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Merge branch 'pkgw-pr-grid3d' into develop
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Added tests

Fixes #470
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@guyer
guyer committed Dec 27, 2015
2 parents b68c39c + efc4abb commit 33d033d
Showing 1 changed file with 175 additions and 18 deletions.
193 changes: 175 additions & 18 deletions fipy/meshes/uniformGrid3D.py
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Original file line number Diff line number Diff line change
Expand Up @@ -169,19 +169,25 @@ def _adjacentCellIDs(self):
def _cellToCellIDs(self):
ids = MA.zeros((6, self.nx, self.ny, self.nz), 'l')
indices = numerix.indices((self.nx, self.ny, self.nz))
ids[0] = indices[0] + (indices[1] + indices[2] * self.ny) * self.nx - 1
ids[1] = indices[0] + (indices[1] + indices[2] * self.ny) * self.nx + 1
ids[2] = indices[0] + (indices[1] + indices[2] * self.ny - self.nz) * self.nx
ids[3] = indices[0] + (indices[1] + indices[2] * self.ny + self.nz) * self.nx
ids[4] = indices[0] + (indices[1] + (indices[2] - 1) * self.ny) * self.nx
ids[5] = indices[0] + (indices[1] + (indices[2] + 1) * self.ny) * self.nx

ids[0, 0, ...] = MA.masked
ids[1,-1, ...] = MA.masked
ids[2,..., 0,...] = MA.masked
ids[3,...,-1,...] = MA.masked
ids[4,..., 0] = MA.masked
ids[5,..., -1] = MA.masked
nxy = self.nx * self.ny
same = indices[0] + indices[1] * self.nx + indices[2] * nxy

ids[0] = same - 1
ids[1] = same + 1
ids[2] = same - self.nx
ids[3] = same + self.nx
ids[4] = same - nxy
ids[5] = same + nxy

if self.nx > 0:
ids[0, 0, ...] = MA.masked
ids[1,-1, ...] = MA.masked
if self.ny > 0:
ids[2,..., 0,...] = MA.masked
ids[3,...,-1,...] = MA.masked
if self.nz > 0:
ids[4,..., 0] = MA.masked
ids[5,..., -1] = MA.masked

return MA.reshape(ids.swapaxes(1,3), (6, self.numberOfCells))

Expand Down Expand Up @@ -275,7 +281,7 @@ def _faceToCellDistanceRatio(self):

return numerix.concatenate((numerix.ravel(XYdis.swapaxes(0,2)),
numerix.ravel(XZdis.swapaxes(0,2)),
numerix.ravel(YZdis.swapaxes(0,2))), axis=1)
numerix.ravel(YZdis.swapaxes(0,2))))

@property
def _orientedFaceNormals(self):
Expand Down Expand Up @@ -328,7 +334,7 @@ def _cellToCellDistances(self):
distances[4,..., 0] = self.dz / 2.
distances[5,..., -1] = self.dz / 2.

return numerix.reshape(distances.swapaxes(1,3), (self.numberOfCells, 6))
return numerix.reshape(distances.swapaxes(1,3), (6, self.numberOfCells))

@property
def _cellNormals(self):
Expand Down Expand Up @@ -761,7 +767,7 @@ def _test(self):
>>> print numerix.allequal(mesh.cellCenters, unpickledMesh.cellCenters)
True
# Bug #130 & #135 are because we only checked a mesh with nz of 1
# Bug #130 & #135 and issue #470 are because we only checked a mesh with nz of 1
>>> nx = 1
>>> ny = 2
Expand All @@ -774,7 +780,42 @@ def _test(self):
... cellVertexIDs + 8, cellVertexIDs + 12, cellVertexIDs + 14))
>>> cellVertexIDs = cellVertexIDs.swapaxes(0,1)
>>> print numerix.allclose(mesh._cellVertexIDs, cellVertexIDs) # doctest: +PROCESSOR_0
1
True
>>> cellToCellIDs = MA.masked_values(((-1,-1,-1,-1,-1,-1),
... (-1,-1,-1,-1,-1,-1),
... (-1, 0,-1, 2,-1, 4),
... ( 1,-1, 3,-1, 5,-1),
... (-1,-1, 0, 1, 2, 3),
... ( 2, 3, 4, 5,-1,-1)), -1)
>>> print numerix.allequal(mesh._cellToCellIDs, cellToCellIDs) # doctest: +PROCESSOR_0
True
>>> cellDistances = numerix.array((dz/2, dz/2, dz, dz, dz, dz, dz/2, dz/2,
... dy/2, dy, dy/2, dy/2, dy, dy/2, dy/2, dy, dy/2,
... dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, ))
>>> print numerix.allclose(cellDistances, mesh._cellDistances, atol = 1e-10, rtol = 1e-10) # doctest: +PROCESSOR_0
True
>>> faceToCellDistances = MA.masked_values(((dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2),
... ( -1, -1, dz/2, dz/2, dz/2, dz/2, -1, -1, -1, dy/2, -1, -1, dy/2, -1, -1, dy/2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1)), -1)
>>> faceToCellDistanceRatios = faceToCellDistances[0] / cellDistances
>>> print numerix.allclose(faceToCellDistanceRatios, mesh._faceToCellDistanceRatio, atol = 1e-10, rtol = 1e-10) # doctest: +PROCESSOR_0
True
>>> cells = numerix.array(((17, 19, 21, 23, 25, 27),
... (18, 20, 22, 24, 26, 28),
... ( 8, 9, 11, 12, 14, 15),
... ( 9, 10, 12, 13, 15, 16),
... ( 0, 1, 2, 3, 4, 5),
... ( 2, 3, 4, 5, 6, 7)))
>>> print numerix.allequal(cells, mesh.cellFaceIDs) # doctest: +PROCESSOR_0
True
>>> cellToCellDistances = numerix.take(cellDistances, cells)
>>> print numerix.allclose(cellToCellDistances, mesh._cellToCellDistances, atol = 1e-10, rtol = 1e-10) # doctest: +PROCESSOR_0
True
>>> nx = 3
>>> ny = 1
Expand All @@ -787,8 +828,124 @@ def _test(self):
... cellVertexIDs + 8, cellVertexIDs + 9, cellVertexIDs + 10))
>>> cellVertexIDs = cellVertexIDs.swapaxes(0,1)
>>> print numerix.allclose(mesh._cellVertexIDs, cellVertexIDs) # doctest: +PROCESSOR_0
1
True
>>> cellToCellIDs = MA.masked_values(((-1, 0, 1,-1, 3, 4),
... ( 1, 2,-1, 4, 5,-1),
... (-1,-1,-1,-1,-1,-1),
... (-1,-1,-1,-1,-1,-1),
... (-1,-1,-1, 0, 1, 2),
... ( 3, 4, 5,-1,-1,-1)), -1)
>>> print numerix.allequal(mesh._cellToCellIDs, cellToCellIDs) # doctest: +PROCESSOR_0
True
>>> cellDistances = numerix.array((dz/2, dz/2, dz/2, dz, dz, dz, dz/2, dz/2, dz/2,
... dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2,
... dx/2, dx, dx, dx/2, dx/2, dx, dx, dx/2))
>>> print numerix.allclose(cellDistances, mesh._cellDistances, atol = 1e-10, rtol = 1e-10) # doctest: +PROCESSOR_0
True
>>> faceToCellDistances = MA.masked_values(((dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2, dx/2),
... ( -1, -1, -1, dz/2, dz/2, dz/2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, dx/2, dx/2, -1, -1, dx/2, dx/2, -1)), -1)
>>> faceToCellDistanceRatios = faceToCellDistances[0] / cellDistances
>>> print numerix.allclose(faceToCellDistanceRatios, mesh._faceToCellDistanceRatio, atol = 1e-10, rtol = 1e-10) # doctest: +PROCESSOR_0
True
>>> cells = numerix.array(((21, 22, 23, 25, 26, 27),
... (22, 23, 24, 26, 27, 28),
... ( 9, 10, 11, 15, 16, 17),
... (12, 13, 14, 18, 19, 20),
... ( 0, 1, 2, 3, 4, 5),
... ( 3, 4, 5, 6, 7, 8)))
>>> print numerix.allequal(cells, mesh.cellFaceIDs) # doctest: +PROCESSOR_0
True
>>> cellToCellDistances = numerix.take(cellDistances, cells)
>>> print numerix.allclose(cellToCellDistances, mesh._cellToCellDistances, atol = 1e-10, rtol = 1e-10) # doctest: +PROCESSOR_0
True
# issue 470
# 3x2x1 mesh above did not exhibit the failure of
# _cellToCellIDs and _cellToCellDistances to present proper results
>>> dx = 0.5
>>> dy = 2.
>>> dz = 4.
>>> nx = 4
>>> ny = 3
>>> nz = 2
>>> mesh = UniformGrid3D(nx=nx, ny=ny, nz=nz, dx=dx, dy=dy, dz=dz)
>>> XYFaceIDs = numerix.array((((0, 12, 24), (4, 16, 28), ( 8, 20, 32)),
... ((1, 13, 25), (5, 17, 29), ( 9, 21, 33)),
... ((2, 14, 26), (6, 18, 30), (10, 22, 34)),
... ((3, 15, 27), (7, 19, 31), (11, 23, 35))))
>>> print numerix.allequal(XYFaceIDs, mesh._XYFaceIDs) # doctest: +PROCESSOR_0
True
>>> XZFaceIDs = numerix.array((((36, 52), (40, 56), (44, 60), (48, 64)),
... ((37, 53), (41, 57), (45, 61), (49, 65)),
... ((38, 54), (42, 58), (46, 62), (50, 66)),
... ((39, 55), (43, 59), (47, 63), (51, 67))))
>>> print numerix.allequal(mesh._XZFaceIDs, XZFaceIDs) # doctest: +PROCESSOR_0
True
>>> YZFaceIDs = numerix.array((((68, 83), (73, 88), (78, 93)),
... ((69, 84), (74, 89), (79, 94)),
... ((70, 85), (75, 90), (80, 95)),
... ((71, 86), (76, 91), (81, 96)),
... ((72, 87), (77, 92), (82, 97))))
>>> print numerix.allequal(mesh._YZFaceIDs, YZFaceIDs) # doctest: +PROCESSOR_0
True
>>> adjacentCellIDs = (numerix.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
... 0, 1, 2, 3, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
... 0, 0, 1, 2, 3, 4, 4, 5, 6, 7, 8, 8, 9, 10, 11, 12, 12, 13, 14, 15, 16, 16, 17, 18, 19, 20, 20, 21, 22, 23]),
... numerix.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
... 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 20, 21, 22, 23,
... 0, 1, 2, 3, 3, 4, 5, 6, 7, 7, 8, 9, 10, 11, 11, 12, 13, 14, 15, 15, 16, 17, 18, 19, 19, 20, 21, 22, 23, 23]))
>>> print numerix.allequal(mesh._adjacentCellIDs, adjacentCellIDs) # doctest: +PROCESSOR_0
True
>>> vertices = numerix.array(((0., 1., 2., 3., 4., 0., 1., 2., 3., 4., 0., 1., 2., 3., 4., 0., 1., 2., 3., 4., 0., 1., 2., 3., 4., 0., 1., 2., 3., 4., 0., 1., 2., 3., 4., 0., 1., 2., 3., 4., 0., 1., 2., 3., 4., 0., 1., 2., 3., 4., 0., 1., 2., 3., 4., 0., 1., 2., 3., 4.),
... (0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 2., 2., 2., 2., 2., 3., 3., 3., 3., 3., 0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 2., 2., 2., 2., 2., 3., 3., 3., 3., 3., 0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 2., 2., 2., 2., 2., 3., 3., 3., 3., 3.),
... (0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.)))
>>> vertices *= numerix.array([[dx], [dy], [dz]])
>>> print numerix.allequal(vertices, mesh.vertexCoords) # doctest: +PROCESSOR_0
True
>>> cellToCellIDs = MA.masked_values(((-1, 0, 1, 2,-1, 4, 5, 6,-1, 8, 9,10,-1,12,13,14,-1,16,17,18,-1,20,21,22),
... ( 1, 2, 3,-1, 5, 6, 7,-1, 9,10,11,-1,13,14,15,-1,17,18,19,-1,21,22,23,-1),
... (-1,-1,-1,-1, 0, 1, 2, 3, 4, 5, 6, 7,-1,-1,-1,-1,12,13,14,15,16,17,18,19),
... ( 4, 5, 6, 7, 8, 9,10,11,-1,-1,-1,-1,16,17,18,19,20,21,22,23,-1,-1,-1,-1),
... (-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9,10,11),
... (12,13,14,15,16,17,18,19,20,21,22,23,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1)), -1)
>>> print numerix.allequal(mesh._cellToCellIDs, cellToCellIDs) # doctest: +PROCESSOR_0
True
>>> cellDistances = numerix.array((dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz, dz, dz, dz, dz, dz, dz, dz, dz, dz, dz, dz, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2, dz/2,
... dy/2, dy/2, dy/2, dy/2, dy, dy, dy, dy, dy, dy, dy, dy, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy/2, dy, dy, dy, dy, dy, dy, dy, dy, dy/2, dy/2, dy/2, dy/2,
... dx/2, dx, dx, dx, dx/2, dx/2, dx, dx, dx, dx/2, dx/2, dx, dx, dx, dx/2, dx/2, dx, dx, dx, dx/2, dx/2, dx, dx, dx, dx/2, dx/2, dx, dx, dx, dx/2))
>>> print numerix.allclose(cellDistances, mesh._cellDistances, atol = 1e-10, rtol = 1e-10) # doctest: +PROCESSOR_0
True
>>> cells = numerix.array(((68, 69, 70, 71, 73, 74, 75, 76, 78, 79, 80, 81, 83, 84, 85, 86, 88, 89, 90, 91, 93, 94, 95, 96),
... (69, 70, 71, 72, 74, 75, 76, 77, 79, 80, 81, 82, 84, 85, 86, 87, 89, 90, 91, 92, 94, 95, 96, 97),
... (36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63),
... (40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67),
... ( 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23),
... (12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35)))
>>> print numerix.allequal(cells, mesh.cellFaceIDs) # doctest: +PROCESSOR_0
True
>>> cellToCellDistances = numerix.take(cellDistances, cells)
>>> print numerix.allclose(cellToCellDistances, mesh._cellToCellDistances, atol = 1e-10, rtol = 1e-10) # doctest: +PROCESSOR_0
True
Oh, how boring. We'll assume the 3x2x1 permutations are good enough for everything else until proven otherwise.
"""

def _test():
Expand Down

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