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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# run within virtual environment (uses Python 3 syntax)
import argparse
import os
import re
from array import array
from collections import Counter
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
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
for coord in range(nDims):
xdmfFile.write(' <DataItem ItemType="Function" Dimensions="{}"\n'.format(nVerts*nCells)) # 1D-array
xdmfFile.write(' Function="JOIN({})">\n'.format(' ; '.join("$" + str(k) for k in range(nVerts))))
writeHyperSlab(xdmfFile, coord, nDims, nCells, nVerts, pyfrm, dataset)
xdmfFile.write(' </DataItem>\n')
xdmfFile.write(' </Geometry>\n')
return
def writeHyperSlab(xdmfFile, coord, nDims, nCells, nVerts, pyfrm, dataset):
"write HyperSlab element"
for vert in range(nVerts):
xdmfFile.write(' <DataItem ItemType="HyperSlab"\n')
xdmfFile.write(' Dimensions="{} 1 1"\n'.format(nCells))
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(' {:<3} 0 {}\n'.format(vert, coord)) # select vertex and co-ordinate (format is vertex, cell, co-ordinate)
xdmfFile.write(' 1 1 1\n') # select every cell, for this vertex and co-ordinate
xdmfFile.write(' 1 {} 1\n'.format(nCells)) # loop over cells
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()
# 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.decode()) # restrict to 'spt' arrays
if spt:
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
writeConnectivities(xfname, partitions[cellType][part],
nverts[cellTypes[cellType]], order[cellType])
writeAttribute(g, part)
g.write(' </Grid>\n')
writeFooter(g)
g.close()
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