#!/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 = {
'grid': ['a','b','c'],
}
mappings = {
'grid': lambda x: int(x),
'grains': lambda x: int(x),
}
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
Generate geometry description and material configuration by standard Voronoi tessellation of given seeds file.
""" + string.replace('$Id$','\n','\\n')
)
parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, \
help='a,b,c grid of hexahedral box [from seed file]')
parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, \
help='x,y,z size of hexahedral box [1.0 along largest grid point number]')
parser.add_option('--homogenization', dest='homogenization', type='int', \
help='homogenization index to be used [%default]')
parser.add_option('--phase', dest='phase', type='int', \
help='phase index to be used [%default]')
parser.add_option('--crystallite', dest='crystallite', type='int', \
help='crystallite index to be used [%default]')
parser.add_option('-c', '--configuration', dest='config', action='store_true', \
help='output material configuration [%default]')
parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
help='output geom file with two-dimensional data arrangement [%default]')
parser.set_defaults(grid = [0,0,0])
parser.set_defaults(size = [0.0,0.0,0.0])
parser.set_defaults(homogenization = 1)
parser.set_defaults(phase = 1)
parser.set_defaults(crystallite = 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 = [file['input'].readline() for i in range(headerlines)]
else:
headerlines = 1
headers = firstline
content = file['input'].readlines()
file['input'].close()
#--- interprete header ----------------------------------------------------------------------------
info = {
'grid': numpy.zeros(3,'i'),
'size': numpy.array(options.size),
'origin': numpy.zeros(3,'d'),
'grains': 0,
'homogenization': 0,
}
new_header = []
for header in headers:
headitems = map(str.lower,header.split())
if headitems[0] == 'resolution': headitems[0] = 'grid'
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'] != len(content):
file['croak'].write('grain data not matching grain count...\n')
info['grains'] = min(info['grains'],len(content))
if 0 not in options.grid: # user-specified grid
info['grid'] = numpy.array(options.grid)
for i in xrange(3):
if info['size'][i] <= 0.0: # any invalid size?
info['size'][i] = float(info['grid'][i])/max(info['grid'])
file['croak'].write('rescaling size %i...\n'%i)
file['croak'].write('grains to map: %i\n'%info['grains'] + \
'grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
'homogenization: %i\n'%info['homogenization'])
if numpy.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n')
sys.exit()
if numpy.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n')
sys.exit()
if info['grains'] == 0:
file['croak'].write('no grain info found.\n')
sys.exit()
#--- 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['size']
eulers[:,i] = map(float,content[i].split()[3:6])
#--- switch according to task ---------------------------------------------------------------------
if options.config: # write config file
file['output'].write('<microstructure>\n')
for i in xrange(info['grains']):
file['output'].write('\n[Grain%s]\n'%(str(i+1).zfill(formatwidth)) + \
'crystallite %i\n'%options.crystallite + \
'(constituent)\tphase %i\ttexture %s\tfraction 1.0\n'%(options.phase,str(i+1).rjust(formatwidth)))
file['output'].write('\n<texture>\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: # write geometry file
twoD = info['grid'][2] < 2
N = info['grid'].prod()
shift = 0.5*info['size']/info['grid'] # 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['size'][0]\
* float(i % info['grid'][0])\
/float(info['grid'][0])
undeformed[1,i] = info['size'][1]\
* float(i//info['grid'][0] % info['grid'][1])\
/float(info['grid'][1])
undeformed[2,i] = info['size'][2]\
* float(i//info['grid'][0]//info['grid'][1] % info['grid'][2])\
/float(info['grid'][2])
undeformed[:,i] += shift
indices = damask.core.math.periodicNearestNeighbor(\
info['size'],\
numpy.eye(3),\
undeformed,coords)//3**3 + 1 # floor division to kill periodic images
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))
#--- write header ---------------------------------------------------------------------------------
new_header.append("$Id$ \n")
new_header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],))
new_header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][2],))
new_header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2],))
new_header.append("microstructures\t%i\n"%(info['grains']-missing))
new_header.append("homogenization\t%i\n"%info['homogenization'])
file['output'].write('%i\theader\n'%(len(new_header)) + ''.join(new_header))
# --- write microstructure information ------------------------------------------------------------
for n in xrange(info['grid'][1:3].prod()): # loop over 2nd and 3rd size
file['output'].write({ True: ' ',
False:'\n'}[options.twoD].\
join(map(lambda x: str(x).rjust(formatwidth),\
indices[n*info['grid'][0]:(n+1)*info['grid'][0]]))+'\n')
#--- 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])