#!/usr/bin/env python # -*- coding: UTF-8 no BOM -*- import os,sys,string,math import numpy as np from optparse import OptionParser import damask scriptID = string.replace('$Id$','\n','\\n') scriptName = scriptID.split()[1][:-3] # -------------------------------------------------------------------- # MAIN # -------------------------------------------------------------------- parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options]', description = """ Generate a geometry file of an osteon enclosing the Harvesian canal and separated by interstitial tissue. The osteon phase is lamellar with a twisted plywood structure. Its fiber orientation is oscillating by +/- amplitude within one period. """, version = scriptID) parser.add_option('-g', '--grid', dest='grid', type='int', nargs=2, metavar = 'int int', \ help='a,b grid of hexahedral box %default') parser.add_option('-s', '--size', dest='size', type='float', nargs=2, metavar = 'float float', \ help='x,y size of hexahedral box %default') parser.add_option('-c', '--canal', dest='canal', type='float', metavar = 'float', \ help='Haversian canal radius [%default]') parser.add_option('-o', '--osteon', dest='osteon', type='float', metavar = 'float', \ help='osteon radius (horizontal) [%default]') parser.add_option('-l', '--lamella', dest='period', type='float', metavar = 'float', \ help='lamella width [%default]') parser.add_option('-a', '--amplitude', dest='amplitude', type='float', metavar = 'float', \ help='amplitude of twisted plywood wiggle in deg [%default]') parser.add_option( '--aspect', dest='aspect', type='float', metavar = 'float', \ help='osteon aspect ratio (vert/horiz) [%default]') parser.add_option('-w', '--omega', dest='omega', type='float', metavar = 'float', \ help='rotation angle (around normal) of osteon [%default]') parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int', \ help='homogenization 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('--configuration', dest='config', action='store_true', \ help='output material configuration [%default]') parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \ help='use two-dimensional geom data arrangement [%default]') parser.set_defaults(canal = 25e-6) parser.set_defaults(osteon = 100e-6) parser.set_defaults(aspect = 1.0) parser.set_defaults(omega = 0.0) parser.set_defaults(period = 5e-6) parser.set_defaults(amplitude = 60) parser.set_defaults(size = np.array([300e-6,300e-6],'d')) parser.set_defaults(grid = np.array([512,512],'i')) parser.set_defaults(homogenization = 1) parser.set_defaults(crystallite = 1) parser.set_defaults(config = False) parser.set_defaults(twoD = False) (options,filename) = parser.parse_args() # ------------------------------------------ setup file handle ------------------------------------- if filename == []: file = {'output':sys.stdout, 'croak':sys.stderr} else: file = {'output':open(filename[0],'w'), 'croak':sys.stderr} if np.any(options.grid < 2): file['croak'].write('grid too small...\n') sys.exit() if np.any(options.size <= 0.0): file['croak'].write('size too small...\n') sys.exit() options.omega *= math.pi/180.0 # rescale ro radians rotation = np.array([[ math.cos(options.omega),math.sin(options.omega),], [-math.sin(options.omega),math.cos(options.omega),]],'d') box = np.dot(np.array([[options.canal,0.],[0.,options.aspect*options.canal]]).transpose(),rotation) info = { 'grid': np.ones(3,'i'), 'size': np.ones(3,'d'), 'origin': np.zeros(3,'d'), 'microstructures': 3, 'homogenization': options.homogenization, } info['grid'][:2] = options.grid info['size'][:2] = options.size info['size'][2] = min(info['size'][0]/info['grid'][0],info['size'][1]/info['grid'][1]) info['origin'] = -info['size']/2.0 X0 = info['size'][0]/info['grid'][0]*\ (np.tile(np.arange(info['grid'][0]),(info['grid'][1],1)) - info['grid'][0]/2 + 0.5) Y0 = info['size'][1]/info['grid'][1]*\ (np.tile(np.arange(info['grid'][1]),(info['grid'][0],1)).transpose() - info['grid'][1]/2 + 0.5) X = X0*rotation[0,0] + Y0*rotation[0,1] # rotate by omega Y = X0*rotation[1,0] + Y0*rotation[1,1] # rotate by omega radius = np.sqrt(X*X + Y*Y/options.aspect/options.aspect) alpha = np.degrees(np.arctan2(Y/options.aspect,X)) beta = options.amplitude*np.sin(2.0*math.pi*(radius-options.canal)/options.period) microstructure = np.where(radius < float(options.canal),1,0) + np.where(radius > float(options.osteon),2,0) alphaOfGrain = np.zeros(info['grid'][0]*info['grid'][1],'d') betaOfGrain = np.zeros(info['grid'][0]*info['grid'][1],'d') for y in xrange(info['grid'][1]): for x in xrange(info['grid'][0]): if microstructure[y,x] == 0: microstructure[y,x] = info['microstructures'] alphaOfGrain[info['microstructures']] = alpha[y,x] betaOfGrain[ info['microstructures']] = beta[y,x] info['microstructures'] += 1 #--- report --------------------------------------------------------------------------------------- else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n') file['croak'].write('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']))) + \ 'microstructures: %i\n'%info['microstructures'] + \ 'homogenization: %i\n'%info['homogenization']) file['croak'].write("bounding box: %s\n"%(np.sqrt(np.sum(box*box,0)))) if np.any(info['grid'] < 1): file['croak'].write('invalid grid a b c.\n') sys.exit() if np.any(info['size'] <= 0.0): file['croak'].write('invalid size x y z.\n') sys.exit() # -------------------------------------- switch according to task ---------------------------------- formatwidth = 1+int(math.floor(math.log10(info['microstructures']-1))) if options.config: file['output'].write('\n') file['output'].write('\n[canal]\n' + \ 'crystallite %i\n'%options.crystallite + \ '(constituent)\tphase 1\ttexture 1\tfraction 1.0\n') file['output'].write('\n[interstitial]\n' + \ 'crystallite %i\n'%options.crystallite + \ '(constituent)\tphase 2\ttexture 2\tfraction 1.0\n') for i in xrange(3,info['microstructures']): file['output'].write('\n[Grain%s]\n'%(str(i).zfill(formatwidth)) + \ 'crystallite %i\n'%options.crystallite + \ '(constituent)\tphase 3\ttexture %s\tfraction 1.0\n'%(str(i).rjust(formatwidth))) file['output'].write('\n\n') file['output'].write('\n[canal]\n') file['output'].write('\n[interstitial]\n') for i in xrange(3,info['microstructures']): file['output'].write('\n[Grain%s]\n'%(str(i).zfill(formatwidth)) + \ '(gauss)\tphi1 %g\tPhi %g\tphi2 0\tscatter 0.0\tfraction 1.0\n'%(\ alphaOfGrain[i],\ betaOfGrain[i])) else: header = [scriptID + ' ' + ' '.join(sys.argv[1:])+'\n'] header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],)) header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][2],)) header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2],)) header.append("microstructures\t%i\n"%info['microstructures']) header.append("homogenization\t%i\n"%info['homogenization']) file['output'].write('%i\theader\n'%(len(header))+''.join(header)) for y in xrange(info['grid'][1]): for x in xrange(info['grid'][0]): file['output'].write(\ str(microstructure[y,x]).rjust(formatwidth) + \ {True:' ',False:'\n'}[options.twoD] ) file['output'].write({True:'\n',False:''}[options.twoD])