From 086746ff58a19456111c9999e91e8a63e7e88acb Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Fri, 11 Mar 2016 21:16:41 +0000
Subject: include LICENSE file and AUTHORS file pyfrm2xdmf: add encoding
comment, allow for triangular cells pyfrs2vtu: add encoding comment
---
pyfrm2xdmf | 222 ++++++++++++++++++++++++++++++++++++++++---------------------
1 file changed, 148 insertions(+), 74 deletions(-)
(limited to 'pyfrm2xdmf')
diff --git a/pyfrm2xdmf b/pyfrm2xdmf
index a45a74e..b7e1be3 100755
--- a/pyfrm2xdmf
+++ b/pyfrm2xdmf
@@ -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()
--
cgit