Henrik,

PETSc's DMPlexCreateGmsh() function does not recognize the "PhysicalNames" field, which is why the reader screws up in neu3.msh

neu4.msh also fails because the boundaries in DMPlex are labeled by physical ID's, which is , not "PhysicalNames" strings.

Also, if you're using the Mesh() function, you need to provide the entire mesh and not just the four 2-node lines? In any case, the GMSH file format (including where the physical ID's are located) can be found here:

9.1 MSH ASCII file format


Thanks,
Justin

On Fri, Dec 18, 2015 at 1:18 AM, Buesing, Henrik <HBuesing@eonerc.rwth-aachen.de> wrote:

Dear all,

 

I create a very simple gmsh file: just a square with “left”, “bottom”, “right” and “top” boundary. I have attached two versions of the mesh.

1) neu3.msh: This has the “PhysicalNames” declared at the beginning. I get a “File is not a valid Gmsh file” error.

2) neu4.msh: This has the “PhysicalNames” declared at the end. But if I now try to set Dirichlet bc for the “left” and “right” boundary, e.g. with

 

bc0 = DirichletBC(W.sub(0), Expression("0.0"), “right”)

 

nothing seems to happen. I guess I’m missing sth. obvious here…

Thank you!

Henrik

 

 

 

 

Error message for neu3.msh

 

Traceback (most recent call last):

  File "charge.py", line 7, in <module>

    mymesh = Mesh("neu3.msh")

  File "<decorator-gen-274>", line 2, in __init__

  File "/home/hb111949/.local/lib/python2.7/site-packages/PyOP2-0.11.0_425_g64db689-py2.7-linux-x86_64.egg/pyop2/profiling.py", line 203, in wrapper

    return f(*args, **kwargs)

  File "/home/hb111949/Code/firedrake/firedrake/mesh.py", line 351, in __init__

    plex = _from_gmsh(meshfile)

  File "/home/hb111949/Code/firedrake/firedrake/mesh.py", line 152, in _from_gmsh

    gmsh_plex = PETSc.DMPlex().createGmsh(gmsh_viewer)

  File "PETSc/DMPlex.pyx", line 115, in petsc4py.PETSc.DMPlex.createGmsh (src/petsc4py.PETSc.c:214898)

petsc4py.PETSc.Error: error code 62

[0] DMPlexCreateGmsh() line 140 in /rwthfs/rz/cluster/home/hb111949/Code/petsc/src/dm/impls/plex/plexgmsh.c

[0] Invalid argument

[0] File is not a valid Gmsh file

 

 

 

--

Dipl.-Math. Henrik Büsing

Institute for Applied Geophysics and Geothermal Energy

E.ON Energy Research Center

RWTH Aachen University

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52074 Aachen, Germany     |    Fax +49 (0)241 80 49889

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hbuesing@eonerc.rwth-aachen.de

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