creation of mesh and solution file conversion scripts

1 files changed, 99 insertions, 0 deletions

diff --git a/pyfrm2xdmf b/pyfrm2xdmf
new file mode 100755
index 0000000..a45a74e
--- /dev/null
+++ 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()