cmaurini / msh2xdmf

Converter from MSH mesh format to XDMF mesh format

msh2xdmf

The code contains a converter from MSH mesh format to XDMF mesh format for the dolfin users.

How to test the installation ?

In order to test the compatibility of the script with the user installation of meshio and dolfin, the following command must be run at the root of the repository:

% python3 -m pytest

How to convert a mesh ?

For this exemple, let us consider a 2D mesh named mesh.msh where 3 physical groups are defined in the mesh.geo file:

// Domain
Physical Surface("domain") = {1};
// Boundaries
Physical Line("left") = {4};
Physical Line("right") = {2};

In order to convert this mesh, the following command must be used:

% python3 msh2xdmf.py -d 2 mesh.msh

This command should outputs the following table (the table should be empty for msh2 format):

+-----------------------------------------+
|     GMSH label     | MeshFunction value |
+--------------------+--------------------+
|        left        |         2          |
|       right        |         3          |
|       domain       |         1          |
+-----------------------------------------+

This table contains the GMSH labels and the value associated to each physical groups. Additionally, two new files are generated: domain.xdmf which contains the domain and boundaries.xdmf which contains the values associated to the boundaries. In order to check the label/value association, the boundaries.xdmf can also be openend with Paraview (or an alternative). It will show the value associated to each boundaries.

In order to import the mesh and its boundaries in dolfin, one can use the utility function import_mesh_from_xdmf which returns the dolfin Mesh object and the MeshFunction object associated to the files.

from msh2xdmf import import_mesh_from_xdmf

mesh, mesh_function = import_mesh_from_xdmf(
    domain="domain.xdmf",
    boundaries="boundaries.xdmf",
    dim=2,
    )

How to convert a multidomain mesh ?

For this exemple, let us consider a mesh named multidomain.msh where 7 physical groups are defined in the multidomain.geo file:

// Domain
Physical Surface("top_domain") = {1};
Physical Surface("bot_domain") = {2};

// Boundaries
Physical Line("middle") = {1};
Physical Line("right") = {2, 5};
Physical Line("top") = {3};
Physical Line("bot") = {6};
Physical Line("left") = {4, 7};

In order to convert this mesh, the following command must be used:

% python3 msh2xdmf.py -d 2 multidomain.msh

This command should outputs the following table (the table should be empty for msh2 format):

+-----------------------------------------+
|     GMSH label     | MeshFunction value |
+--------------------+--------------------+
|       middle       |         3          |
|       right        |         4          |
|        top         |         5          |
|        bot         |         6          |
|        left        |         7          |
|     top_domain     |         1          |
|     bot_domain     |         2          |
+-----------------------------------------+

This table contains the GMSH labels and the value associated to each physical groups. Additionally, two new files are generated: domain.xdmf which contains the domain and the values associated to each subdomains and boundaries.xdmf which contains the values associated to the boundaries. In order to check the label/value association, both files can be openend with Paraview (or an alternative) to check the values associated to each boundaries and subdomains.

In order to import the mesh and the value asosociated to the subdomains and the boundaries in dolfin, one can use the utility function import_mesh_from_xdmf which returns the dolfin Mesh object and the MeshFunction object associated to the files.

from msh2xdmf import import_mesh_from_xdmf

mesh, boundaries_mf, subdomains_mf = import_mesh_from_xdmf(
    domain="domain.xdmf",
    boundaries="boundaries.xdmf",
    dim=2,
    subdomains=True
    )

In this exemple, boundaries_mf is the MeshFunction object associated to the boundaries and subdomains_mf is the MeshFunction associated to the subdomains.