On Thu, May 30, 2013 at 5:14 AM, Michelangelo Formisano <
[email protected]> wrote:
> Hi Daniel. Here you find the output. Thanks,
>
>From the output attached it is evident that Gmsh doesn't seem to be working
correctly. Unfortunately failures of the form
> File
> "/usr/local/lib/python2.7/dist-packages/fipy/models/levelSet/electroChem/gapFillMesh.py",
> line 230, in fipy.models.levelSet.electroChem.gapFillMesh.TrenchMesh
> Failed example:
> print numerix.sqrt(localErrors[argmax]) < 0.051 # doctest: +GMSH
> Expected:
> 1
> Got:
> False
>
are not helpful as they don't show the actual issue, which is the Gmsh
installation in all likelihood (or FiPy's interaction with Gmsh). I think
the first thing to do is to actually test the Gmsh installation to make
sure it is working correctly. Put the following in a file called "tmp.geo"
cellSize = 0.05;
Point(1) = {0.0, 0.0, 0.0, cellSize};
Point(2) = {5.0, 0.0, 0.0, cellSize};
Point(3) = {5.0, 2.0, 0.0, cellSize};
Point(4) = {2.0, 2.0, 0.0, cellSize};
Point(5) = {2.0, 1.0, 0.0, cellSize};
Point(6) = {0.0, 1.0, 0.0, cellSize};
Line(1) = {1, 2};
Line(2) = {2, 3};
Line(3) = {3, 4};
Line(4) = {4, 5};
Line(5) = {5, 6};
Line(6) = {6, 1};
Line Loop(6) = {1, 2, 3, 4, 5, 6};
Plane Surface(6) = {6};
Physical Line(7) = {4};
Physical Line(8) = {1, 3};
Physical Line(9) = {2};
Physical Surface(10) = {6};
and run "gmsh tmp.geo -format msh -2 -nopopup tmp.msh" at the command line
and see what output is produced. There should be something in "tmp.msh"
assuming it worked. The output should look like:
Info : Running 'gmsh tmp.geo -format msh -2 -nopopup tmp.msh' [Gmsh
2.6.2, 1 node, max. 8 threads]
Info : Started on Thu May 30 11:11:02 2013
Info : Reading 'tmp.geo'...
Info : Done reading 'tmp.geo'
Info : Reading 'tmp.msh'...
Info : 218 vertices
Info : Vertex numbering is dense
Info : 217 elements
Info : Done reading 'tmp.msh'
Info : Meshing 2D...
Info : Meshing surface 6 (Plane, Delaunay)
Info : Done meshing 2D (0.004 s)
Info : 218 vertices 217 elements
Info : Writing 'tmp.msh'...
Info : Done writing 'tmp.msh'
Info : Stopped on Thu May 30 11:11:02 2013
It should produce some vertices and elements and not zero vertices and zero
elements as the output showed in your first email. Try this to check for
sure that the Gmsh installation is messed up.
--
Daniel Wheeler
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