#!/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('\n') xdmfFile.write('\n') xdmfFile.write('\n') xdmfFile.write(' \n') return def writeTopology(xdmfFile, nCells, connFile): "write Topology element" xdmfFile.write(' \n'.format(nCells)) xdmfFile.write(' \n'.format(connFile)) xdmfFile.write(' \n') return def writeGeometry(xdmfFile, nDims, nCells, nVerts, pyfrm, dataset): "write Geometry element" if nDims == 2: xdmfFile.write(' \n') # co-ordinates in separate arrays else: xdmfFile.write(' \n') # co-ordinates in separate arrays writeHyperSlab(xdmfFile, nDims, nCells, nVerts, pyfrm, dataset) xdmfFile.write(' \n') return def writeHyperSlab(xdmfFile, nDims, nCells, nVerts, pyfrm, dataset): "write HyperSlab element" for coord in range(nDims): xdmfFile.write(' \n') xdmfFile.write(' \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(' \n') xdmfFile.write(' \n') xdmfFile.write(' {}:/{}\n'.format(pyfrm, dataset)) xdmfFile.write(' \n') xdmfFile.write(' \n') return def writeAttribute(xdmfFile, tag): "write Attribute element" xdmfFile.write(' \n') xdmfFile.write(' \n') xdmfFile.write(' {}\n'.format(tag)) # tag with partition number xdmfFile.write(' \n') xdmfFile.write(' \n') return def writeConnectivities(connFile, nCells, nVerts, orderDict): "write connectivities to xml file" cf = open(connFile, 'w') cf.write('\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('\n') cf.close() print('connectivities written to ' + connFile) return def writeFooter(xdmfFile): "write XDMF footer" xdmfFile.write(' \n') xdmfFile.write('\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(' \n'.format(part)) else: g.write(' \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(' \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(' \n') # connectivities file writeConnectivities(xfname, partitions[cellType][part], nverts[cellTypes[cellType]], order[cellType]) writeAttribute(g, part) g.write(' \n') writeFooter(g) g.close()