def _translate(self, vector):
"""
Test for ticket:298.
>>> from fipy import *
>>> m = PeriodicGrid3DLeftRight(nx=2, ny=2, nz=1) + [[-1], [0], [0]]
>>> orderedCellVertexIDs = [[13, 14, 16, 17],
... [12, 13, 15, 16],
... [10, 11, 13, 14],
... [9, 10, 12, 13],
... [4, 5, 7, 8],
... [3, 4, 6, 7],
... [1, 2, 4, 5],
... [0, 1, 3, 4]]
>>> print(numerix.allclose(m._orderedCellVertexIDs, orderedCellVertexIDs)) # doctest: +PROCESSOR_0
True
>>> print(CellVariable(mesh=m, value=m.cellCenters[0]))
[-0.5 0.5 -0.5 0.5]
"""
newCoords = self.vertexCoords + vector
newmesh = self.__class__(**self.args)
from fipy.meshes.mesh import Mesh
Mesh.__init__(newmesh,
newCoords,
self.faceVertexIDs,
self._nonPeriodicCellFaceIDs,
communicator=self.communicator)
newmesh._makePeriodic()
return newmesh
def _translate(self, vector):
"""
Test for ticket:298.
>>> from fipy import *
>>> m = PeriodicGrid3DLeftRight(nx=2, ny=2, nz=1) + [[-1], [0], [0]]
>>> orderedCellVertexIDs = [[13, 14, 16, 17],
... [12, 13, 15, 16],
... [10, 11, 13, 14],
... [9, 10, 12, 13],
... [4, 5, 7, 8],
... [3, 4, 6, 7],
... [1, 2, 4, 5],
... [0, 1, 3, 4]]
>>> print(numerix.allclose(m._orderedCellVertexIDs, orderedCellVertexIDs)) # doctest: +PROCESSOR_0
True
>>> print(CellVariable(mesh=m, value=m.cellCenters[0]))
[-0.5 0.5 -0.5 0.5]
"""
newCoords = self.vertexCoords + vector
newmesh = self.__class__(**self.args)
from fipy.meshes.mesh import Mesh
Mesh.__init__(newmesh, newCoords, self.faceVertexIDs, self._nonPeriodicCellFaceIDs, communicator=self.communicator)
newmesh._makePeriodic()
return newmesh
def __init__(self, dx = 1., dy = 1., dz = 1., nx = None, ny = None, nz = None, overlap=2, communicator=parallelComm,
_RepresentationClass=_Grid3DRepresentation, _TopologyClass=_Grid3DTopology):
builder = _NonuniformGrid3DBuilder()
self.args = {
'dx': dx,
'dy': dy,
'dz' :dz,
'nx': nx,
'ny': ny,
'nz': nz,
'overlap': overlap,
'communicator': communicator
}
builder.buildGridData([dx, dy, dz], [nx, ny, nz], overlap,
communicator)
([self.dx, self.dy, self.dz],
[self.nx, self.ny, self.nz],
self.dim,
scale,
self.globalNumberOfCells,
self.globalNumberOfFaces,
self.overlap,
self.offset,
self.numberOfVertices,
self.numberOfFaces,
self.numberOfCells,
self.shape,
self.physicalShape,
self._meshSpacing,
self.numberOfXYFaces,
self.numberOfXZFaces,
self.numberOfYZFaces,
self.numberOfHorizontalRows,
self.numberOfVerticalColumns,
self.numberOfLayersDeep,
vertices,
faces,
cells,
self.Xoffset, self.Yoffset, self.Zoffset) = builder.gridData
Mesh.__init__(self, vertices, faces, cells, communicator=communicator,
_RepresentationClass=_RepresentationClass, _TopologyClass=_TopologyClass)
self._setScale(scaleLength = scale)
def __init__(self, dx = 1., dy = 1., dz = 1., nx = None, ny = None, nz = None, overlap=2, communicator=parallelComm,
_RepresentationClass=_Grid3DRepresentation, _TopologyClass=_Grid3DTopology):
builder = _NonuniformGrid3DBuilder()
self.args = {
'dx': dx,
'dy': dy,
'dz': dz,
'nx': nx,
'ny': ny,
'nz': nz,
'overlap': overlap,
}
builder.buildGridData([dx, dy, dz], [nx, ny, nz], overlap,
communicator)
([self.dx, self.dy, self.dz],
[self.nx, self.ny, self.nz],
self.dim,
scale,
self.globalNumberOfCells,
self.globalNumberOfFaces,
self.overlap,
self.offset,
self.numberOfVertices,
self.numberOfFaces,
self.numberOfCells,
self.shape,
self.physicalShape,
self._meshSpacing,
self.numberOfXYFaces,
self.numberOfXZFaces,
self.numberOfYZFaces,
self.numberOfHorizontalRows,
self.numberOfVerticalColumns,
self.numberOfLayersDeep,
vertices,
faces,
cells,
self.Xoffset, self.Yoffset, self.Zoffset) = builder.gridData
Mesh.__init__(self, vertices, faces, cells, communicator=communicator,
_RepresentationClass=_RepresentationClass, _TopologyClass=_TopologyClass)
self._setScale(scaleLength = scale)
def setstate(mesh, state):
"""Populate a new `Mesh` from ``pickled`` persistent storage.
"""
from fipy.meshes.mesh import Mesh
Mesh.__init__(mesh, **state)
def setstate(mesh, state):
"""Populate a new `Mesh` from ``pickled`` persistent storage.
"""
from fipy.meshes.mesh import Mesh
Mesh.__init__(mesh, **state)
def _extrude(self, mesh, extrudeFunc, layers):
## should extrude self rather than creating a new mesh?
## the following allows the 2D mesh to be in 3D space, this can be the case for a
## Gmsh2DIn3DSpace which would then be extruded.
oldVertices = mesh.vertexCoords
if oldVertices.shape[0] == 2:
oldVertices = numerix.resize(oldVertices, (3, len(oldVertices[0])))
oldVertices[2] = 0
NCells = mesh.numberOfCells
NFac = mesh.numberOfFaces
NFacPerCell = mesh._maxFacesPerCell
## set up the initial data arrays
new_shape = (max(NFacPerCell, 4), (1 + layers)*NCells + layers*NFac)
faces = numerix.MA.masked_values(-numerix.ones(new_shape, 'l'), value = -1)
orderedVertices = mesh._orderedCellVertexIDs
faces[:NFacPerCell, :NCells] = orderedVertices
vertices = oldVertices
vert0 = mesh.faceVertexIDs
faceCount = NCells
for layer in range(layers):
## need this later
initialFaceCount = faceCount
## build the vertices
newVertices = extrudeFunc(oldVertices)
vertices = numerix.concatenate((vertices, newVertices), axis=1)
## build the faces along the layers
faces[:NFacPerCell, faceCount: faceCount + NCells] = orderedVertices + len(oldVertices[0]) * (layer + 1)
try:
# numpy 1.1 doesn't copy right side before assigning slice
# See: http://www.mail-archive.com/[email protected]/msg09843.html
faces[:NFacPerCell, faceCount: faceCount + NCells] = faces[:NFacPerCell, faceCount: faceCount + NCells][::-1,:].copy()
except:
faces[:NFacPerCell, faceCount: faceCount + NCells] = faces[:NFacPerCell, faceCount: faceCount + NCells][::-1,:]
faceCount = faceCount + NCells
vert1 = (vert0 + len(oldVertices[0]))[::-1,:]
## build the faces between the layers
faces[:4, faceCount: faceCount + NFac] = numerix.concatenate((vert0, vert1), axis = 0)[::-1,:]
vert0 = vert0 + len(oldVertices[0])
NCells = mesh.numberOfCells
## build the cells, the first layer has slightly different ordering
if layer == 0:
c0 = numerix.reshape(numerix.arange(NCells), (1, NCells))
cells = numerix.concatenate((c0, c0 + NCells, mesh.cellFaceIDs + 2 * NCells), axis = 0)
else:
newCells = numerix.concatenate((c0, c0 + initialFaceCount, mesh.cellFaceIDs + faceCount), axis=0)
newCells[0] = cells[1, -NCells:]
cells = numerix.concatenate((cells, newCells), axis=1)
## keep a count of things for the next layer
faceCount = faceCount + NFac
oldVertices = newVertices
## return a new mesh, extrude could just as easily act on self
return Mesh(vertices, faces, cells, communicator=mesh.communicator)