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-rwxr-xr-xpyfrm2xdmf177
1 files changed, 123 insertions, 54 deletions
diff --git a/pyfrm2xdmf b/pyfrm2xdmf
index 172b76c..93dd9d3 100755
--- a/pyfrm2xdmf
+++ b/pyfrm2xdmf
@@ -14,6 +14,8 @@ def meshFile(param):
base, ext = os.path.splitext(param)
if ext.lower() != '.pyfrm':
raise argparse.ArgumentTypeError('Mesh file must have a .pyfrm extension')
+ if not os.path.exists(param):
+ raise argparse.ArgumentTypeError("{} not found".format(param))
return param
def writeHeader(xdmfFile):
@@ -26,58 +28,58 @@ def writeHeader(xdmfFile):
def writeTopology(xdmfFile, tType, nCells, connFile):
"write Topology element"
- xdmfFile.write(' <Topology TopologyType="{}" NumberOfElements="{}">\n'.format(tType, nCells))
- xdmfFile.write(' <xi:include href="{}"/>\n'.format(connFile))
- xdmfFile.write(' </Topology>\n')
+ xdmfFile.write(' <Topology TopologyType="{}" NumberOfElements="{}">\n'.format(tType, nCells))
+ xdmfFile.write(' <xi:include href="{}"/>\n'.format(connFile))
+ xdmfFile.write(' </Topology>\n')
return
def writeGeometry(xdmfFile, nDims, nCells, nodeArray, pyfrm, dataset):
"write Geometry element"
nVerts = len(nodeArray)
if nDims == 2:
- xdmfFile.write(' <Geometry GeometryType="X_Y">\n') # co-ordinates in separate arrays
+ xdmfFile.write(' <Geometry GeometryType="X_Y">\n') # co-ordinates in separate arrays
else:
- xdmfFile.write(' <Geometry GeometryType="X_Y_Z">\n') # co-ordinates in separate arrays
+ xdmfFile.write(' <Geometry GeometryType="X_Y_Z">\n') # co-ordinates in separate arrays
for coord in range(nDims):
- xdmfFile.write(' <DataItem ItemType="Function" Dimensions="{}"\n'.format(nVerts*nCells)) # 1D-array
- xdmfFile.write(' Function="JOIN({})">\n'.format(' ; '.join("$" + str(k) for k in range(nVerts))))
+ xdmfFile.write(' <DataItem ItemType="Function" Dimensions="{}"\n'.format(nVerts*nCells)) # 1D-array
+ xdmfFile.write(' Function="JOIN({})">\n'.format(' ; '.join("$" + str(k) for k in range(nVerts))))
writeHyperSlab(xdmfFile, coord, nDims, nCells, nodeArray, pyfrm, dataset)
- xdmfFile.write(' </DataItem>\n')
- xdmfFile.write(' </Geometry>\n')
+ xdmfFile.write(' </DataItem>\n')
+ xdmfFile.write(' </Geometry>\n')
return
def writeHyperSlab(xdmfFile, coord, nDims, nCells, nodeArray, pyfrm, dataset):
"write HyperSlab element"
nVerts = len(nodeArray)
for vert in nodeArray:
- xdmfFile.write(' <DataItem ItemType="HyperSlab"\n')
- xdmfFile.write(' Dimensions="{} 1 1"\n'.format(nCells))
- xdmfFile.write(' Type="HyperSlab">\n')
- xdmfFile.write(' <DataItem\n') # start, stride and count of hyperslab region
- xdmfFile.write(' Dimensions="3 3"\n')
- xdmfFile.write(' Format="XML">\n')
- xdmfFile.write(' {:<3} 0 {}\n'.format(vert, coord)) # select vertex and co-ordinate (format is vertex, cell, co-ordinate)
- xdmfFile.write(' 1 1 1\n') # select every cell, for this vertex and co-ordinate
- xdmfFile.write(' 1 {} 1\n'.format(nCells)) # loop over cells
+ xdmfFile.write(' <DataItem ItemType="HyperSlab"\n')
+ xdmfFile.write(' Dimensions="{} 1 1"\n'.format(nCells))
+ xdmfFile.write(' Type="HyperSlab">\n')
+ xdmfFile.write(' <DataItem\n') # start, stride and count of hyperslab region
+ xdmfFile.write(' Dimensions="3 3"\n')
+ xdmfFile.write(' Format="XML">\n')
+ xdmfFile.write(' {:<3} 0 {}\n'.format(vert, coord)) # select vertex and co-ordinate (format is vertex, cell, co-ordinate)
+ xdmfFile.write(' 1 1 1\n') # select every cell, for this vertex and co-ordinate
+ xdmfFile.write(' 1 {} 1\n'.format(nCells)) # loop over cells
+ xdmfFile.write(' </DataItem>\n')
+ xdmfFile.write(' <DataItem\n')
+ xdmfFile.write(' Name="Points" \n')
+ xdmfFile.write(' Dimensions="{} {} {}"\n'.format(nVerts, nCells, nDims))
+ xdmfFile.write(' Format="HDF">\n')
+ xdmfFile.write(' {}:/{}\n'.format(pyfrm, dataset))
xdmfFile.write(' </DataItem>\n')
- xdmfFile.write(' <DataItem\n')
- xdmfFile.write(' Name="Points" \n')
- xdmfFile.write(' Dimensions="{} {} {}"\n'.format(nVerts, nCells, nDims))
- xdmfFile.write(' Format="HDF">\n')
- xdmfFile.write(' {}:/{}\n'.format(pyfrm, dataset))
- xdmfFile.write(' </DataItem>\n')
- xdmfFile.write(' </DataItem>\n')
+ xdmfFile.write(' </DataItem>\n')
return
def writeAttribute(xdmfFile, tag):
"write Attribute element"
- xdmfFile.write(' <Attribute Name="Partition" Center="Grid">\n')
- xdmfFile.write(' <DataItem\n')
- xdmfFile.write(' Dimensions="1"\n')
- xdmfFile.write(' Format="XML">\n')
- xdmfFile.write(' {}\n'.format(tag)) # tag with partition number
- xdmfFile.write(' </DataItem>\n')
- xdmfFile.write(' </Attribute>\n')
+ xdmfFile.write(' <Attribute Name="Partition" Center="Grid">\n')
+ xdmfFile.write(' <DataItem\n')
+ xdmfFile.write(' Dimensions="1"\n')
+ xdmfFile.write(' Format="XML">\n')
+ xdmfFile.write(' {}\n'.format(tag)) # tag with partition number
+ xdmfFile.write(' </DataItem>\n')
+ xdmfFile.write(' </Attribute>\n')
return
def writeConnectivities(connFile, nCells, nVerts):
@@ -120,7 +122,7 @@ def readH5lsOutput(os_output):
partno = int(re.search('\d+', chunk[0]).group())
nnodes = int(re.search('(\d+),', line.decode()).group(1))
ncells = int(re.search(' (\d+),', line.decode()).group(1))
- if re.search('quad', line.decode()): # check whether cell is quadrangular
+ if re.search('quad', line.decode()): # check whether cells are quadrilaterals
if nnodes == 4:
quad4[partno] = ncells
elif nnodes == 9:
@@ -133,7 +135,7 @@ def readH5lsOutput(os_output):
quad36[partno] = ncells
else:
print("unknown cell order")
- elif re.search('tri', line.decode()): # check whether cell is triangular
+ elif re.search('tri', line.decode()): # check whether cells are triangles
if nnodes == 3:
tri3[partno] = ncells
elif nnodes == 6:
@@ -146,7 +148,7 @@ def readH5lsOutput(os_output):
tri21[partno] = ncells
else:
print("unknown cell order")
- elif re.search('hex', line.decode()): # check whether cell is hexahedral
+ elif re.search('hex', line.decode()): # check whether cells are hexahedrons
if nnodes == 8:
hex8[partno] = ncells
elif nnodes == 27:
@@ -159,6 +161,51 @@ def readH5lsOutput(os_output):
hex216[partno] = ncells
else:
print("unknown cell order")
+ elif re.search('pyr', line.decode()): # check whether cells are pyramids
+ if nnodes == 5:
+ pyr5[partno] = ncells
+ elif nnodes == 14:
+ pyr14[partno] = ncells
+ elif nnodes == 30:
+ pyr30[partno] = ncells
+ elif nnodes == 55:
+ pyr55[partno] = ncells
+ elif nnodes == 91:
+ pyr91[partno] = ncells
+ elif nnodes == 140:
+ pyr140[partno] = ncells
+ else:
+ print("unknown cell order")
+ elif re.search('pri', line.decode()): # check whether cells are prisms
+ if nnodes == 6:
+ pri6[partno] = ncells
+ elif nnodes == 18:
+ pri18[partno] = ncells
+ elif nnodes == 40:
+ pri40[partno] = ncells
+ elif nnodes == 75:
+ pri75[partno] = ncells
+ elif nnodes == 126:
+ pri126[partno] = ncells
+ elif nnodes == 196:
+ pri196[partno] = ncells
+ else:
+ print("unknown cell order")
+ elif re.search('tet', line.decode()): # check whether cells are tetrahedrons
+ if nnodes == 4:
+ tet4[partno] = ncells
+ elif nnodes == 10:
+ tet10[partno] = ncells
+ elif nnodes == 20:
+ tet20[partno] = ncells
+ elif nnodes == 35:
+ tet35[partno] = ncells
+ elif nnodes == 56:
+ tet56[partno] = ncells
+ elif nnodes == 84:
+ tet84[partno] = ncells
+ else:
+ print("unknown cell order")
else:
print("unknown cell type")
break
@@ -196,28 +243,55 @@ ndims = {'quad': 2, 'tri': 2, 'hex': 3, 'pyr': 3, 'pri': 3, 'tet':3
xdmfTopologyType = {'quad': 'Quadrilateral', 'tri': 'Triangle', 'hex': 'Hexahedron',
'pyr' : 'Pyramid', 'pri': 'Wedge', 'tet': 'Tetrahedron'}
-# node identification (see pyfr/readers/nodemaps.py): reduce high-order cells to first order
+# node identification (see pyfr/readers/nodemaps.py): reduces high-order cells to first order
+# example, for second-order pyramid:
+# >>> from pyfr.readers.nodemaps import GmshNodeMaps
+# >>> [GmshNodeMaps.to_pyfr['pyr', 14][i] for i in range(5)]
nodeIDs = {}
nodeIDs[29] = [0, 2, 8, 6] # quad9
nodeIDs[28] = [0, 1, 3, 2] # quad4
+nodeIDs[24] = [0, 2, 5] # tri6
nodeIDs[23] = [0, 1, 2] # tri3
nodeIDs[19] = [0, 2, 8, 6, 18, 20, 26, 24] # hex27
nodeIDs[18] = [0, 1, 3, 2, 4, 5, 7, 6] # hex8
+nodeIDs[13] = [0, 2, 8, 6, 13] # pyr14
+nodeIDs[12] = [0, 1, 3, 2, 4] # pyr5
+nodeIDs[7] = [0, 2, 5, 12, 14, 17] # pri18
+nodeIDs[6] = [0, 1, 2, 3, 4, 5] # pri6
+nodeIDs[1] = [0, 2, 5, 9] # tet10
+nodeIDs[0] = [0, 1, 2, 3] # tet4
-# sort datasets
-hex8Keys = list(nhex8.keys()) # keys are partition numbers
+# keys are partition numbers
+tet4Keys = list(ntet4.keys())
+tet10Keys = list(ntet10.keys())
+pri6Keys = list(npri6.keys())
+pri18Keys = list(npri18.keys())
+pyr5Keys = list(npyr5.keys())
+pyr14Keys = list(npyr14.keys())
+hex8Keys = list(nhex8.keys())
hex27Keys = list(nhex27.keys())
-quad4Keys = list(nquad4.keys())
tri3Keys = list(ntri3.keys())
-allKeys = quad4Keys + tri3Keys + hex8Keys + hex27Keys # concatenate keys
-numTypes = Counter(allKeys) # number of types present in each partition
-partKeys = list(numTypes.keys()) # partition keys
+tri6Keys = list(ntri6.keys())
+quad4Keys = list(nquad4.keys())
+quad9Keys = list(nquad9.keys())
+# concatenate keys
+allKeys = (tet4Keys + tet10Keys +
+ pri6Keys + pri18Keys +
+ pyr5Keys + pyr14Keys +
+ hex8Keys + hex27Keys +
+ tri3Keys + tri6Keys +
+ quad4Keys + quad9Keys)
+# number of types present in each partition
+numTypes = Counter(allKeys)
+# list of partition keys
+partKeys = list(numTypes.keys())
+# list of cell dictionaries
partitions = [ntet4, ntet10, ntet20, ntet35, ntet56, ntet84,
npri6, npri18, npri40, npri75, npri126, npri196,
npyr5, npyr14, npyr30, npyr55, npyr91, npyr140,
nhex8, nhex27, nhex64, nhex125, nhex216,
ntri3, ntri6, ntri10, ntri15, ntri21,
- nquad4, nquad9, nquad16, nquad25, nquad36] # list of cell dictionaries
+ nquad4, nquad9, nquad16, nquad25, nquad36]
numCellTypes = len(partitions)
if partKeys:
@@ -226,31 +300,26 @@ if partKeys:
writeHeader(g)
for part in partKeys:
- if numTypes[part] > 1: # check whether partition contain multiple cell types
- g.write(' <Grid Name="Partition{}" GridType="Collection">\n'.format(part))
- else:
- g.write(' <Grid Name="Partition{}" GridType="Uniform">\n'.format(part))
-
+ g.write(' <Grid Name="Partition{}" GridType="Collection">\n'.format(part))
for cellType in range(numCellTypes):
if part in partitions[cellType]: # check whether these cells exist in this partition
xfname = os.path.join('con_' + firstOrderCellType[cellType] + '_p' + str(part) + '.xml')
dname = os.path.join('spt_' + firstOrderCellType[cellType] + '_p' + str(part))
- if numTypes[part] > 1:
- g.write(' <Grid Name="cellType{}" GridType="Uniform">\n'.format(cellType))
+ g.write(' <Grid Name="{}s[{}]" GridType="Uniform">\n'.format(xdmfTopologyType[firstOrderCellType[cellType]], part))
writeTopology(g, xdmfTopologyType[firstOrderCellType[cellType]],
partitions[cellType][part], xfname)
writeGeometry(g, ndims[firstOrderCellType[cellType]],
partitions[cellType][part],
nodeIDs[cellType],
args.mesh, dname)
- if numTypes[part] > 1:
- g.write(' </Grid>\n')
+ writeAttribute(g, part)
+ g.write(' </Grid>\n')
# connectivities file
writeConnectivities(xfname, partitions[cellType][part],
len(nodeIDs[cellType]))
-
- writeAttribute(g, part)
g.write(' </Grid>\n')
writeFooter(g)
g.close()
+else:
+ print("mesh does not contain any supported cell types")