#!/usr/bin/env python # -*- coding: utf-8 -*- import os,sys,math,string,re,numpy, damask from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP # ----------------------------- class extendedOption(Option): # ----------------------------- # used for definition of new option parser action 'extend', which enables to take multiple option arguments # taken from online tutorial http://docs.python.org/library/optparse.html ACTIONS = Option.ACTIONS + ("extend",) STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",) TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",) ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",) def take_action(self, action, dest, opt, value, values, parser): if action == "extend": lvalue = value.split(",") values.ensure_value(dest, []).extend(lvalue) else: Option.take_action(self, action, dest, opt, value, values, parser) # -------------------------------------------------------------------- # MAIN # -------------------------------------------------------------------- identifiers = { 'resolution': ['a','b','c'], } mappings = { 'resolution': lambda x: int(x), 'grains': lambda x: int(x), } parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """ generates geom file and material_config file using seeds file """ + string.replace('$Id$','\n','\\n') ) parser.add_option('-r', '--resolution', dest='resolution', type='int', nargs = 3, \ help='a,b,c resolution of periodic box') parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs = 3, \ help='x,y,z dimension of periodic box') parser.add_option('--homogenization', dest='homogenization', type='int', \ help='homogenization index to be used') parser.add_option('--phase', dest='phase', type='int', \ help='phase index to be used') parser.add_option('-c', '--configuration', dest='config', action='store_true', \ help='output material configuration') parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \ help='output geom file with two-dimensional data arrangement') parser.set_defaults(resolution = [0,0,0]) parser.set_defaults(dimension = [0.0,0.0,0.0]) parser.set_defaults(homogenization = 1) parser.set_defaults(phase = 1) parser.set_defaults(config = False) parser.set_defaults(twoD = False) (options,filenames) = parser.parse_args() # ------------------------------------------ setup file handles --------------------------------------- files = [] if filenames == []: files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr, }) else: for name in filenames: if os.path.exists(name): files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stdout, }) # ------------------------------------------ loop over input files --------------------------------------- for file in files: if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n') firstline = file['input'].readline() m = re.search('(\d+)\s*head', firstline.lower()) if m: headerlines = int(m.group(1)) headers = [firstline]+[file['input'].readline() for i in range(headerlines)] else: headerlines = 1 headers = firstline content = file['input'].readlines() file['input'].close() info = {'grains': 0, 'resolution': numpy.array([0,0,0]), 'dimension': numpy.array(options.dimension), 'origin': numpy.array([0.0,0.0,0.0]), 'homogenization': options.homogenization, } new_header = [] for header in headers: headitems = map(str.lower,header.split()) if headitems[0] in mappings.keys(): if headitems[0] in identifiers.keys(): for i in xrange(len(identifiers[headitems[0]])): info[headitems[0]][i] = \ mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1]) else: info[headitems[0]] = mappings[headitems[0]](headitems[1]) if info['grains'] == 0: file['croak'].write('no grains found.\n') continue if info['grains'] != len(content): file['croak'].write('grain data not matching grain count...\n') info['grains'] = min(info['grains'],len(content)) if 0 not in options.resolution: # user-specified resolution info['resolution'] = numpy.array(options.resolution) if numpy.all(info['resolution'] == 0): file['croak'].write('no resolution info found.\n') continue twoD = info['resolution'][2] < 2 for i in xrange(3): if info['dimension'][i] <= 0.0: # any invalid dimension? info['dimension'][i] = float(info['resolution'][i])/max(info['resolution']) file['croak'].write('rescaling dimension %i...\n'%i) file['croak'].write('grains: %i\n'%info['grains'] + \ 'resolution: %s\n'%(' x '.join(map(str,info['resolution']))) + \ 'dimension: %s\n'%(' x '.join(map(str,info['dimension']))) + \ 'origin: %s\n'%(' : '.join(map(str,info['origin']))) + \ 'homogenization: %i\n'%info['homogenization']) new_header.append("resolution\ta %i\tb %i\tc %i\n"%( info['resolution'][0], info['resolution'][1], info['resolution'][2],)) new_header.append("dimension\tx %f\ty %f\tz %f\n"%( info['dimension'][0], info['dimension'][1], info['dimension'][2],)) new_header.append("origin\tx %f\ty %f\tz %f\n"%( info['origin'][0], info['origin'][1], info['origin'][2],)) new_header.append("homogenization\t%i\n"%info['homogenization']) # -------------------------------------- prepare data ---------------------------------- formatwidth = 1+int(math.log10(info['grains'])) coords = numpy.zeros((3,info['grains']),'d') eulers = numpy.zeros((3,info['grains']),'d') for i in xrange(info['grains']): coords[:,i] = map(float,content[i].split()[:3])*info['dimension'] eulers[:,i] = map(float,content[i].split()[3:6]) # -------------------------------------- switch according to task ---------------------------------- if options.config: file['output'].write('\n') for i in xrange(info['grains']): file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \ 'crystallite 1\n' + \ '(constituent)\tphase %i\ttexture %s\tfraction 1.0\n'%(options.phase,str(i+1).rjust(formatwidth))) file['output'].write('\n\n') for i in xrange(info['grains']): file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \ '(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0\n'%(eulers[0,i],eulers[1,i],eulers[2,i])) else: file['output'].write('%i\theader\n'%(len(new_header)) + ''.join(new_header)) N = info['resolution'].prod() shift = 0.5*info['dimension']/info['resolution'] # shift by half of side length to center of element undeformed = numpy.zeros((3,N),'d') for i in xrange(N): undeformed[0,i] = info['dimension'][0]\ * float(i % info['resolution'][0])\ /float(info['resolution'][0]) undeformed[1,i] = info['dimension'][1]\ * float(i//info['resolution'][0] % info['resolution'][1])\ /float(info['resolution'][1]) undeformed[2,i] = info['dimension'][2]\ * float(i//info['resolution'][0]//info['resolution'][1] % info['resolution'][2])\ /float(info['resolution'][2]) undeformed[:,i] += shift indices = damask.core.math.math_nearestNeighborSearch(3,\ numpy.array(([1.0,0.0,0.0],\ [0.0,1.0,0.0],\ [0.0,0.0,1.0]),'d'),\ info['dimension'],\ N,info['grains'],undeformed,coords)//3**3 + 1 # floor division to kill periodic images for n in xrange(info['resolution'][1:3].prod()): # loop over 2nd and 3rd dimension file['output'].write({ True: ' ', False:'\n'}[options.twoD].\ join(map(lambda x: str(x).rjust(formatwidth),\ indices[n*info['resolution'][0]:(n+1)*info['resolution'][0]]))+'\n') missing = 0 for i in xrange(info['grains']): if i+1 not in indices: missing += 1 file['croak'].write({True:'all',False:'only'}[missing == 0] + ' %i grains mapped.\n'%(info['grains']-missing)) # ------------------------------------------ output finalization --------------------------------------- if file['name'] != 'STDIN': file['output'].close() os.rename(file['name']+'_tmp',os.path.splitext(file['name'])[0] + \ {True: '_material.config', False:'.geom'}[options.config])