def WriteHalos(halos, filename):
"""
Write a Fluidity .halo file
"""
xmlfile = xml.dom.minidom.Document()
halosRootEle = xmlfile.createElement("halos")
halosRootEle.setAttribute("process", str(halos.GetProcess()))
halosRootEle.setAttribute("nprocs", str(halos.GetNProcesses()))
xmlfile.appendChild(halosRootEle)
halos = halos.LevelHaloDict()
for level in halos.keys():
halo = halos[level]
haloEle = xmlfile.createElement("halo")
haloEle.setAttribute("level", str(level))
haloEle.setAttribute("n_private_nodes", str(halo.GetNOwnedNodes()))
halosRootEle.appendChild(haloEle)
for i, process in enumerate(range(halo.GetNProcesses())):
haloDataEle = xmlfile.createElement("halo_data")
haloDataEle.setAttribute("process", str(i))
haloEle.appendChild(haloDataEle)
sendEle = xmlfile.createElement("send")
haloDataEle.appendChild(sendEle)
if level > 0:
sendText = xmlfile.createTextNode(utils.FormLine(utils.OffsetList(utils.ExpandList(halo.GetSends(process = i)), 1), delimiter = " ", newline = False))
else:
sendText = xmlfile.createTextNode(utils.FormLine(utils.ExpandList(halo.GetSends(process = i)), delimiter = " ", newline = False))
sendEle.appendChild(sendText)
receiveEle = xmlfile.createElement("receive")
haloDataEle.appendChild(receiveEle)
if level > 0:
receiveText = xmlfile.createTextNode(utils.FormLine(utils.OffsetList(utils.ExpandList(halo.GetReceives(process = i)), 1), delimiter = " ", newline = False))
else:
receiveText = xmlfile.createTextNode(utils.FormLine(utils.ExpandList(halo.GetReceives(process = i)), delimiter = " ", newline = False))
receiveEle.appendChild(receiveText)
handle = open(filename, "w")
if XmlExtSupport():
xml.dom.ext.PrettyPrint(xmlfile, handle)
else:
xmlfile.writexml(handle)
handle.flush()
handle.close()
return
def WriteGid(mesh, filename):
"""
Write a GiD file with the given filename
"""
debug.dprint("Writing GiD mesh with filename " + filename)
fileHandle = open(filename, "w")
# Write the header
fileHandle.write(utils.FormLine(["MESH", "dimension", mesh.GetDim(), "ElemType", "Unknown", "Nnode", mesh.VolumeElementFixedNodeCount()]))
# Write the nodes
fileHandle.write("Coordinates\n")
for i, nodeCoord in enumerate(mesh.GetNodeCoords()):
fileHandle.write(" " + utils.FormLine([i + 1, nodeCoord]))
fileHandle.write("end coordinates\n")
# Write the volume elements
fileHandle.write("Elements\n")
for i, element in enumerate(mesh.GetVolumeElements()):
# Note: GiD file indexes nodes from 1, Mesh s index nodes from 0
fileHandle.write(" " + utils.FormLine([i + 1, ToGidNodeOrder(utils.OffsetList(element.GetNodes(), 1), elements.ElementType(dim = mesh.GetDim(), nodeCount = element.NodeCount()))]))
fileHandle.write("end elements\n")
fileHandle.close()
debug.dprint("Finished writing GiD mesh")
return mesh
def WriteTriangle(mesh, baseName):
"""
Write triangle files with the given base name
"""
def FileFooter():
return "# Created by triangletools.WriteTriangle\n" + \
"# Command: " + " ".join(sys.argv) + "\n" + \
"# " + str(time.ctime()) + "\n"
debug.dprint("Writing triangle mesh with base name " + baseName)
# Write the .node file
debug.dprint("Writing .node file")
nodeHandle = open(baseName + ".node", "w")
# Write the meta data
nodeHandle.write(utils.FormLine([mesh.NodeCount(), mesh.GetDim(), 0, 0]))
# Write the nodes
for i in range(mesh.NodeCount()):
nodeHandle.write(utils.FormLine([i + 1, mesh.GetNodeCoord(i)]))
nodeHandle.write(FileFooter())
nodeHandle.close()
if mesh.GetDim() == 1:
# Write the .bound file
debug.dprint("Writing .bound file")
boundHandle = open(baseName + ".bound", "w")
# Write the meta data
nBoundIds = 0
for i in range(mesh.SurfaceElementCount()):
if i == 0:
nBoundIds = len(mesh.GetSurfaceElement(i).GetIds())
else:
assert(nBoundIds == len(mesh.GetSurfaceElement(i).GetIds()))
boundHandle.write(utils.FormLine([mesh.SurfaceElementCount(), nBoundIds]))
# Write the bounds
for i in range(mesh.SurfaceElementCount()):
boundHandle.write(utils.FormLine([i + 1, utils.OffsetList(mesh.GetSurfaceElement(i).GetNodes(), 1), mesh.GetSurfaceElement(i).GetIds()]))
boundHandle.write(FileFooter())
boundHandle.close()
elif mesh.GetDim() == 2:
# Write the .edge file
debug.dprint("Writing .edge file")
edgeHandle = open(baseName + ".edge", "w")
# Write the meta data
nEdgeIds = 0
for i in range(mesh.SurfaceElementCount()):
if i == 0:
nEdgeIds = len(mesh.GetSurfaceElement(i).GetIds())
else:
assert(nEdgeIds == len(mesh.GetSurfaceElement(i).GetIds()))
edgeHandle.write(utils.FormLine([mesh.SurfaceElementCount(), nEdgeIds]))
# Write the edges
for i in range(mesh.SurfaceElementCount()):
edgeHandle.write(utils.FormLine([i + 1, utils.OffsetList(mesh.GetSurfaceElement(i).GetNodes(), 1), mesh.GetSurfaceElement(i).GetIds()]))
edgeHandle.write(FileFooter())
edgeHandle.close()
elif mesh.GetDim() == 3:
# Write the .face file
debug.dprint("Writing .face file")
faceHandle = open(baseName + ".face", "w")
# Write the meta data
nFaceIds = 0
for i in range(mesh.SurfaceElementCount()):
if i == 0:
nFaceIds = len(mesh.GetSurfaceElement(i).GetIds())
else:
assert(nFaceIds == len(mesh.GetSurfaceElement(i).GetIds()))
faceHandle.write(utils.FormLine([mesh.SurfaceElementCount(), nFaceIds]))
# Write the faces
for i in range(mesh.SurfaceElementCount()):
faceHandle.write(utils.FormLine([i + 1, utils.OffsetList(mesh.GetSurfaceElement(i).GetNodes(), 1), mesh.GetSurfaceElement(i).GetIds()]))
faceHandle.write(FileFooter())
faceHandle.close()
# Write the .ele file
debug.dprint("Writing .ele file")
eleHandle = open(baseName + ".ele", "w")
# Write the meta data
nNodesPerEle = 0
nEleIds = 0
for i in range(mesh.VolumeElementCount()):
if i == 0:
nEleIds = len(mesh.GetVolumeElement(i).GetIds())
nNodesPerEle = mesh.GetVolumeElement(i).GetLoc()
else:
assert(nEleIds == len(mesh.GetVolumeElement(i).GetIds()))
assert(nNodesPerEle == mesh.GetVolumeElement(i).GetLoc())
eleHandle.write(utils.FormLine([mesh.VolumeElementCount(), nNodesPerEle, nEleIds]))
# Write the eles
for i in range(mesh.VolumeElementCount()):
# Note: Triangle mesh indexes nodes from 1, Mesh s index nodes from 0
eleHandle.write(utils.FormLine([i + 1, utils.OffsetList(mesh.GetVolumeElement(i).GetNodes(), 1), mesh.GetVolumeElement(i).GetIds()]))
eleHandle.write(FileFooter())
eleHandle.close()
halos = mesh.GetHalos()
if halos.HaloCount() > 0:
# Write the .halo file
debug.dprint("Writing .halo file")
if mesh_halos.HaloIOSupport():
mesh_halos.WriteHalos(halos, baseName + ".halo")
else:
debug.deprint("Warning: No .halo I/O support")
debug.dprint("Finished writing triangle file")
return
def WritePoly(mesh, filename, holeMesh=None):
"""
Write a .poly file with the given base name
"""
def FileFooter():
return "# Created by WritePoly\n" + \
"# Command: " + " ".join(sys.argv) + "\n" + \
"# " + str(time.ctime()) + "\n"
polyHandle = open(filename, "w")
# Write the node meta data
polyHandle.write("# Nodes\n")
polyHandle.write(utils.FormLine([mesh.NodeCount(), mesh.GetDim(), 0, 0]))
# Write the nodes
for i in range(mesh.NodeCount()):
polyHandle.write(utils.FormLine([i + 1, mesh.GetNodeCoord(i)]))
# Write the facets meta data
polyHandle.write("# Facets\n")
nFacetIds = 0
for i in range(mesh.SurfaceElementCount()):
if i == 0:
nFacetIds = len(mesh.GetSurfaceElement(i).GetIds())
else:
assert (nFacetIds == len(mesh.GetSurfaceElement(i).GetIds()))
polyHandle.write(utils.FormLine([mesh.SurfaceElementCount(), nFacetIds]))
# Write the facets
if mesh.GetDim() == 2:
# This is the facet specification as in the Triangle documentation
# http://www.cs.cmu.edu/~quake/triangle.poly.html
for i in range(mesh.SurfaceElementCount()):
# Note: .poly indexes nodes from 1, Mesh s index nodes from 0
polyHandle.write(
utils.FormLine([
i + 1,
utils.OffsetList(mesh.GetSurfaceElement(i).GetNodes(), 1),
mesh.GetSurfaceElement(i).GetIds()
]))
else:
# This is the facet specification as in the Tetgen documentation
# http://tetgen.berlios.de/fformats.poly.html
for i in range(mesh.SurfaceElementCount()):
polyHandle.write(
utils.FormLine([1, 0, mesh.GetSurfaceElement(i).GetIds()]))
# Note: .poly indexes nodes from 1, Mesh s index nodes from 0
polyHandle.write(
utils.FormLine([
mesh.GetSurfaceElement(i).NodeCount(),
utils.OffsetList(mesh.GetSurfaceElement(i).GetNodes(), 1)
]))
# Write the hole list meta data
polyHandle.write("# Holes\n")
if holeMesh is None:
polyHandle.write(utils.FormLine([0]))
else:
polyHandle.write(utils.FormLine([holeMesh.NodeCount()]))
# Write the holes
for i in range(holeMesh.NodeCount()):
polyHandle.write(utils.FormLine([i + 1, holeMesh.GetNodeCoord(i)]))
polyHandle.write(FileFooter())
polyHandle.close()
return
def WriteMsh(mesh, filename, binary = True):
"""
Write a Gmsh msh file
"""
if binary:
# Binary format
fileHandle = open(filename, "wb")
# Write the MeshFormat section
fileHandle.write("$MeshFormat\n")
version = 2.1
fileType = 1
dataSize = ctypes.sizeof(ctypes.c_double)
fileHandle.write(utils.FormLine([version, fileType, dataSize]))
iArr = array.array("i", [1])
iArr.tofile(fileHandle)
fileHandle.write("\n")
fileHandle.write("$EndMeshFormat\n")
# Write the Nodes section
fileHandle.write("$Nodes\n")
fileHandle.write(utils.FormLine([mesh.NodeCoordsCount()]))
for i, nodeCoord in enumerate(mesh.GetNodeCoords()):
nodeCoord = list(nodeCoord)
while len(nodeCoord) < 3:
nodeCoord.append(0.0)
assert(len(nodeCoord) == 3)
iArr = array.array("i", [i + 1])
rArr = array.array("d", nodeCoord)
iArr.tofile(fileHandle)
rArr.tofile(fileHandle)
fileHandle.write("\n")
fileHandle.write("$EndNodes\n")
# Write the Elements section
fileHandle.write("$Elements\n")
fileHandle.write(utils.FormLine([mesh.SurfaceElementCount() + mesh.VolumeElementCount()]))
eleSort = {}
for ele in mesh.GetSurfaceElements() + mesh.GetVolumeElements():
eleType = ele.GetType()
gmshType = GmshElementType(dim = eleType.GetDim(), nodeCount = eleType.GetNodeCount())
key = (gmshType.GetGmshElementTypeId(), len(ele.GetIds()))
if key in eleSort:
eleSort[key].append(ele)
else:
eleSort[key] = [ele]
index = 1
for gmshEleId, nIds in eleSort:
eles = eleSort[(gmshEleId, nIds)]
iArr = array.array("i", [gmshEleId, len(eles), nIds])
iArr.tofile(fileHandle)
for ele in eles:
iArr = array.array("i", [index] + list(ele.GetIds()) + utils.OffsetList(ToGmshNodeOrder(ele.GetNodes(), ele.GetType()), 1))
iArr.tofile(fileHandle)
index += 1
assert(index == mesh.SurfaceElementCount() + mesh.VolumeElementCount() + 1)
fileHandle.write("\n")
fileHandle.write("$EndElements\n")
else:
# ASCII format
fileHandle = open(filename, "w")
# Write the MeshFormat section
fileHandle.write("$MeshFormat\n")
version = 2.1
fileType = 0
dataSize = ctypes.sizeof(ctypes.c_double)
fileHandle.write(utils.FormLine([version, fileType, dataSize]))
fileHandle.write("$EndMeshFormat\n")
# Write the Nodes section
fileHandle.write("$Nodes\n")
fileHandle.write(utils.FormLine([mesh.NodeCoordsCount()]))
for i, nodeCoord in enumerate(mesh.GetNodeCoords()):
nodeCoord = list(nodeCoord)
while len(nodeCoord) < 3:
nodeCoord.append(0.0)
assert(len(nodeCoord) == 3)
fileHandle.write(utils.FormLine([i + 1, nodeCoord]))
fileHandle.write("$EndNodes\n")
# Write the Elements section
fileHandle.write("$Elements\n")
fileHandle.write(utils.FormLine([mesh.SurfaceElementCount() + mesh.VolumeElementCount()]))
for i, ele in enumerate(mesh.GetSurfaceElements() + mesh.GetVolumeElements()):
eleType = ele.GetType()
gmshType = GmshElementType(dim = eleType.GetDim(), nodeCount = eleType.GetNodeCount())
ids = ele.GetIds()
fileHandle.write(utils.FormLine([i + 1, gmshType.GetGmshElementTypeId(), len(ids), ids, utils.OffsetList(ToGmshNodeOrder(ele.GetNodes(), eleType), 1)]))
fileHandle.write("$EndElements\n")
return
def ReadMsh(filename):
"""
Read a Gmsh msh file
"""
def ReadNonCommentLine(fileHandle):
line = fileHandle.readline()
while len(line) > 0:
line = line.strip()
if len(line) > 0:
return line
line = fileHandle.readline()
return line
fileHandle = open(filename, "r")
basename = filename.split(".")[0]
hasHalo = filehandling.FileExists(basename + ".halo")
# Read the MeshFormat section
line = ReadNonCommentLine(fileHandle)
assert(line == "$MeshFormat")
line = ReadNonCommentLine(fileHandle)
lineSplit = line.split()
assert(len(lineSplit) == 3)
version = float(lineSplit[0])
fileType = int(lineSplit[1])
dataSize = int(lineSplit[2])
if fileType == 1:
# Binary format
if dataSize == 4:
realFormat = "f"
elif dataSize == 8:
realFormat = "d"
else:
raise Exception("Unrecognised real size " + str(dataSize))
iArr = array.array("i")
iArr.fromfile(fileHandle, 1)
if iArr[0] == 1:
swap = False
else:
iArr.byteswap()
if iArr[0] == 1:
swap = True
else:
raise Exception("Invalid one byte")
line = ReadNonCommentLine(fileHandle)
assert(line == "$EndMeshFormat")
# Read the Nodes section
line = ReadNonCommentLine(fileHandle)
assert(line == "$Nodes")
line = ReadNonCommentLine(fileHandle)
nNodes = int(line)
# Assume dense node IDs, but not necessarily ordered
seenNode = [False for i in range(nNodes)]
nodeIds = []
nodes = []
lbound = [calc.Inf() for i in range(3)]
ubound = [-calc.Inf() for i in range(3)]
for i in range(nNodes):
iArr = array.array("i")
rArr = array.array(realFormat)
iArr.fromfile(fileHandle, 1)
rArr.fromfile(fileHandle, 3)
if swap:
iArr.byteswap()
rArr.byteswap()
nodeId = iArr[0]
coord = rArr
assert(nodeId > 0)
assert(not seenNode[nodeId - 1])
seenNode[nodeId - 1] = True
nodeIds.append(nodeId)
nodes.append(coord)
for j in range(3):
lbound[j] = min(lbound[j], coord[j])
ubound[j] = max(ubound[j], coord[j])
line = ReadNonCommentLine(fileHandle)
assert(line == "$EndNodes")
nodes = utils.KeyedSort(nodeIds, nodes)
bound = bounds.BoundingBox(lbound, ubound)
indices = bound.UsedDimIndices()
dim = len(indices)
if dim < 3:
nodes = [[coord[index] for index in indices] for coord in nodes]
mesh = meshes.Mesh(dim)
mesh.AddNodeCoords(nodes)
# Read the Elements section
line = ReadNonCommentLine(fileHandle)
assert(line == "$Elements")
line = ReadNonCommentLine(fileHandle)
nEles = int(line)
i = 0
while i < nEles:
iArr = array.array("i")
iArr.fromfile(fileHandle, 3)
if swap:
iArr.byteswap()
typeId = iArr[0]
nSubEles = iArr[1]
nIds = iArr[2]
type = GmshElementType(gmshElementTypeId = typeId)
for j in range(nSubEles):
iArr = array.array("i")
iArr.fromfile(fileHandle, 1 + nIds + type.GetNodeCount())
if swap:
iArr.byteswap()
eleId = iArr[0]
assert(eleId > 0)
ids = iArr[1:1 + nIds]
nodes = FromGmshNodeOrder(utils.OffsetList(iArr[-type.GetNodeCount():], -1), type)
element = elements.Element(nodes, ids)
if type.GetDim() == dim - 1:
mesh.AddSurfaceElement(element)
elif type.GetDim() == dim:
mesh.AddVolumeElement(element)
else:
debug.deprint("Warning: Element of type " + str(type) + " encountered in " + str(dim) + " dimensions")
i += nSubEles
assert(i == nEles)
line = ReadNonCommentLine(fileHandle)
assert(line == "$EndElements")
elif fileType == 0:
# ASCII format
line = ReadNonCommentLine(fileHandle)
assert(line == "$EndMeshFormat")
# Read the Nodes section
line = ReadNonCommentLine(fileHandle)
assert(line == "$Nodes")
line = ReadNonCommentLine(fileHandle)
nNodes = int(line)
# Assume dense node IDs, but not necessarily ordered
seenNode = [False for i in range(nNodes)]
nodeIds = []
nodes = []
lbound = [calc.Inf() for i in range(3)]
ubound = [-calc.Inf() for i in range(3)]
for i in range(nNodes):
line = ReadNonCommentLine(fileHandle)
lineSplit = line.split()
assert(len(lineSplit) == 4)
nodeId = int(lineSplit[0])
coord = [float(comp) for comp in lineSplit[1:]]
assert(nodeId > 0)
assert(not seenNode[nodeId - 1])
seenNode[nodeId - 1] = True
nodeIds.append(nodeId)
nodes.append(coord)
for j in range(3):
lbound[j] = min(lbound[j], coord[j])
ubound[j] = max(ubound[j], coord[j])
line = ReadNonCommentLine(fileHandle)
assert(line == "$EndNodes")
nodes = utils.KeyedSort(nodeIds, nodes)
bound = bounds.BoundingBox(lbound, ubound)
indices = bound.UsedDimIndices()
dim = len(indices)
if dim < 3:
nodes = [[coord[index] for index in indices] for coord in nodes]
mesh = meshes.Mesh(dim)
mesh.AddNodeCoords(nodes)
# Read the Elements section
line = ReadNonCommentLine(fileHandle)
assert(line == "$Elements")
line = ReadNonCommentLine(fileHandle)
nEles = int(line)
for i in range(nEles):
line = ReadNonCommentLine(fileHandle)
lineSplit = line.split()
assert(len(lineSplit) > 3)
eleId = int(lineSplit[0])
assert(eleId > 0)
typeId = int(lineSplit[1])
nIds = int(lineSplit[2])
type = GmshElementType(gmshElementTypeId = typeId)
ids = [int(id) for id in lineSplit[3:3 + nIds]]
nodes = FromGmshNodeOrder([int(node) - 1 for node in lineSplit[-type.GetNodeCount():]], type)
element = elements.Element(nodes, ids)
if type.GetDim() == dim - 1:
mesh.AddSurfaceElement(element)
elif type.GetDim() == dim:
mesh.AddVolumeElement(element)
else:
debug.deprint("Warning: Element of type " + str(type) + " encountered in " + str(dim) + " dimensions")
line = ReadNonCommentLine(fileHandle)
assert(line == "$EndElements")
# Ignore all remaining sections
else:
raise Exception("File type " + str(fileType) + " not recognised")
fileHandle.close()
if hasHalo:
# Read the .halo file
debug.dprint("Reading .halo file")
if mesh_halos.HaloIOSupport():
halos = mesh_halos.ReadHalos(basename + ".halo")
mesh.SetHalos(halos)
else:
debug.deprint("Warning: No .halo I/O support")
return mesh
def ReadBinaryMshV4(fileHandle, dataSize):
if dataSize == 4:
sizeFormat = "i"
elif dataSize == 8:
sizeFormat = "l"
else:
raise Exception("Unrecognised size_t size " + str(dataSize))
swap = ByteSwap(fileHandle)
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndMeshFormat")
# skip ahead to Nodes section (possibly bypassing Entities)
while line != "$Nodes":
line = ReadNonCommentLine(fileHandle)
assert (line == "$Nodes")
# numEntityBlock(size_t) numNodes(size_t)
# minNodeTag(size_t) maxNodeTag(size_t)
#
# entityDim(int) entityTag(int) parametric(int) numNodes(size_t)
#
# nodeTag(size_t) ...
# x(double) y(double) z(double) ...
# ...
sArr = array.array(sizeFormat)
sArr.fromfile(fileHandle, 4)
if swap:
sArr.byteswap()
numBlocks = sArr[0]
numNodes = sArr[1]
# assume dense nodes (we can check using the min/max id fields)
seenNode = [False] * numNodes
nodeIds = []
nodes = []
lbound = [calc.Inf() for i in range(3)]
ubound = [-calc.Inf() for i in range(3)]
for b in range(numBlocks):
iArr = array.array("i")
sArr = array.array(sizeFormat)
iArr.fromfile(fileHandle, 3)
sArr.fromfile(fileHandle, 1)
if swap:
iArr.byteswap()
sArr.byteswap()
subNodes = sArr[0]
tagArr = array.array(sizeFormat)
tagArr.fromfile(fileHandle, subNodes)
if swap:
tagArr.byteswap()
for i in range(subNodes):
rArr = array.array("d")
rArr.fromfile(fileHandle, 3)
if swap:
rArr.byteswap()
nodeId = tagArr[i]
coord = rArr
assert (nodeId > 0)
assert (not seenNode[nodeId - 1])
seenNode[nodeId - 1] = True
nodeIds.append(nodeId)
nodes.append(coord)
for j in range(3):
lbound[j] = min(lbound[j], coord[j])
ubound[j] = max(ubound[j], coord[j])
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndNodes")
nodes = utils.KeyedSort(nodeIds, nodes)
bound = bounds.BoundingBox(lbound, ubound)
indices = bound.UsedDimIndices()
dim = len(indices)
if dim < 3:
nodes = [[coord[index] for index in indices] for coord in nodes]
mesh = meshes.Mesh(dim)
mesh.AddNodeCoords(nodes)
# read the Elements section
line = ReadNonCommentLine(fileHandle)
assert (line == "$Elements")
# numEntityBlocks(size_t) numElements(size_t)
# minElementTag(size_t) maxElementTag(size_t)
#
# entityDim(int) entityTag(int) elementType(int) numElems(size_t)
# elementTag(size_t) nodeTag(size_t) ...
# ...
# ...
sArr = array.array(sizeFormat)
sArr.fromfile(fileHandle, 4)
if swap:
sArr.byteswap()
numEntities = sArr[0]
numElems = sArr[1]
for i in range(numEntities):
iArr = array.array("i")
sArr = array.array(sizeFormat)
iArr.fromfile(fileHandle, 3)
sArr.fromfile(fileHandle, 1)
if swap:
iArr.byteswap()
sArr.byteswap()
entityDim = iArr[0]
entityTag = iArr[1]
elementType = iArr[2]
elemsInBlock = sArr[0]
type = GmshElementType(gmshElementTypeId=elementType)
for j in range(elemsInBlock):
sArr = array.array(sizeFormat)
sArr.fromfile(1 + type.GetNodeCount())
if swap:
sArr.byteswap()
ids = [entityTag, sArr[0]]
nodes = FromGmshNodeOrder(utils.OffsetList(sArr[1:], -1), type)
element = elements.Element(nodes, ids)
if type.GetDim() == dim - 1:
mesh.AddSurfaceElement(element)
elif type.GetDim() == dim:
mesh.AddVolumeElement(element)
else:
debug.deprint("Warning: Element of type " + str(type) +
" encountered in " + str(dim) + " dimensions")
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndElements")
return mesh
def ReadBinaryMshV2(fileHandle, dataSize):
if dataSize == 4:
realFormat = "f"
elif dataSize == 8:
realFormat = "d"
else:
raise Exception("Unrecognised real size " + str(dataSize))
swap = ByteSwap(fileHandle)
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndMeshFormat")
# Read the Nodes section (no PhysicalNames section in binary)
line = ReadNonCommentLine(fileHandle)
assert (line == "$Nodes")
# number-of-nodes
# node-number x-coord y-coord z-coord
# ...
line = ReadNonCommentLine(fileHandle)
nNodes = int(line)
# Assume dense node IDs, but not necessarily ordered
seenNode = [False for i in range(nNodes)]
nodeIds = []
nodes = []
lbound = [calc.Inf() for i in range(3)]
ubound = [-calc.Inf() for i in range(3)]
for i in range(nNodes):
iArr = array.array("i")
rArr = array.array(realFormat)
iArr.fromfile(fileHandle, 1)
rArr.fromfile(fileHandle, 3)
if swap:
iArr.byteswap()
rArr.byteswap()
nodeId = iArr[0]
coord = rArr
assert (nodeId > 0)
assert (not seenNode[nodeId - 1])
seenNode[nodeId - 1] = True
nodeIds.append(nodeId)
nodes.append(coord)
for j in range(3):
lbound[j] = min(lbound[j], coord[j])
ubound[j] = max(ubound[j], coord[j])
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndNodes")
nodes = utils.KeyedSort(nodeIds, nodes)
bound = bounds.BoundingBox(lbound, ubound)
indices = bound.UsedDimIndices()
dim = len(indices)
if dim < 3:
nodes = [[coord[index] for index in indices] for coord in nodes]
mesh = meshes.Mesh(dim)
mesh.AddNodeCoords(nodes)
# Read the Elements section
line = ReadNonCommentLine(fileHandle)
assert (line == "$Elements")
# number-of-elements
# element-header-binary
# element-binary
# ...
# where element-header-binary is: elm-type num-elm num-tags
# where element-binary is:
# num-elm * (4 + num-tags*4 + node-num*4)
# node-num physical-tag elementary-tag node-nums ...
line = ReadNonCommentLine(fileHandle)
nEles = int(line)
i = 0
while i < nEles:
iArr = array.array("i")
iArr.fromfile(fileHandle, 3)
if swap:
iArr.byteswap()
typeId = iArr[0]
nSubEles = iArr[1]
nIds = iArr[2]
type = GmshElementType(gmshElementTypeId=typeId)
for j in range(nSubEles):
iArr = array.array("i")
iArr.fromfile(fileHandle, 1 + nIds + type.GetNodeCount())
if swap:
iArr.byteswap()
eleId = iArr[0]
assert (eleId > 0)
ids = iArr[1:1 + nIds]
nodes = FromGmshNodeOrder(
utils.OffsetList(iArr[-type.GetNodeCount():], -1), type)
element = elements.Element(nodes, ids)
if type.GetDim() == dim - 1:
mesh.AddSurfaceElement(element)
elif type.GetDim() == dim:
mesh.AddVolumeElement(element)
else:
debug.deprint("Warning: Element of type " + str(type) +
" encountered in " + str(dim) + " dimensions")
i += nSubEles
assert (i == nEles)
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndElements")
return mesh
def ReadHalos(filename):
"""
Read a Fluidity .halo file
"""
xmlFile = xml.dom.minidom.parse(filename)
halosRootEle = xmlFile.getElementsByTagName("halos")
assert(len(halosRootEle) == 1)
halosRootEle = halosRootEle[0]
haloProcess = int(halosRootEle.attributes["process"].nodeValue)
nprocs = int(halosRootEle.attributes["nprocs"].nodeValue)
halosEle = halosRootEle.getElementsByTagName("halo")
halos = Halos(process = haloProcess, nProcesses = nprocs)
for haloEle in halosEle:
try:
level = int(haloEle.attributes["level"].nodeValue)
except KeyError:
# Backwards compatibility
level = int(haloEle.attributes["tag"].nodeValue)
n_private_nodes = int(haloEle.attributes["n_private_nodes"].nodeValue)
halo = Halo(process = haloProcess, nProcesses = nprocs, nOwnedNodes = n_private_nodes)
processes = []
haloDataEles = haloEle.getElementsByTagName("halo_data")
for haloDataEle in haloDataEles:
process = int(haloDataEle.attributes["process"].nodeValue)
assert(process >= 0 and process < nprocs)
assert(not process in processes)
processes.append(process)
sendEle = haloDataEle.getElementsByTagName("send")
assert(len(sendEle) == 1)
sendEle = sendEle[0]
sendEleChildren = sendEle.childNodes
sends = None
for child in sendEleChildren:
if child.nodeType == child.TEXT_NODE:
sends = map(int, child.nodeValue.split())
break
if not sends is None:
if level > 0:
halo.SetSends(utils.OffsetList(sends, -1), process = process)
else:
halo.SetSends(sends, process = process)
receiveEle = haloDataEle.getElementsByTagName("receive")
assert(len(receiveEle) == 1)
receiveEle = receiveEle[0]
receiveEleChildren = receiveEle.childNodes
receives = None
for child in receiveEleChildren:
if child.nodeType == child.TEXT_NODE:
receives = map(int, child.nodeValue.split())
break
if not receives is None:
if level > 0:
halo.SetReceives(utils.OffsetList(receives, -1), process = process)
else:
halo.SetReceives(receives, process = process)
if level > 0:
assert(not halos.HasNodeHalo(level))
halos.SetNodeHalo(level, halo)
else:
assert(not halos.HasElementHalo(-level))
halos.SetElementHalo(-level, halo)
return halos
