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authorPaul Garlick <pgarlick@tourbillion-technology.com>2016-03-07 15:07:18 +0000
committerPaul Garlick <pgarlick@tourbillion-technology.com>2016-03-07 15:07:18 +0000
commit730cc34523c9ff93eba95a62d7d3c6fa0bb811f8 (patch)
treec72f04e0b11afdea325bb9edc6ed0109b5c0d3a4 /pyfrm2xdmf
downloadpyfrUtils-730cc34523c9ff93eba95a62d7d3c6fa0bb811f8.tar.gz
creation of mesh and solution file conversion scripts
Diffstat (limited to 'pyfrm2xdmf')
-rwxr-xr-xpyfrm2xdmf99
1 files changed, 99 insertions, 0 deletions
diff --git a/pyfrm2xdmf b/pyfrm2xdmf
new file mode 100755
index 0000000..a45a74e
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+++ b/pyfrm2xdmf
@@ -0,0 +1,99 @@
+#!/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()