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#!/usr/bin/env python
import argparse
import os
import re
import string
from subprocess import check_output
def meshFile(param):
global base
base, ext = os.path.splitext(param)
if ext.lower() != '.pyfrm':
raise argparse.ArgumentTypeError('Mesh file must have a .pyfrm extension')
return param
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])
for line in h5ls_output.splitlines():
spt = re.search('spt', line) # 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')
# 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')
g.close()
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