260 lines
11 KiB
Python
Executable File
260 lines
11 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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# --------------------------------------------------------------------
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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('--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.set_defaults(grid = (0,0,0))
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parser.set_defaults(size = (0.0,0.0,0.0))
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parser.set_defaults(origin = (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(secondphase = 0.0)
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parser.set_defaults(config = 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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file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n')
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table = damask.ASCIItable(file['input'],file['output'],buffered = False)
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table.head_read()
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labels = ['x','y','z']
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index = 0
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eulerCol = table.labels_index('phi1')
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hasEulers = np.all(table.labels_index(['phi1','Phi','phi2'])) != -1
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grainCol = table.labels_index('microstructure')
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hasGrains = grainCol != -1
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if hasEulers:
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labels += ['phi1','Phi','phi2']
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index += 3
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if hasGrains:
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labels += ['microstructure']
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index += 1
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table.data_readArray(labels)
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coords = table.data[:,0:3]
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eulers = table.data[:,eulerCol:eulerCol+3] if hasEulers else np.zeros(3*len(coords))
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grain = table.data[:,grainCol] if hasGrains else 1+np.arange(len(eulers))
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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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coords = (coords*info['size']).transpose()
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eulers = eulers.transpose()
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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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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:]))
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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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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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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({True:'all',False:'only'}[newInfo['microstructures'] == info['microstructures'] ] +
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' %i'%newInfo['microstructures'] +
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{True:'',False:' out of %i'%info['microstructures']}[newInfo['microstructures'] == 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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if file['name'] != 'STDIN':
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table.input_close()
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table.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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