Gmsh2D does not respect background mesh #326

guyer · 2014-09-19T21:34:08Z

>>> from fipy import *
>>> geo = *
... // A mesh consisting of a square
...                        
... // define the basic dimensions of the mesh
...                        
... cellSize = 1;
... side = 1;
...                        
... // define the corners of the square
... 
... Point(1) = {side/2, side/2, 0, cellSize};
... Point(2) = {-side/2, side/2, 0, cellSize};
... Point(3) = {-side/2, -side/2, 0, cellSize};
... Point(4) = {side/2, -side/2, 0, cellSize};
... 
... // define the square
... 
... Line(1) = {1, 2};
... Line(2) = {2, 3};
... Line(3) = {3, 4};
... Line(4) = {4, 1};
... 
... // define the boundary
... 
... Line Loop(1) = {1, 2, 3, 4};
... 
... // define the domain
... 
... Plane Surface(1) = {1};
... *
>>> square = Gmsh2D(geo)
>>> x, y = square.cellCenters
>>> var = CellVariable(mesh=square, value=abs(x) + 0.1)
>>> vw = Viewer(vars=var)

>>> square2 = Gmsh2D(geo, background=var)
>>> x2, y2 = square2.cellCenters
>>> var2 = CellVariable(mesh=square2, value=abs(x2) + 0.1)
>>> vw2 = Viewer(vars=var2)

The same mesh is generated in both cases.

This turns out to be a problem with the writing of the POSFile for the background

>>> f = openPOSFile("test.pos", "w")
>>> f.write(var)
>>> f.close()
>>> f = open("test.pos", "r")
>>> print "".join(f.readlines())
$PostFormat
1.4 0 8
$EndPostFormat
$View
 1
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0
0 0 0 0
0
$EndView
>>> f.close()

There are a couple of problems with this.

No elements are output (the counts are all zero and no elements are output)
- [trunk/fipy/meshes/gmshImport.py @5233#L352 POSFile._writevalues()] is finding no cells with cellTopology == t["triangle"]
- [trunk/fipy/meshes/topologies/meshTopology.py @5233#L56 _MeshTopology._cellTopology()] only defines 3D cell topologies!
The view-name (just after $View) is empty
- This is because var.name is ''

It turns out that some other 2D meshes don't even get this far

>>> trisquare = Tri2D(nx=1, ny=1) + [[-0.5], [-0.5]]
>>> x3, y3 = trisquare.cellCenters
>>> var3 = CellVariable(mesh=trisquare, value=abs(x3) + 0.1)
>>> square3 = Gmsh2D(geo, background=var3)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "fipy/meshes/gmshImport.py", line 1559, in __init__
background=background)
  File "fipy/meshes/gmshImport.py", line 209, in openMSHFile
f.write(background)
  File "fipy/meshes/gmshImport.py", line 342, in write
self._writeValues(var=obj, dimensions=dimensions, time=time, timeindex=timeindex)
  File "fipy/meshes/gmshImport.py", line 438, in _writeValues
value=value[..., i])
  File "fipy/meshes/gmshImport.py", line 549, in _writeNodesAndValues
nodes = nodes[!= -1](nodes)
IndexError: invalid index to scalar variable.

This turns out to be due to nodes[~nodes.mask] in [trunk/fipy/meshes/gmshImport.py @5233#L352 POSFile._writeValue()]

Imported from trac ticket #448, created by guyer on 06-29-2012 at 09:02, last modified: 09-30-2013 at 21:44

The text was updated successfully, but these errors were encountered:

guyer · 2014-09-19T21:34:09Z

In the course of diagnosing and fixing this, I found that

there's really no documentation of background
the GmshGrid2D class takes a background= argument, but it doesn't make any sense since Gmsh ignores the background for extruded meshes

Trac comment by guyer on 06-29-2012 at 14:41

guyer · 2014-09-19T21:34:09Z

Fixed with r5253

Trac comment by guyer on 06-29-2012 at 16:22

fipymigrate · 2014-09-19T21:34:10Z

In 557e653:

#CommitTicketReference repository="fipy" revision="557e6538b5587eb08404d2a148be9fd7872fea7a"
tests re issue #326


git-svn-id: svn+ssh://code.matforge.org/fipy/branches/ticket448@5249 d80e17d7-ff13-0410-a124-85740d801063