changes to gmshImport.py caused --inline problems

[guyer]

r5209 has induced [http://build.cmi.kent.edu:8010/builders/Mac_OS_X%7Etrunk%7Efull/builds/21/steps/trial_4/logs/problems five --inline failures]

The problem is visible in this 3 cell reduction of examples/diffusion/steadyState/otherMeshes/prism.py

from fipy import *

valueLeft = 0.
valueRight = 1.

mesh = GmshGrid3D(dx=1, dy=1, dz=1, nx=3, ny=1, nz=1)

var = CellVariable(name = "solution variable",
mesh = mesh,
value = valueLeft)

exteriorFaces = mesh.exteriorFaces
xFace = mesh.faceCenters[0]

var.constrain(valueLeft, exteriorFaces & (xFace ** 2 < 0.000000000000001))
var.constrain(valueRight, exteriorFaces & ((xFace - 3) ** 2 < 0.000000000000001))

DiffusionTerm().solve(var)

print var

Normal (Python) output:

[ 0.16666667  0.5         0.83333333]

--inline output:

[ 0.25  0.25  0.75]

The problem is traceable to a discrepancy in the [trunk/fipy/terms/abstractDiffusionTerm.py@5211#L350 divergence calculation on constraints]

Imported from trac ticket #438, created by guyer on 04-12-2012 at 11:35, last modified: 04-13-2012 at 09:07

[guyer]

Replying to [guyer](issue #316):

The problem is traceable to a discrepancy in the [trunk/fipy/terms/abstractDiffusionTerm.py@5211#L350 divergence calculation on constraints]

This is further isolated to trunk/fipy/variables/addOverFacesVariable.py@5211#L58, where ids is C_CONTIGUOUS in r5160 and F_CONTIGUOUS in r5209.

In trunk/fipy/meshes/gmshImport.py@5160#L795, the call to formatForFiPy does both a swapaxes() and a [::-1] reversal, producing an array which is neither C_CONTIGUOUS nor F_CONTIGUOUS. A later call to MA.masked_values() produces a C_CONTIGUOUS array.

The reversal of cellFaceIDs caused problems and was removed in r5209, but the result is an F_CONTIGUOUS array, which remains F_CONTIGUOUS after MA.masked_values(), which our weave code can't handle. The solution is to force this array to be C_CONTIGUOUS on construction.

Trac comment by guyer on 04-12-2012 at 11:43

[guyer]

Fixed with r5213

Trac comment by guyer on 04-13-2012 at 09:07