msh2exo

A Gmsh (Gmsh msh format) to Exodus (ExodusII format) mesh conversion utility

License

msh2exo is distributed under the terms of the GNU General Public License

Copyright (C) 2022 Weston Ortiz

See the LICENSE file for license information.

Third Party Libraries

Various third party libraries are included in tpls/ please see their respective licenses for usage

Requirements

• CMake >= 3.13 (binaries available at https://cmake.org/download/)
• ExodusII library https://github.com/sandialabs/seacas
• (optional) Gmsh SDK (available prebuilt through pip or the Gmsh website https://gmsh.info/#Download) when built with Gmsh SDK, Gmsh will be used to read the msh files
• C++14 compatible compiler (e.g. GCC > 5)

Usage

msh2exo: mesh conversion utility
Usage: ./build/msh2exo [OPTIONS] input_file output_file

Positionals:
  input_file TEXT:FILE REQUIRED
                              Input (Gmsh msh) mesh file
  output_file TEXT REQUIRED   Output (ExodusII) mesh file

Options:
  -h,--help                   Print this help message and exit
  -V,--version                print version and basic info
  -b,--builtin                Use builtin gmsh file reader
  -v,--verbose                increase verbosity

Examples

Examples are available at msh2exo-examples

Supported Elements

• Quadrilateral elements (First and Second Order: QUAD4, QUAD8, QUAD9)
• Triangular elements (First and Second Order: TRI3, TRI6)
• Tetrahedral elements (First Order: TET4)
• Hexahedral elements (First Order: HEX8)

Conversion from Physical Groups to ExodusII data

• ExodusII Blocks are created from physical groups with the largest dimension (MAX_DIM)

  • e.g. if you have a physical volume, a physical surface, and a physical curve then the volume will represent an exodus block

• ExodusII Sidesets are created from physical groups of dimension MAX_DIM - 1, a nodeset of the same name and id will also be created

• ExodusII Nodesets will be created from physical groups of dimensions less than MAX_DIM

ExodusII data numbering

• ExodusII nodes are renumbered to 1 to N_Nodes

• ExodusII elements are renumbered to 1 to N_Elements

• ExodusII blocks are renumbered to 1 to N_Blocks

• ExodusII sidesets and nodesets keep the same number as the physical group

ExodusII data naming

• Names should be preserved for blocks, sidesets, and nodesets

Building

For notes on building for windows see Windows Build Notes

1. A working SEACASExodus install is required

   See build instructions in the SEACAS repository:

   https://github.com/sandialabs/seacas/#get-the-sources

   Or Build with spack https://github.com/sandialabs/seacas/#spack

   spack install seacas spack load seacas

2. Instructions for building msh2exo

   The following commands show an example build:

   <path to seacas> is the pass where SEACAS was installed, usually the seacas git folder, if installed with spack this can be skipped

   <install prefix> is where you want the executable, will install to <install prefix>/bin

   <path to gmsh sdk> is the path to a downloaded gmsh SDK which contains include/gmsh.h and the gmsh library under the lib folder.

   $ git clone --recursive https://github.com/wortiz/msh2exo
   $ mkdir msh2exo/build
   $ cd msh2exo/build
   $ cmake .. -DSEACASExodus_DIR=<path to seacas>/lib/cmake/SEACASExodus \
        -DCMAKE_INSTALL_PREFIX=<install prefix> \ # optional
        -DGmsh_DIR=<path to gmsh sdk> # optional
   $ make # should create a msh2exo executable in msh2exo/build folder
   $ make install # optional, will install to <install prefix>/bin

Windows Build Notes

A working build for Windows 10 with Visual Studio 2019 was done as follows:

Prerequisites:

• Git
• vcpkg
• Visual Studio tested with 2019 community
• CMake

My vcpkg was installed to C:\src\vcpkg the following will need to be adjusted if another location is used I did vcpkg integrate install to integrate with Visual Studio

1. Install Exodus prerequisites:

   This was done in powershell terminal from C:\src\vcpkg

   .\vcpkg install fmt --triplet=x64-windows
   .\vcpkg install netcdf-c --triplet=x64-windows
   

2. Build and Install Exodus

   In C:\src I cloned SEACAS

   cd C:\src
   git clone https://github.com/sandialabs/seacas
   

   Then using CMake configure SEACAS to build ExodusII, modified from appveyor config in SEACAS repository. Adjust locations specified with C:\ to preferred locations

   If cmake is not on path use full path to cmake.exe

   cd C:\src\seacas
   
   mkdir build
   
   cd build
   
   cmake .. -G "Visual Studio 16 2019" -A x64 -DCMAKE_TOOLCHAIN_FILE=C:/Tools/vcpkg/scripts/buildsystems/vcpkg.cmake -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="/wd4478 /EHsc" -DCMAKE_C_FLAGS="/wd4478" -DCMAKE_INSTALL_PREFIX=C:\src\seacas\install -DHDF5_ROOT:PATH=C:\src\vcpkg\installed\x64-windows -DMatio_INCLUDE_DIRS:PATH=C:\src\vcpkg\installed\x64-windows\include -DNetCDF_ROOT:PATH=C:\src\vcpkg\installed\x64-windows -DSEACASExodus_ENABLE_THREADSAFE:BOOL=OFF -DSEACASIoss_ENABLE_THREADSAFE:BOOL=OFF -DSeacas_ENABLE_SEACASExodus:BOOL=ON -DSeacas_ENABLE_DOXYGEN:BOOL=OFF -DSeacas_ENABLE_Fortran=OFF -DSeacas_ENABLE_TESTS=OFF -DSeacas_ENABLE_Zoltan:BOOL=OFF -DSeacas_HIDE_DEPRECATED_CODE:BOOL=ON -DSeacas_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=ON -DTPL_ENABLE_ADIOS2:BOOL=OFF -DTPL_ENABLE_CGNS:BOOL=OFF -DTPL_ENABLE_Kokkos:BOOL=OFF -DTPL_ENABLE_MPI:BOOL=OFF -DTPL_ENABLE_Matio:BOOL=OFF -DTPL_ENABLE_Netcdf:BOOL=ON -DTPL_ENABLE_Pamgen:BOOL=OFF -DTPL_ENABLE_Pthread:BOOL=OFF -DTPL_ENABLE_X11:BOOL=OFF -DCMAKE_SH="CMAKE_SH-NOTFOUND" -DTPL_ENABLE_gtest:BOOL=OFF
   

   Building Exodus using CMake (from within build directory where cmake was run above):

   cmake --build . --config Release
   

   Installing Exodus to CMAKE_INSTALL_PREFIX using CMake (again from build directory):

   cmake --install . --config Release
   

3. Building msh2exo

   Clone repo

   cd C:\src
   
   git clone --recursive https://github.com/wortiz/msh2exo
   

   configure msh2exo (adjust paths if necessary)

   cd C:\src\msh2exo
   
   mkdir build
   
   cd build
   
   cmake .. -DSEACASExodus_DIR=C:\src\seacas\install\lib\cmake\SEACASExodus -DCMAKE_INSTALL_PREFIX=C:\src\msh2exo\install -G "Visual Studio 16 2019" -A x64
   

   Build msh2exo (from build directory)

   cmake --build . --config Release
   

   Installing msh2exo to CMAKE_INSTALL_PREFIX using CMake (again from build directory):

   cmake --install . --config Release
   

   Currently the dll's need to be copied from the build directory to the install bin directory.

   The following are created in the build/Release directory on my machine and should be copied to the installed bin/ directory where msh2exo.exe is placed

   hdf5.dll
   hdf5_hl.dll
   libcurl.dll
   netcdf.dll
   zlib1.dll