316 lines
14 KiB
Python
Executable File
316 lines
14 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,re,sys,math,string
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import numpy as np
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from optparse import OptionParser
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import damask
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scriptID = string.replace('$Id$','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
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def meshgrid2(*arrs):
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'''
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code inspired by http://stackoverflow.com/questions/1827489/numpy-meshgrid-in-3d
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'''
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arrs = tuple(reversed(arrs))
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arrs = tuple(arrs)
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lens = np.array(map(len, arrs))
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dim = len(arrs)
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ans = []
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for i, arr in enumerate(arrs):
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slc = np.ones(dim,'i')
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slc[i] = lens[i]
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arr2 = np.asarray(arr).reshape(slc)
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for j, sz in enumerate(lens):
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if j != i:
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arr2 = arr2.repeat(sz, axis=j)
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ans.insert(0,arr2)
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return tuple(ans)
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def laguerreTessellation(undeformed, coords, weights, grain):
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weight = np.power(np.tile(weights, 27),2) # Laguerre weights (squared)
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micro = np.zeros(undeformed.shape[0])
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N = coords.shape[0] # Number of seeds points
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periodic = np.array([
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[ -1,-1,-1 ],
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[ 0,-1,-1 ],
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[ 1,-1,-1 ],
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[ -1, 0,-1 ],
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[ 0, 0,-1 ],
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[ 1, 0,-1 ],
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[ -1, 1,-1 ],
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[ 0, 1,-1 ],
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[ 1, 1,-1 ],
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[ -1,-1, 0 ],
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[ 0,-1, 0 ],
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[ 1,-1, 0 ],
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[ -1, 0, 0 ],
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[ 0, 0, 0 ],
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[ 1, 0, 0 ],
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[ -1, 1, 0 ],
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[ 0, 1, 0 ],
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[ 1, 1, 0 ],
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[ -1,-1, 1 ],
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[ 0,-1, 1 ],
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[ 1,-1, 1 ],
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[ -1, 0, 1 ],
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[ 0, 0, 1 ],
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[ 1, 0, 1 ],
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[ -1, 1, 1 ],
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[ 0, 1, 1 ],
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[ 1, 1, 1 ],
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]).astype(float)
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for i,vec in enumerate(periodic):
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seeds = np.append(seeds, coords+vec, axis=0) if i > 0 else coords+vec
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for i,point in enumerate(undeformed):
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tmp = np.repeat(point.reshape(3,1), N*27, axis=1).T
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dist = np.sum((tmp - seeds)*(tmp - seeds),axis=1) - weight
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micro[i] = grain[np.argmin(dist)%N]
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return micro
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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identifiers = {
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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'origin': ['x','y','z'],
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}
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mappings = {
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'grid': lambda x: int(x),
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'size': lambda x: float(x),
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'origin': lambda x: float(x),
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'homogenization': lambda x: int(x),
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'microstructures': lambda x: int(x),
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}
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parser = OptionParser(option_class=damask.extendableOption, 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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""", version = scriptID)
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parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, metavar=' '.join(['int']*3),
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help='a,b,c grid of hexahedral box [from seeds file]')
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parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, metavar=' '.join(['float']*3),
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help='x,y,z size of hexahedral box [1.0 along largest grid point number]')
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parser.add_option('-o', '--origin', dest='origin', type='float', nargs = 3, metavar=' '.join(['float']*3),
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help='offset from old to new origin of grid')
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parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int',
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help='homogenization index to be used [%default]')
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parser.add_option('--phase', dest='phase', type='int', metavar = 'int',
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help='phase index to be used [%default]')
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parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int',
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help='crystallite index to be used [%default]')
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parser.add_option('-c', '--configuration', dest='config', action='store_true',
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help='output material configuration [%default]')
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parser.add_option('-r', '--rnd', dest='randomSeed', type='int', metavar='int',
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help='seed of random number generator for second phase distribution [%default]')
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parser.add_option('--secondphase', type='float', dest='secondphase', metavar= 'float',
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help='volume fraction of randomly distribute second phase [%default]')
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parser.add_option('-l', '--laguerre', dest='laguerre', action='store_true',
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help='use Laguerre (weighted Voronoi) tessellation [%default]')
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parser.set_defaults(grid = (0,0,0),
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size = (0.0,0.0,0.0),
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origin = (0.0,0.0,0.0),
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homogenization = 1,
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phase = 1,
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crystallite = 1,
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secondphase = 0.0,
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config = False,
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laguerre = False,
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randomSeed = None,
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)
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(options,filenames) = parser.parse_args()
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if options.secondphase > 1.0 or options.secondphase < 0.0:
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parser.error('volume fraction of second phase (%f) out of bounds...'%options.secondphase)
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []:
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filenames = ['STDIN']
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for name in filenames:
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if name == 'STDIN':
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file = {'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr}
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file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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else:
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if not os.path.exists(name): continue
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file = {'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr}
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file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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table = damask.ASCIItable(file['input'],file['output'],buffered=False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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labels = []
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if np.all(table.label_index(['1_coords','2_coords','3_coords']) != -1):
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coords = ['1_coords','2_coords','3_coords']
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elif np.all(table.label_index(['x','y','z']) != -1):
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coords = ['x','y','z']
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else:
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file['croak'].write('no coordinate data (1/2/3_coords | x/y/z) found ...')
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continue
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labels += coords
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hasEulers = np.all(table.label_index(['phi1','Phi','phi2']) != -1)
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if hasEulers:
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labels += ['phi1','Phi','phi2']
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hasGrains = table.label_index('microstructure') != -1
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if hasGrains:
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labels += ['microstructure']
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hasWeight = table.label_index('weight') != -1
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if hasWeight:
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labels += ['weight']
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table.data_readArray(labels)
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coords = table.data[:,table.label_index(coords)]
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eulers = table.data[:,table.label_index(['phi1','Phi','phi2'])] if hasEulers else np.zeros(3*len(coords))
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grain = table.data[:,table.label_index('microstructure')] if hasGrains else 1+np.arange(len(coords))
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weights = table.data[:,table.label_index('weight')] if hasWeight else np.zeros(len(coords))
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grainIDs = np.unique(grain).astype('i')
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#--- interpret header ----------------------------------------------------------------------------
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info = {
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'grid': np.zeros(3,'i'),
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'size': np.array(options.size),
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'origin': np.zeros(3,'d'),
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'microstructures': 0,
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'homogenization': options.homogenization,
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}
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newInfo = {
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'microstructures': 0,
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}
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extra_header = []
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for header in table.info:
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headitems = map(str.lower,header.split())
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if len(headitems) == 0: continue
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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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else:
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extra_header.append(header)
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if info['microstructures'] != len(grainIDs):
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file['croak'].write('grain data not matching grain count (%i)...\n'%(len(grainIDs)))
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info['microstructures'] = len(grainIDs)
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if 0 not in options.grid: # user-specified grid
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info['grid'] = np.array(options.grid)
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for i in xrange(3):
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if info['size'][i] <= 0.0: # any invalid size?
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info['size'][i] = float(info['grid'][i])/max(info['grid'])
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file['croak'].write('rescaling size %s...\n'%{0:'x',1:'y',2:'z'}[i])
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file['croak'].write('grains to map: %i\n'%info['microstructures'] + \
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'grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
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'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
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'homogenization: %i\n'%info['homogenization'])
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if np.any(info['grid'] < 1):
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file['croak'].write('invalid grid a b c.\n')
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continue
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if np.any(info['size'] <= 0.0):
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file['croak'].write('invalid size x y z.\n')
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continue
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if info['microstructures'] == 0:
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file['croak'].write('no grain info found.\n')
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continue
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#--- prepare data ---------------------------------------------------------------------------------
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eulers = eulers.T
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#--- switch according to task ---------------------------------------------------------------------
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if options.config: # write config file
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phase = np.empty(info['microstructures'],'i')
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phase.fill(options.phase)
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phase[0:int(float(info['microstructures'])*options.secondphase)] = options.phase+1
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randomSeed = int(os.urandom(4).encode('hex'), 16) if options.randomSeed == None else options.randomSeed # radom seed per file for second phase
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np.random.seed(randomSeed)
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np.random.shuffle(phase)
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formatwidth = 1+int(math.log10(info['microstructures']))
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file['output'].write('#' + scriptID + ' ' + ' '.join(sys.argv[1:])+'\n')
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if options.secondphase > 0.0: file['output'].write('# random seed for second phase %i\n'%randomSeed)
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file['output'].write('\n<microstructure>\n')
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for i,ID in enumerate(grainIDs):
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file['output'].write('\n[Grain%s]\n'%(str(ID).zfill(formatwidth)) + \
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'crystallite %i\n'%options.crystallite + \
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'(constituent)\tphase %i\ttexture %s\tfraction 1.0\n'%(phase[i],str(ID).rjust(formatwidth)))
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file['output'].write('\n<texture>\n')
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for ID in grainIDs:
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eulerID = np.nonzero(grain == ID)[0][0] # find first occurrence of this grain id
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file['output'].write('\n[Grain%s]\n'%(str(ID).zfill(formatwidth)) + \
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'(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0\n'%(eulers[0,eulerID],
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eulers[1,eulerID],
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eulers[2,eulerID]))
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else: # write geometry file
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x = (np.arange(info['grid'][0])+0.5)*info['size'][0]/info['grid'][0]
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y = (np.arange(info['grid'][1])+0.5)*info['size'][1]/info['grid'][1]
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z = (np.arange(info['grid'][2])+0.5)*info['size'][2]/info['grid'][2]
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if not options.laguerre:
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coords = (coords*info['size']).T
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undeformed = np.vstack(map(np.ravel, meshgrid2(x, y, z)))
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file['croak'].write('tessellating...\n')
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indices = damask.core.math.periodicNearestNeighbor(\
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info['size'],\
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np.eye(3),\
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undeformed,coords)//3**3 + 1 # floor division to kill periodic images
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indices = grain[indices-1]
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else :
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undeformed = np.vstack(np.meshgrid(x, y, z)).reshape(3,-1).T
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indices = laguerreTessellation(undeformed, coords, weights, grain)
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newInfo['microstructures'] = info['microstructures']
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for i in grainIDs:
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if i not in indices: newInfo['microstructures'] -= 1
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file['croak'].write(('all' if newInfo['microstructures'] == info['microstructures'] else 'only') +
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' %i'%newInfo['microstructures'] +
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('' if newInfo['microstructures'] == info['microstructures'] else \
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' out of %i'%info['microstructures']) +
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' grains mapped.\n')
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#--- write header ---------------------------------------------------------------------------------
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table.labels_clear()
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table.info_clear()
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table.info_append(extra_header+[
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scriptID + ' ' + ' '.join(sys.argv[1:]),
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"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],),
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"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],),
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"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],),
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"homogenization\t%i"%info['homogenization'],
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"microstructures\t%i"%(newInfo['microstructures']),
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])
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table.head_write()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = 1+int(math.log10(newInfo['microstructures']))
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table.data = indices.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
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table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
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#--- output finalization --------------------------------------------------------------------------
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table.close()
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if file['name'] != 'STDIN':
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os.rename(file['name']+'_tmp',
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os.path.splitext(file['name'])[0] +'%s'%('_material.config' if options.config else '.geom'))
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