From e1c71927734cfacbcc7f12c664fb7f651847b20f Mon Sep 17 00:00:00 2001
From: Wenqing Wang <wenqing.wang@ufz.de>
Date: Mon, 9 May 2016 17:05:56 +0200
Subject: [PATCH] [PMesh] Added a mesh partitioning tool as a utility
---
Applications/Utils/CMakeLists.txt | 1 +
.../Utils/PartitionMesh/CMakeLists.txt | 23 ++++++
.../Utils/PartitionMesh/MeshPartitioning.cpp | 51 +++++++++++++
.../Utils/PartitionMesh/MeshPartitioning.h | 58 +++++++++++++++
.../Utils/PartitionMesh/PartitionMesh.cpp | 72 +++++++++++++++++++
5 files changed, 205 insertions(+)
create mode 100644 Applications/Utils/PartitionMesh/CMakeLists.txt
create mode 100644 Applications/Utils/PartitionMesh/MeshPartitioning.cpp
create mode 100644 Applications/Utils/PartitionMesh/MeshPartitioning.h
create mode 100644 Applications/Utils/PartitionMesh/PartitionMesh.cpp
diff --git a/Applications/Utils/CMakeLists.txt b/Applications/Utils/CMakeLists.txt
index 8c39fbc8274..b59b53186da 100644
--- a/Applications/Utils/CMakeLists.txt
+++ b/Applications/Utils/CMakeLists.txt
@@ -3,6 +3,7 @@ add_subdirectory(GeoTools)
add_subdirectory(MeshGeoTools)
add_subdirectory(MeshEdit)
add_subdirectory(ModelPreparation)
+add_subdirectory(PartitionMesh)
add_subdirectory(SimpleMeshCreation)
if(OGS_BUILD_GUI)
diff --git a/Applications/Utils/PartitionMesh/CMakeLists.txt b/Applications/Utils/PartitionMesh/CMakeLists.txt
new file mode 100644
index 00000000000..0c85505cfd2
--- /dev/null
+++ b/Applications/Utils/PartitionMesh/CMakeLists.txt
@@ -0,0 +1,23 @@
+
+include_directories(
+ ${CMAKE_SOURCE_DIR}/Utils/PartitionMesh
+ ${CMAKE_SOURCE_DIR}/BaseLib
+ ${CMAKE_SOURCE_DIR}/FileIO
+ ${CMAKE_SOURCE_DIR}/MeshLib
+)
+
+add_executable(partmesh PartitionMesh.cpp MeshPartitioning.h MeshPartitioning.cpp)
+set_target_properties(partmesh PROPERTIES FOLDER Utilities)
+target_link_libraries(partmesh FileIO)
+ADD_VTK_DEPENDENCY(partmesh)
+
+####################
+### Installation ###
+####################
+install(TARGETS partmesh RUNTIME DESTINATION bin COMPONENT ogs_partmesh)
+
+cpack_add_component(ogs_partmesh
+ DISPLAY_NAME "Mesh partitioning tool"
+ DESCRIPTION "Mesh partitioning tool."
+ GROUP Utilities
+)
diff --git a/Applications/Utils/PartitionMesh/MeshPartitioning.cpp b/Applications/Utils/PartitionMesh/MeshPartitioning.cpp
new file mode 100644
index 00000000000..ead10df8c64
--- /dev/null
+++ b/Applications/Utils/PartitionMesh/MeshPartitioning.cpp
@@ -0,0 +1,51 @@
+/*!
+ \file MeshPartitioning.cpp
+ \date 2016.05
+
+ \brief Define the members of class MeshPartitioning
+
+ \copyright
+ Copyright (c) 2012-2016, 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 "MeshPartitioning.h"
+
+#include <fstream>
+
+#include "MeshLib/Elements/Element.h"
+
+namespace MeshLib
+{
+void MeshPartitioning :: write2METIS(const std::string& file_name)
+{
+ std::ofstream os(file_name.data(), std::ios::trunc);
+ os << _elements.size() <<" \n";
+ for (const auto elem : _elements)
+ {
+ for (unsigned j=0; j<elem->getNNodes(); j++)
+ {
+ os << elem->getNodeIndex(j) + 1 <<" ";
+ }
+ os << std::endl;
+ }
+}
+
+void MeshPartitioning :: partitionByNode()
+{
+
+}
+
+void MeshPartitioning :: writeNodePartitionedMeshASCII()
+{
+}
+
+void MeshPartitioning :: writeNodePartitionedMeshBinary()
+{
+}
+
+} // namespace MeshLib
+
diff --git a/Applications/Utils/PartitionMesh/MeshPartitioning.h b/Applications/Utils/PartitionMesh/MeshPartitioning.h
new file mode 100644
index 00000000000..ae1270479be
--- /dev/null
+++ b/Applications/Utils/PartitionMesh/MeshPartitioning.h
@@ -0,0 +1,58 @@
+/*!
+ \file MeshPartitioning.h
+ \date 2016.05
+
+ \brief Declare a class to perform mesh partitioning
+
+ \copyright
+ Copyright (c) 2012-2016, OpenGeoSys Community (http://www.opengeosys.org)
+ Distributed under a Modified BSD License.
+ See accompanying file LICENSE.txt or
+ http://www.opengeosys.org/project/license
+
+*/
+
+#ifndef MESH_PARTITIONING_H_
+#define MESH_PARTITIONING_H_
+
+#include <vector>
+#include <string>
+
+#include "MeshLib/Mesh.h"
+
+namespace MeshLib
+{
+
+/// A subdomain mesh.
+class MeshPartitioning : public Mesh
+{
+ public:
+ /// Copy constructor
+ MeshPartitioning(const MeshLib::Mesh &mesh) : Mesh(mesh)
+ {}
+
+ /// Write mesh to METIS input file
+ void write2METIS(const std::string& file_name);
+
+ /// Partition by element.
+ void partitionByElement()
+ {
+ /* to be decided */
+ }
+
+ /// Partition by node.
+ void partitionByNode();
+
+ /// Write the partitioned mesh into ASCII files.
+ void writeNodePartitionedMeshASCII();
+
+ /// Write the partitioned mesh into binary files.
+ void writeNodePartitionedMeshBinary();
+
+ private:
+
+};
+
+} // namespace MeshLib
+
+#endif // MESH_PARTITIONING_H_
diff --git a/Applications/Utils/PartitionMesh/PartitionMesh.cpp b/Applications/Utils/PartitionMesh/PartitionMesh.cpp
new file mode 100644
index 00000000000..b277abddb8e
--- /dev/null
+++ b/Applications/Utils/PartitionMesh/PartitionMesh.cpp
@@ -0,0 +1,72 @@
+/*!
+ \file PartitionMesh.cpp
+ \date 2016.05
+
+ \brief A tool for mesh partitioning.
+
+ \copyright
+ Copyright (c) 2012-2016, 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 "logog/include/logog.hpp"
+
+#include "LogogSimpleFormatter.h"
+#include "BaseLib/FileTools.h"
+
+#include "FileIO/VtkIO/VtuInterface.h"
+#include "Legacy/MeshIO.h"
+
+#include "MeshPartitioning.h"
+
+int main (int argc, char* argv[])
+{
+ LOGOG_INITIALIZE();
+ logog::Cout* logog_cout (new logog::Cout);
+ BaseLib::LogogSimpleFormatter *custom_format (new BaseLib::LogogSimpleFormatter);
+ logog_cout->SetFormatter(*custom_format);
+
+ std::string m_str = "Partition a mesh for parallel computing."
+ "The tasks of this tool are in twofold:\n"
+ "1. Convert mesh file to the input file of the partitioning tool,\n"
+ "2. Partition a mesh using the partitioning tool,\n"
+ "\tcreate the mesh data of each partition,\n"
+ "\trenumber the node indicies of each partition,\n"
+ "\tand output the results for parallel computing.";
+
+ TCLAP::CmdLine cmd(m_str, ' ', "0.1");
+ TCLAP::ValueArg<std::string> mesh_in("i", "mesh-input-file",
+ "the name of the file containing the input mesh", true,
+ "", "file name of input mesh");
+
+ TCLAP::SwitchArg ogs2metis_flag("1", "ogs2metis",
+ "Indicator to convert the ogs mesh file to METIS input file", cmd, false);
+
+ cmd.parse(argc, argv);
+
+ const std::string ifile_name = mesh_in.getValue();
+
+ MeshLib::MeshPartitioning* mesh = dynamic_cast<MeshLib::MeshPartitioning*>
+ (FileIO::VtuInterface::readVTUFile(ifile_name));
+ INFO("Mesh read: %d nodes, %d elements.", mesh->getNNodes(), mesh->getNElements());
+
+ if ( ogs2metis_flag.getValue() )
+ {
+ mesh->write2METIS(BaseLib::dropFileExtension(ifile_name) + ".mesh");
+ }
+ else
+ {
+
+ }
+
+ delete custom_format;
+ delete logog_cout;
+ LOGOG_SHUTDOWN();
+
+ return 0;
+}
--
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