DAMASK_EICMD/processing/pre/geom_fromVoronoiTessellatio...

254 lines
11 KiB
Python
Executable File

#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,re,sys,math,string
import numpy as np
from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
def meshgrid2(*arrs):
'''
code inspired by http://stackoverflow.com/questions/1827489/numpy-meshgrid-in-3d
'''
arrs = tuple(reversed(arrs))
arrs = tuple(arrs)
lens = np.array(map(len, arrs))
dim = len(arrs)
ans = []
for i, arr in enumerate(arrs):
slc = np.ones(dim,'i')
slc[i] = lens[i]
arr2 = np.asarray(arr).reshape(slc)
for j, sz in enumerate(lens):
if j != i:
arr2 = arr2.repeat(sz, axis=j)
ans.insert(0,arr2)
return tuple(ans)
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
identifiers = {
'grid': ['a','b','c'],
'size': ['x','y','z'],
'origin': ['x','y','z'],
}
mappings = {
'grid': lambda x: int(x),
'size': lambda x: float(x),
'origin': lambda x: float(x),
'homogenization': lambda x: int(x),
'microstructures': lambda x: int(x),
}
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Generate geometry description and material configuration by standard Voronoi tessellation of given seeds file.
""", version = scriptID)
parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, metavar=' '.join(['int']*3),
help='a,b,c grid of hexahedral box [from seeds file]')
parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, metavar=' '.join(['float']*3),
help='x,y,z size of hexahedral box [1.0 along largest grid point number]')
parser.add_option('-o', '--origin', dest='origin', type='float', nargs = 3, metavar=' '.join(['float']*3),
help='offset from old to new origin of grid')
parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int',
help='homogenization index to be used [%default]')
parser.add_option('--phase', dest='phase', type='int', metavar = 'int',
help='phase index to be used [%default]')
parser.add_option('--crystallite', dest='crystallite', type='int', metavar = '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('--secondphase', type='float', dest='secondphase', metavar= 'float',
help='volume fraction of randomly distribute second phase [%default]')
parser.set_defaults(grid = (0,0,0))
parser.set_defaults(size = (0.0,0.0,0.0))
parser.set_defaults(origin = (0.0,0.0,0.0))
parser.set_defaults(homogenization = 1)
parser.set_defaults(phase = 1)
parser.set_defaults(crystallite = 1)
parser.set_defaults(secondphase = 0.0)
parser.set_defaults(config = 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:
file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n')
table = damask.ASCIItable(file['input'],file['output'],buffered = False)
table.head_read()
coordsCol = table.labels_index('1_coords')
if coordsCol < 0:
coordsCol = table.labels_index('x') # try if file is in legacy format
if coordsCol < 0:
file['croak'].write('column 1_coords/x not found...\n')
continue
eulerCol = table.labels_index('phi1')
hasEulers = np.all(table.labels_index(['phi1','Phi','phi2'])) != -1
grainCol = table.labels_index('microstructure')
hasGrains = grainCol != -1
table.data_readArray()
coords = table.data[:,coordsCol:coordsCol+3]
eulers = table.data[:,eulerCol:eulerCol+3] if hasEulers else np.zeros(3*len(coords))
grain = table.data[:,grainCol] if hasGrains else 1+np.arange(len(eulers))
grainIDs = np.unique(grain).astype('i')
#--- interpret header ----------------------------------------------------------------------------
info = {
'grid': np.zeros(3,'i'),
'size': np.array(options.size),
'origin': np.zeros(3,'d'),
'microstructures': 0,
'homogenization': options.homogenization,
}
newInfo = {
'microstructures': 0,
}
extra_header = []
for header in table.info:
headitems = map(str.lower,header.split())
if len(headitems) == 0: continue
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])
else:
extra_header.append(header)
if info['microstructures'] != len(grainIDs):
file['croak'].write('grain data not matching grain count (%i)...\n'%(len(grainIDs)))
info['microstructures'] = len(grainIDs)
if 0 not in options.grid: # user-specified grid
info['grid'] = np.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 %s...\n'%{0:'x',1:'y',2:'z'}[i])
file['croak'].write('grains to map: %i\n'%info['microstructures'] + \
'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 np.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n')
continue
if np.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n')
continue
if info['microstructures'] == 0:
file['croak'].write('no grain info found.\n')
continue
#--- prepare data ---------------------------------------------------------------------------------
coords = (coords*info['size']).T
eulers = eulers.T
#--- switch according to task ---------------------------------------------------------------------
if options.config: # write config file
phase=np.empty(info['microstructures'],'i')
phase.fill(options.phase)
phase[0:int(float(info['microstructures'])*options.secondphase)] = options.phase+1
np.random.shuffle(phase)
formatwidth = 1+int(math.log10(info['microstructures']))
file['output'].write('#' + scriptID + ' ' + ' '.join(sys.argv[1:]))
file['output'].write('\n<microstructure>\n')
for i,ID in enumerate(grainIDs):
file['output'].write('\n[Grain%s]\n'%(str(ID).zfill(formatwidth)) + \
'crystallite %i\n'%options.crystallite + \
'(constituent)\tphase %i\ttexture %s\tfraction 1.0\n'%(phase[i],str(ID).rjust(formatwidth)))
file['output'].write('\n<texture>\n')
for ID in grainIDs:
eulerID = np.nonzero(grain == ID)[0][0] # find first occurrence of this grain id
file['output'].write('\n[Grain%s]\n'%(str(ID).zfill(formatwidth)) + \
'(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0\n'%(eulers[0,eulerID],
eulers[1,eulerID],
eulers[2,eulerID]))
else: # write geometry file
x = (np.arange(info['grid'][0])+0.5)*info['size'][0]/info['grid'][0]
y = (np.arange(info['grid'][1])+0.5)*info['size'][1]/info['grid'][1]
z = (np.arange(info['grid'][2])+0.5)*info['size'][2]/info['grid'][2]
undeformed = np.vstack(map(np.ravel, meshgrid2(x, y, z)))
file['croak'].write('tessellating...\n')
indices = damask.core.math.periodicNearestNeighbor(\
info['size'],\
np.eye(3),\
undeformed,coords)//3**3 + 1 # floor division to kill periodic images
indices = grain[indices-1]
newInfo['microstructures'] = info['microstructures']
for i in grainIDs:
if i not in indices: newInfo['microstructures'] -= 1
file['croak'].write({True:'all',False:'only'}[newInfo['microstructures'] == info['microstructures'] ] +
' %i'%newInfo['microstructures'] +
{True:'',False:' out of %i'%info['microstructures']}[newInfo['microstructures'] == info['microstructures']] +
' grains mapped.\n')
#--- write header ---------------------------------------------------------------------------------
table.labels_clear()
table.info_clear()
table.info_append(extra_header+[
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
"homogenization\t%i"%info['homogenization'],
"microstructures\t%i"%(newInfo['microstructures']),
])
table.head_write()
# --- write microstructure information ------------------------------------------------------------
formatwidth = 1+int(math.log10(newInfo['microstructures']))
table.data = indices.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
#--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN':
table.input_close()
table.output_close()
os.rename(file['name']+'_tmp',os.path.splitext(file['name'])[0] + \
{True: '_material.config',
False:'.geom'}[options.config])