter = 0;
+    while (!npart_in.eof())
+    {
+        npart_in >> partition_ids[counter++] >> std::ws;
+        if (counter == number_of_nodes)
+        {
+            break;
+        }
+    }
+
+    if (npart_in.bad())
+    {
+        OGS_FATAL("Error while reading file %s.", fname_parts.data());
+    }
+
+    if (counter != number_of_nodes)
+    {
+        OGS_FATAL("Error: data in %s are less than expected.",
+                  fname_parts.data());
+    }
+
+    return partition_ids;
+}
+
+void removeMetisPartitioningFiles(std::string const& file_name_base,
+                                  long const number_of_partitions)
+{
+    const std::string npartitions_str = std::to_string(number_of_partitions);
+
+    std::remove((file_name_base + ".mesh.npart." + npartitions_str).c_str());
+    std::remove((file_name_base + ".mesh.epart." + npartitions_str).c_str());
+}
+}  // namespace ApplicationUtils

Applications/Utils/ModelPreparation/PartitionMesh/Metis.h

@@ -0,0 +1,44 @@
+/**
+ * \file
+ *
+ * \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
+ *
+ */
+
+#pragma once
+
+#include <string>
+#include <vector>
+
+namespace MeshLib
+{
+class Element;
+}
+
+namespace ApplicationUtils
+{
+/// Write elements as METIS graph file
+/// \param elements The mesh elements.
+/// \param file_name File name with an extension of mesh.
+void writeMETIS(std::vector<MeshLib::Element*> const& elements,
+                const std::string& file_name);
+
+/// Read metis data
+/// \param file_name_base The prefix of the filename.
+/// \param number_of_partitions The number is used to compose the full filename
+///                             and forms the postfix.
+/// \param number_of_nodes Expected/required number of nodes to be read.
+std::vector<std::size_t> readMetisData(const std::string& file_name_base,
+                                       long number_of_partitions,
+                                       std::size_t number_of_nodes);
+
+/// Removes the F.mesh.npart.P and F.mesh.epart.P files, where F is file name
+/// base and P is the number of partitions.
+void removeMetisPartitioningFiles(std::string const& file_name_base,
+                                  long number_of_partitions);
+
+}  // namespace ApplicationUtils