diff options
| -rwxr-xr-x | pyfrm2xdmf | 177 |
1 files changed, 123 insertions, 54 deletions
@@ -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") |