#!/usr/bin/env python # -*- coding: UTF-8 no BOM -*- import os,sys,string,math import numpy as np from optparse import OptionParser import damask scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptID = ' '.join([scriptName,damask.version]) # -------------------------------------------------------------------- # 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='horizontal osteon radius [%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='vertical/horizontal osteon aspect ratio [%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.set_defaults(canal = 25e-6, osteon = 100e-6, aspect = 1.0, omega = 0.0, period = 5e-6, amplitude = 60, size = (300e-6,300e-6), grid = (512,512), homogenization = 1, crystallite = 1) (options,filename) = parser.parse_args() if np.any(options.grid < 2): parser('invalid grid a b c.') if np.any(options.size <= 0.0): parser('invalid size x y z.') # --- open input files ---------------------------------------------------------------------------- if filename == []: filename = [None] table = damask.ASCIItable(outname = filename[0], buffered = False) damask.util.report(scriptName,filename[0]) 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] = np.array(options.grid,'i') info['size'][:2] = np.array(options.size,'d') 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 --------------------------------------------------------------------------------------- damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))), 'size x y z: %s'%(' x '.join(map(str,info['size']))), 'origin x y z: %s'%(' : '.join(map(str,info['origin']))), 'homogenization: %i'%info['homogenization'], 'microstructures: %i'%info['microstructures']]) # -------------------------------------- switch according to task ---------------------------------- formatwidth = 1+int(math.floor(math.log10(info['microstructures']-1))) header = [scriptID + ' ' + ' '.join(sys.argv[1:])] header.append('') header.append('[canal]') header.append('crystallite %i'%options.crystallite) header.append('(constituent)\tphase 1\ttexture 1\tfraction 1.0') header.append('[interstitial]') header.append('crystallite %i'%options.crystallite) header.append('(constituent)\tphase 2\ttexture 2\tfraction 1.0') for i in xrange(3,info['microstructures']): header.append('[Grain%s]'%(str(i).zfill(formatwidth))) header.append('crystallite %i'%options.crystallite) header.append('(constituent)\tphase 3\ttexture %s\tfraction 1.0'%(str(i).rjust(formatwidth))) header.append('') header.append('[canal]') header.append('[interstitial]') for i in xrange(3,info['microstructures']): header.append('[Grain%s]'%(str(i).zfill(formatwidth))) header.append('(gauss)\tphi1 %g\tPhi %g\tphi2 0\tscatter 0.0\tfraction 1.0'\ %(alphaOfGrain[i],betaOfGrain[i])) header.append([ "grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']), "size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']), "origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']), "homogenization\t{homog}".format(homog=info['homogenization']), "microstructures\t{microstructures}".format(microstructures=info['microstructures'])]) table.info_append(header) table.head_write() # --- write microstructure information ------------------------------------------------------------ table.data = microstructure.reshape(info['grid'][1]*info['grid'][2],info['grid'][0]) table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ') #--- output finalization -------------------------------------------------------------------------- table.close()