DAMASK_EICMD/processing/pre/geom_fromVoronoiTessellatio...

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#!/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, \
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help='a,b,c resolution of periodic box')
parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs = 3, \
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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)
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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('<microstructure>\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<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:
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])