dolfin-convert

dolfin-convert, a Python code which can convert a mesh file from Gmsh, MEDIT, METIS or SCOTCH format to an XML format suitable for use by DOLFIN or FENICS, by Anders Logg.

The conversions carried out by this function include:

• Medit mesh to DOLFIN XML;
• Gmsh msh to DOLFIN XML; (The Gmsh file can only contain linear 3-node triangles or linear 4-node tetrahedrons)
• Old DOLFIN XML to DOLFIN XML;
• METIS Graph to DOLFIN Graph XML;
• SCOTCH Graph to DOLFIN Graph XML.

Note that the examples of converting a 3D GMSH file to DOLFIN XML file have failed. This is because the GMSH 3D tetrahedral elements are listed as type 29, whereas DOLFIN-CONVERT is expecting an element type of 4. Thanks to Sean Breckling for reporting this issue, 13 May 2016.

Licensing:

The computer codes made available on this web page are distributed under the MIT license

Languages:

dolfin-convert is available in a Python version.

Related Data and Software:

dolfin_xml a data directory which contains examples of xml files that describe 3d finite element meshes as used by dolfin and fenics.

fenics, examples which illustrate the use of fenics, a collection of free software with an extensive list of features for automated, efficient solution of differential equations.

gmsh, examples which illustrate the use of the gmsh program, a 3d mesh generator for the finite element method (fem).

gmsh_to_fem, a fortran90 program which reads a mesh data file created by the gmsh program and writes a pair of node and element files that correspond to the fem format.

medit, examples which illustrate the use of medit, an interactive graphics program developed to visualize numerical simulation results on unstructured meshes in two and three dimensions. scalar, vector and tensor fields can be easily associated and displayed with meshes. the program is by pascal frey.

mitchell_fenics, examples which illustrate the implementation of the Mitchell elliptic test problems using FENICS.

msh, a data directory of examples of MSH files, the native 3D mesh format used by Gmsh.

xml, a data directory which contains examples of XML files, a standard, general datafile format.

Author:

Anders Logg

Reference:

• Anders Logg, Garth Wells,
  DOLFIN: Automated finite element computing,
  ACM Transactions on Mathematical Software,
  Volume 37, Number 2, Article 20, April 2010.
• Anders Logg, Kent-Andre Mardal, Garth Wells,
  Automated Solution of Differential Equations by the Finite Element Method: The FEniCS Book,
  Lecture Notes in Computational Science and Engineering,
  Springer, 2011,
  ISBN13: 978-3642230981,
  LC:
• https://www.fenics.org, the web site for the FEniCS project.

Source Code:

• dolfin-convert.py, the source code.
• dolfin-convert.sh, runs all the tests.

CYLINDER_2D is a 2D mesh for a cylinder.

• cylinder_2d.msh, the mesh in GMSH format.
• cylinder_2d.xml, the mesh converted by dolfin-convert to XML format.

CYLINDER_3D is a 3D mesh for a cylinder.

• cylinder_3d.msh, the mesh in GMSH format.
• cylinder_3d.xml, the mesh converted by dolfin-convert to XML format.

ELL_2D is a 2D mesh for the L-shaped region.

• ell_2d.msh, the mesh in GMSH format.
• ell_2d.xml, the mesh converted by dolfin-convert to XML format.

PINCH is a 2D channel formed by starting with a long rectangular channel and creating a narrow neck by removing elliptical portions from the top and bottom. The resulting mesh has 4,325 nodes and 8,656 elements.

• pinch.msh, the GMSH mesh file created from the geometry file.
• pinch.xml, the XML mesh file.

STEP_2D is a 2D mesh for a step.

• step_2d.msh, the mesh in GMSH format.
• step_2d.xml, the mesh converted by dolfin-convert to XML format.

STEP_3D is a 3D mesh for a step.

• step_3d.msh, the mesh in GMSH format.
• step_3d.xml, the mesh converted by dolfin-convert to XML format.

TEST02 is the upside down L-shaped region, for the Mitchell test problem #2.

• test02.msh, the GMSH mesh file.
• test02.xml, the mesh, converted by dolfin-convert to XML format.

TEST03 is the square [-1,+1]x[-1,+1] with a slit from (0,0) to (1,0), for the Mitchell test problem #3.

• test03.msh, the GMSH mesh file.
• test03.xml, the mesh, converted by dolfin-convert to XML format.