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