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, five new files are generated: mesh_domain.xdmf and mesh_domain.h5 which contain the domain, mesh_boundaries.xdmf and mesh_boundaries.h5 which contain the values associated to the boundaries and mesh_association_table.ini which contains the association table. In order to check the label/value association, the .xdmf files can also be openend with Paraview (or an alternative). It will show the value associated to each domains/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, the MeshFunction object associated to the files and a dictionnary containing the association_table.

from msh2xdmf import import_mesh_from_xdmf

mesh, mesh_function, association_table = import_mesh_from_xdmf(
    prefix="mesh" # it the file name of the msh file without the extension
    dim=2,
    )

In order to get the value associated to get the MeshFunction value associated to the left, one must use: association_table["left"].

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, four new files are generated: multidomain_domain.xdmf and multidomain_domain.h5 which contain the domain and the values associated to each subdomains, multidomain_boundaries.xdmf and multidomain_boundaries.h5 which contains the values associated to the boundaries and mesh_association_table.ini which contains the association table. 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, association_table = import_mesh_from_xdmf(
    prefix="multidomain", # it is the file name of the msh file without the extension
    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.

In order to get the value associated to get the MeshFunction value associated to the left, one must use: association_table["left"]. The same dictionnary can also be used for the subdomains.

First commit by Amir.