def TetrahedralizePoly(polyFilename, commandLineSwitches=[]):
"""
Tetrahedralise the given poly using TetGen
"""
assert (filehandling.FileExtension(polyFilename) == ".poly")
tempDir = tempfile.mkdtemp()
tempFile = os.path.join(tempDir, os.path.basename(polyFilename))
filehandling.Cp(polyFilename, tempFile)
command = ["tetgen", "-p"]
if debug.GetDebugLevel() > 1:
command.append("-V")
stdout = None
stderr = None
else:
stdout = subprocess.PIPE
stderr = subprocess.PIPE
command += commandLineSwitches
command.append(tempFile)
debug.dprint("Tetrahedralization command: " +
utils.FormLine(command, delimiter=" ", newline=False))
proc = subprocess.Popen(command, stdout=stdout, stderr=stderr)
proc.wait()
assert (proc.returncode == 0)
mesh = triangletools.ReadTriangle(tempFile[:-5] + ".1")
filehandling.Rmdir(tempDir, force=True)
return mesh
def testPolyIo(self):
tempDir = tempfile.mkdtemp()
oldMesh = meshes.Mesh(2)
oldMesh.AddNodeCoord([0.0, 0.0])
oldMesh.AddNodeCoord([1.0, 0.0])
oldMesh.AddNodeCoord([0.0, 1.0])
oldMesh.AddSurfaceElement(elements.Element(nodes=[0, 1]))
oldMesh.AddSurfaceElement(elements.Element(nodes=[0, 2]))
oldMesh.AddSurfaceElement(elements.Element(nodes=[1, 2]))
oldHoleMesh = meshes.Mesh(2)
oldHoleMesh.AddNodeCoord([0.1, 0.1])
oldHoleMesh.AddNodeCoord([0.2, 0.2])
filename = os.path.join(tempDir, "temp.poly")
WritePoly(oldMesh, filename, holeMesh=oldHoleMesh)
newMesh, newHoleMesh = ReadPoly(filename)
self.assertEquals(oldHoleMesh.GetDim(), newHoleMesh.GetDim())
self.assertEquals(oldHoleMesh.NodeCount(), newHoleMesh.NodeCount())
self.assertEquals(oldHoleMesh.SurfaceElementCount(),
newHoleMesh.SurfaceElementCount())
self.assertEquals(oldHoleMesh.VolumeElementCount(),
newHoleMesh.VolumeElementCount())
self.assertEquals(oldHoleMesh.GetDim(), newHoleMesh.GetDim())
self.assertEquals(oldHoleMesh.NodeCount(), newHoleMesh.NodeCount())
self.assertEquals(oldHoleMesh.SurfaceElementCount(),
newHoleMesh.SurfaceElementCount())
self.assertEquals(oldHoleMesh.VolumeElementCount(),
newHoleMesh.VolumeElementCount())
oldMesh = meshes.Mesh(3)
oldMesh.AddNodeCoord([0.0, 0.0, 0.0])
oldMesh.AddNodeCoord([1.0, 0.0, 0.0])
oldMesh.AddNodeCoord([0.0, 1.0, 0.0])
oldMesh.AddNodeCoord([0.0, 0.0, 1.0])
oldMesh.AddSurfaceElement(elements.Element(nodes=[0, 1, 2]))
oldMesh.AddSurfaceElement(elements.Element(nodes=[0, 1, 3]))
oldMesh.AddSurfaceElement(elements.Element(nodes=[0, 2, 3]))
oldMesh.AddSurfaceElement(elements.Element(nodes=[1, 2, 3]))
oldHoleMesh = meshes.Mesh(3)
oldHoleMesh.AddNodeCoord([0.1, 0.1, 0.1])
oldHoleMesh.AddNodeCoord([0.2, 0.2, 0.2])
filename = os.path.join(tempDir, "temp.poly")
WritePoly(oldMesh, filename, holeMesh=oldHoleMesh)
newMesh, newHoleMesh = ReadPoly(filename)
self.assertEquals(oldHoleMesh.GetDim(), newHoleMesh.GetDim())
self.assertEquals(oldHoleMesh.NodeCount(), newHoleMesh.NodeCount())
self.assertEquals(oldHoleMesh.SurfaceElementCount(),
newHoleMesh.SurfaceElementCount())
self.assertEquals(oldHoleMesh.VolumeElementCount(),
newHoleMesh.VolumeElementCount())
self.assertEquals(oldHoleMesh.GetDim(), newHoleMesh.GetDim())
self.assertEquals(oldHoleMesh.NodeCount(), newHoleMesh.NodeCount())
self.assertEquals(oldHoleMesh.SurfaceElementCount(),
newHoleMesh.SurfaceElementCount())
self.assertEquals(oldHoleMesh.VolumeElementCount(),
newHoleMesh.VolumeElementCount())
filehandling.Rmdir(tempDir, force=True)
return
def testHalosIO(self): halo1 = Halo(process = 0, nProcesses = 1, nOwnedNodes = 3, sends = [[0, 1]], receives = [[3, 4]]) halo2 = Halo(process = 0, nProcesses = 1, nOwnedNodes = 3, sends = [[0, 2, 1]], receives = [[3, 5, 4]]) halos = Halos(process = 0, nProcesses = 1, nodeHalos = [halo1, halo2]) tempDir = tempfile.mkdtemp() filename = os.path.join(tempDir, "halos") WriteHalos(halos, filename) halos = ReadHalos(filename) self.assertEquals(halos.NodeHaloLevels(), [1, 2]) self.assertEquals(halos.ElementHaloLevels(), []) halo1, halo2 = halos.GetNodeHalos() self.assertEquals(halo1.GetProcess(), 0) self.assertEquals(halo2.GetProcess(), 0) self.assertEquals(halo1.GetNProcesses(), 1) self.assertEquals(halo2.GetNProcesses(), 1) self.assertEquals(halo1.GetSends(process = 0), [0, 1]) self.assertEquals(halo2.GetSends(process = 0), [0, 2, 1]) self.assertEquals(halo1.GetReceives(process = 0), [3, 4]) self.assertEquals(halo2.GetReceives(process = 0), [3, 5, 4]) filehandling.Rmdir(tempDir, force = True) return
def testMshIo(self):
tempDir = tempfile.mkdtemp()
oldMesh = meshes.Mesh(2)
oldMesh.AddNodeCoord([0.0, 0.0])
oldMesh.AddNodeCoord([1.0, 0.0])
oldMesh.AddNodeCoord([0.0, 1.0])
oldMesh.AddVolumeElement(elements.Element(nodes=[0, 1, 2]))
oldMesh.AddSurfaceElement(elements.Element(nodes=[0, 1]))
oldMesh.AddSurfaceElement(elements.Element(nodes=[0, 2]))
oldMesh.AddSurfaceElement(elements.Element(nodes=[1, 2]))
filename = os.path.join(tempDir, "temp")
WriteMsh(oldMesh, filename, binary=False)
newMesh = ReadMsh(filename)
filehandling.Rmdir(tempDir, force=True)
self.assertEquals(oldMesh.GetDim(), newMesh.GetDim())
self.assertEquals(oldMesh.NodeCount(), newMesh.NodeCount())
self.assertEquals(oldMesh.SurfaceElementCount(),
newMesh.SurfaceElementCount())
self.assertEquals(oldMesh.VolumeElementCount(),
newMesh.VolumeElementCount())
tempDir = tempfile.mkdtemp()
oldMesh = meshes.Mesh(2)
oldMesh.AddNodeCoord([0.0, 0.0])
oldMesh.AddNodeCoord([1.0, 0.0])
oldMesh.AddNodeCoord([0.0, 1.0])
oldMesh.AddVolumeElement(elements.Element(nodes=[0, 1, 2]))
oldMesh.AddSurfaceElement(elements.Element(nodes=[0, 1]))
oldMesh.AddSurfaceElement(elements.Element(nodes=[0, 2]))
oldMesh.AddSurfaceElement(elements.Element(nodes=[1, 2]))
filename = os.path.join(tempDir, "temp")
WriteMsh(oldMesh, filename, binary=True)
newMesh = ReadMsh(filename)
filehandling.Rmdir(tempDir, force=True)
self.assertEquals(oldMesh.GetDim(), newMesh.GetDim())
self.assertEquals(oldMesh.NodeCount(), newMesh.NodeCount())
self.assertEquals(oldMesh.SurfaceElementCount(),
newMesh.SurfaceElementCount())
self.assertEquals(oldMesh.VolumeElementCount(),
newMesh.VolumeElementCount())
return
def TetrahedralizeMesh(mesh, holeMesh=None, commandLineSwitches=[]):
"""
Tetrahedralise the given mesh using TetGen
"""
tempDir = tempfile.mkdtemp()
polyFilename = os.path.join(tempDir, "temp.poly")
WritePoly(mesh, polyFilename, holeMesh=holeMesh)
mesh = TetrahedralizePoly(polyFilename,
commandLineSwitches=commandLineSwitches)
filehandling.Rmdir(tempDir, force=True)
return mesh
def TriangulateMesh(mesh, holeMesh=None, commandLineSwitches=[]):
"""
Triangulate the given mesh file using Triangle
"""
tempDir = tempfile.mkdtemp()
polyFilename = os.path.join(tempDir, "temp.poly")
WritePoly(mesh, polyFilename, holeMesh=holeMesh)
mesh = TriangulatePoly(polyFilename,
commandLineSwitches=commandLineSwitches)
filehandling.Rmdir(tempDir, force=True)
return mesh
def testFindPvtuVtuFilenames(self):
tempDir = tempfile.mkdtemp()
project = os.path.join(tempDir, "project")
for i in range(2, 4):
for j in range(3):
filehandling.Touch(project + "_" + str(i) + "_" + str(j) +
".vtu")
filehandling.Touch(project + "_" + str(i) + ".pvtu")
filenames = FindPvtuVtuFilenames(project, firstId=2, lastId=3)
self.assertEquals(len(filenames), 6)
filehandling.Rmdir(tempDir, force=True)
return
def testScatterPlot(self):
plot = ScatterPlot([0.0, 1.0], [1.0, 2.0], xLabel="x", yLabel="y")
# Set data again, to test figure close
plot.SetData([0.0, 1.0], [1.0, 2.0])
tempDir = tempfile.mkdtemp()
plot.Save(os.path.join(tempDir, "temp.png"))
plot.Save(os.path.join(tempDir, "temp.svg"))
filehandling.Rmdir(tempDir, force=True)
self.assertTrue(isinstance(plot.Widget(), gtk.Widget))
return
def testTriangulatePoly(self):
tempDir = tempfile.mkdtemp()
mesh = meshes.Mesh(2)
mesh.AddNodeCoords([[0.0, 0.0], [1.0, 0.0], [0.0, 1.0], [0.1, 0.1]])
mesh.AddSurfaceElement(elements.Element([0, 1]))
mesh.AddSurfaceElement(elements.Element([1, 2]))
mesh.AddSurfaceElement(elements.Element([2, 0]))
filename = os.path.join(tempDir, "test.poly")
WritePoly(mesh, filename)
mesh = TriangulatePoly(filename, commandLineSwitches=["-YY"])
self.assertEquals(mesh.NodeCount(), 4)
self.assertEquals(mesh.VolumeElementCount(), 3)
self.assertEquals(mesh.SurfaceElementCount(), 0)
filehandling.Rmdir(tempDir, force=True)
return
basename = sys.argv[1]
debug.dprint("vtu basename: " + basename)
nPieces = fluiditytools.FindMaxVtuId(basename) + 1
debug.dprint("Number of pieces: " + str(nPieces))
# Write to a temporary directory so that the first piece isn't overwritten
tempDir = tempfile.mkdtemp()
# Create the parallel writer
writer = vtk.vtkXMLPUnstructuredGridWriter()
writer.SetNumberOfPieces(nPieces)
writer.WriteSummaryFileOn()
pvtuName = basename + ".pvtu"
writer.SetFileName(os.path.join(tempDir, pvtuName))
# Load in the first piece, so that the parallel writer has something to do (and
# knows which fields we have)
pieceName = fluiditytools.VtuFilenames(basename, 0)[0]
pieceVtu = vtktools.vtu(pieceName)
if vtk.vtkVersion.GetVTKMajorVersion() <= 5:
writer.SetInput(0, pieceVtu.ugrid)
else:
writer.SetInputData(0, pieceVtu.ugrid)
# Write
writer.Write()
# Move the output back and clean up
filehandling.Move(os.path.join(tempDir, pvtuName), pvtuName)
filehandling.Rmdir(tempDir, force=True)
