diff options
| -rw-r--r-- | AUTHORS | 1 | ||||
| -rw-r--r-- | LICENSE | 28 | ||||
| -rwxr-xr-x | pyfrm2xdmf | 222 | ||||
| -rwxr-xr-x | pyfrs2vtu | 2 |
4 files changed, 179 insertions, 74 deletions
@@ -0,0 +1 @@ +Paul Garlick <pgarlick@tourbillion-technology.com> @@ -0,0 +1,28 @@ +Copyright (c) 2016, Tourbillion Technology Limited + +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + a. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + b. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + c. Neither the name of the copyright holder nor the names of its contributors + may be used to endorse or promote products derived from this software + without specific prior written permission. + + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY +OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH +DAMAGE. @@ -1,8 +1,12 @@ #!/usr/bin/env python +# -*- coding: utf-8 -*- +# run within virtual environment (uses Python 3 syntax) + import argparse import os import re -import string +from array import array +from collections import Counter from subprocess import check_output def meshFile(param): @@ -12,88 +16,158 @@ def meshFile(param): raise argparse.ArgumentTypeError('Mesh file must have a .pyfrm extension') return param +def writeHeader(xdmfFile): + "write XDMF header" + xdmfFile.write('<?xml version="1.0" ?>\n') + xdmfFile.write('<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>\n') + xdmfFile.write('<Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">\n') + xdmfFile.write(' <Domain>\n') + return + +def writeTopology(xdmfFile, nCells, connFile): + "write Topology element" + xdmfFile.write(' <Topology TopologyType="Quadrilateral" NumberOfElements="{}">\n'.format(nCells)) + xdmfFile.write(' <xi:include href="{}"/>\n'.format(connFile)) + xdmfFile.write(' </Topology>\n') + return + +def writeGeometry(xdmfFile, nDims, nCells, nVerts, pyfrm, dataset): + "write Geometry element" + if nDims == 2: + 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 + writeHyperSlab(xdmfFile, nDims, nCells, nVerts, pyfrm, dataset) + xdmfFile.write(' </Geometry>\n') + return + +def writeHyperSlab(xdmfFile, nDims, nCells, nVerts, pyfrm, dataset): + "write HyperSlab element" + for coord in range(nDims): + xdmfFile.write(' <DataItem ItemType="HyperSlab"\n') + xdmfFile.write(' Dimensions="{} 1 1"\n'.format(nCells*nVerts)) + 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(' 0 0 {}\n'.format(coord)) # select co-ordinate + xdmfFile.write(' 1 1 1\n') # select every vertex in every cell + xdmfFile.write(' {:<3} {} 1\n'.format(nVerts, nCells)) # loop over cells (first) and vertices (second) + 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') + 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') + return + +def writeConnectivities(connFile, nCells, nVerts, orderDict): + "write connectivities to xml file" + cf = open(connFile, 'w') + cf.write('<DataItem DataType="Int"\n') + cf.write(' Dimensions="{} {}"\n'.format(nCells, nVerts)) + cf.write(' Format="XML">\n') + + for i in range (0, nCells): + cf.write(' ') + for j in range (1, nVerts+1): + cf.write(' ' + repr(orderDict[j]*nCells+i).ljust(1)) + cf.write('\n') + + cf.write('</DataItem>\n') + cf.close() + print('connectivities written to ' + connFile) + return + +def writeFooter(xdmfFile): + "write XDMF footer" + xdmfFile.write(' </Domain>\n') + xdmfFile.write('</Xdmf>\n') + return + parser = argparse.ArgumentParser(description="extract connectivities from mesh file") parser.add_argument("mesh", help="mesh file (.pyfrm)", type=meshFile) args = parser.parse_args() -# Xdmf file -g = open(os.path.join(base + '.xdmf'), 'w') - -g.write('<?xml version="1.0" ?>\n') -g.write('<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>\n') -g.write('<Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">\n') -g.write(' <Domain>\n') - # use 'h5ls' command to provide array dimensions h5ls_output = check_output(["h5ls", args.mesh]) +nquads = {} +ntris = {} for line in h5ls_output.splitlines(): - spt = re.search('spt', line) # restrict to 'spt' arrays + spt = re.search('spt', line.decode()) # restrict to 'spt' arrays if spt: - quad = re.search('quad', line) # restrict to quad cells - if quad: - order = {1:0, 2:1, 3:3, 4:2} # XDMF:PyFR vertex numbering - ncells = int(re.search(' (\d+),', line).group(1)) - nverts = 4 - ndims = 2 - chunk = string.split(line) - bname = re.sub('spt', 'con', chunk[0]) - fname = os.path.join(bname + '.xml') - partn = int(re.search('\d+', bname).group()) - g.write(' <Grid Name="Partition{}" GridType="Uniform">\n'.format(partn)) - g.write(' <Topology TopologyType="Quadrilateral" NumberOfElements="{}">\n'.format(ncells)) - g.write(' <xi:include href="{}"/>\n'.format(fname)) - g.write(' </Topology>\n') - if ndims == 2: - g.write(' <Geometry GeometryType="X_Y">\n') # co-ordinates in separate arrays - elif ndims == 3: - g.write(' <Geometry GeometryType="X_Y_Z">\n') # co-ordinates in separate arrays - for coord in range(ndims): - g.write(' <DataItem ItemType="HyperSlab"\n') - g.write(' Dimensions="{} 1 1"\n'.format(ncells*nverts)) - g.write(' Type="HyperSlab">\n') - g.write(' <DataItem\n') # start, stride and count of hyperslab region - g.write(' Dimensions="3 3"\n') - g.write(' Format="XML">\n') - g.write(' 0 0 {}\n'.format(coord)) # select co-ordinate - g.write(' 1 1 1\n') # select every vertex in every cell - g.write(' {:<3} {} 1\n'.format(nverts, ncells)) # loop over cells (first) and vertices (second) - g.write(' </DataItem>\n') - g.write(' <DataItem\n') - g.write(' Name="Points" \n') - g.write(' Dimensions="{} {} {}"\n'.format(nverts, ncells, ndims)) - g.write(' Format="HDF">\n') - g.write(' {}:/{}\n'.format(args.mesh, chunk[0])) - g.write(' </DataItem>\n') - g.write(' </DataItem>\n') - - g.write(' </Geometry>\n') - g.write(' <Attribute Name="Partition" Center="Grid">\n') - g.write(' <DataItem\n') - g.write(' Dimensions="1"\n') - g.write(' Format="XML">\n') - g.write(' {}\n'.format(partn)) # tag with partition number - g.write(' </DataItem>\n') - g.write(' </Attribute>\n') - g.write(' </Grid>\n') + chunk = line.decode().split() + npart = int(re.search('\d+', chunk[0]).group()) + ncells = int(re.search(' (\d+),', line.decode()).group(1)) + if re.search('quad', line.decode()): # check whether cell is quadrilateral + nquads[npart] = ncells + elif re.search('tri', line.decode()): # check whether cell is triangular + ntris[npart] = ncells + else: + print("unknown cell type") + break + +# cell types +cellTypes = ['quad', 'tri'] +numCellTypes = len(cellTypes) +nverts = {cellTypes[0]: 4, cellTypes[1]: 3} +ndims = {cellTypes[0]: 2, cellTypes[1]: 2} + +# XDMF:PyFR vertex numbering +order = [] +order.append({1:0, 2:1, 3:3, 4:2}) # quad order +order.append({1:0, 2:1, 3:2}) # tri order +# sort datasets +quadKeys = list(nquads.keys()) # keys are partition numbers +triKeys = list(ntris.keys()) # keys are partition numbers +allKeys = quadKeys + triKeys # concatenate keys +numTypes = Counter(allKeys) # number of types present in each partition +partKeys = list(numTypes.keys()) # partition keys +partitions = [nquads, ntris] # list of dictionaries + +# write files +g = open(os.path.join(base + '.xdmf'), 'w') +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)) + + for cellType in range(numCellTypes): + if part in partitions[cellType]: # check whether these cells exist in this partition + xfname = os.path.join('con_' + cellTypes[cellType] + '_p' + str(part) + '.xml') + dname = os.path.join('spt_' + cellTypes[cellType] + '_p' + str(part)) + if numTypes[part] > 1: + g.write(' <Grid Name="cellType{}" GridType="Uniform">\n'.format(cellType)) + writeTopology(g, partitions[cellType][part], xfname) + writeGeometry(g, ndims[cellTypes[cellType]], + partitions[cellType][part], + nverts[cellTypes[cellType]], args.mesh, dname) + if numTypes[part] > 1: + g.write(' </Grid>\n') # connectivities file - f = open(fname, 'w') - - f.write('<DataItem DataType="Int"\n') - f.write(' Dimensions="{} {}"\n'.format(ncells, nverts)) - f.write(' Format="XML">\n') - - for i in range (0, ncells): - f.write(' ') - for j in range (1, nverts+1): - f.write(' ' + repr(order[j]*ncells+i).ljust(1)) - f.write('\n') - - f.write('</DataItem>\n') - f.close() - print('connectivities written to ' + fname) - -g.write(' </Domain>\n') -g.write('</Xdmf>\n') + writeConnectivities(xfname, partitions[cellType][part], + nverts[cellTypes[cellType]], order[cellType]) + + writeAttribute(g, part) + g.write(' </Grid>\n') + +writeFooter(g) g.close() @@ -1,4 +1,6 @@ #!/usr/bin/env python +# -*- coding: utf-8 -*- + import argparse import os from sys import stdout |