#!/usr/bin/env python2.7 # -*- coding: UTF-8 no BOM -*- import threading,time,os,sys,random import numpy as np from optparse import OptionParser from cStringIO import StringIO import damask scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptID = ' '.join([scriptName,damask.version]) mismatch = None currentSeedsName = None #--------------------------------------------------------------------------------------------------- class myThread (threading.Thread): """perturbes seed in seed file, performes Voronoi tessellation, evaluates, and updates best match""" def __init__(self, threadID): threading.Thread.__init__(self) self.threadID = threadID def run(self): global bestSeedsUpdate global bestSeedsVFile global nMicrostructures global delta global points global target global match global baseFile global maxSeeds s.acquire() bestMatch = match s.release() random.seed(options.randomSeed+self.threadID) # initializes to given seeds knownSeedsUpdate = bestSeedsUpdate -1.0 # trigger update of local best seeds randReset = True # aquire new direction myBestSeedsVFile = StringIO() # store local copy of best seeds file perturbedSeedsVFile = StringIO() # perturbed best seeds file perturbedGeomVFile = StringIO() # tessellated geom file #--- still not matching desired bin class ---------------------------------------------------------- while bestMatch < options.threshold: s.acquire() # ensure only one thread acces global data if bestSeedsUpdate > knownSeedsUpdate: # write best fit to virtual file knownSeedsUpdate = bestSeedsUpdate bestSeedsVFile.reset() myBestSeedsVFile.close() myBestSeedsVFile = StringIO() i=0 for line in bestSeedsVFile: myBestSeedsVFile.write(line) s.release() if randReset: # new direction because current one led to worse fit randReset = False NmoveGrains = random.randrange(1,maxSeeds) selectedMs = [] direction = [] for i in range(NmoveGrains): selectedMs.append(random.randrange(1,nMicrostructures)) direction.append(np.array(((random.random()-0.5)*delta[0], (random.random()-0.5)*delta[1], (random.random()-0.5)*delta[2]))) perturbedSeedsVFile.close() # reset virtual file perturbedSeedsVFile = StringIO() myBestSeedsVFile.reset() perturbedSeedsTable = damask.ASCIItable(myBestSeedsVFile,perturbedSeedsVFile,labeled=True) # write best fit to perturbed seed file perturbedSeedsTable.head_read() perturbedSeedsTable.head_write() outputAlive=True ms = 1 i = 0 while outputAlive and perturbedSeedsTable.data_read(): # perturbe selected microstructure if ms in selectedMs: newCoords=np.array(tuple(map(float,perturbedSeedsTable.data[0:3]))+direction[i]) newCoords=np.where(newCoords>=1.0,newCoords-1.0,newCoords) # ensure that the seeds remain in the box newCoords=np.where(newCoords <0.0,newCoords+1.0,newCoords) perturbedSeedsTable.data[0:3]=[format(f, '8.6f') for f in newCoords] direction[i]*=2. i+= 1 ms+=1 perturbedSeedsTable.data_write() #--- do tesselation with perturbed seed file ---------------------------------------------------------- perturbedGeomVFile.close() perturbedGeomVFile = StringIO() perturbedSeedsVFile.reset() perturbedGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+ ' -g '+' '.join(map(str, options.grid)),streamIn=perturbedSeedsVFile)[0]) perturbedGeomVFile.reset() #--- evaluate current seeds file ---------------------------------------------------------------------- perturbedGeomTable = damask.ASCIItable(perturbedGeomVFile,None,labeled=False,readonly=True) perturbedGeomTable.head_read() for i in perturbedGeomTable.info: if i.startswith('microstructures'): myNmicrostructures = int(i.split('\t')[1]) perturbedGeomTable.data_readArray() perturbedGeomTable.output_flush() currentData=np.bincount(perturbedGeomTable.data.astype(int).ravel())[1:]/points currentError=[] currentHist=[] for i in range(nMicrostructures): # calculate the deviation in all bins per histogram currentHist.append(np.histogram(currentData,bins=target[i]['bins'])[0]) currentError.append(np.sqrt(np.square(np.array(target[i]['histogram']-currentHist[i])).sum())) # as long as not all grains are within the range of the target, use the deviation to left and right as error if currentError[0]>0.0: currentError[0] *=((target[0]['bins'][0]-np.min(currentData))**2.0+ (target[0]['bins'][1]-np.max(currentData))**2.0)**0.5 # norm of deviations by number of usual bin deviation s.acquire() # do the evaluation serially bestMatch = match #--- count bin classes with no mismatch ---------------------------------------------------------------------- myMatch=0 for i in range(nMicrostructures): if currentError[i] > 0.0: break myMatch = i+1 if myNmicrostructures == nMicrostructures: for i in range(min(nMicrostructures,myMatch+options.bins)): if currentError[i] > target[i]['error']: # worse fitting, next try randReset = True break elif currentError[i] < target[i]['error']: # better fit bestSeedsUpdate = time.time() # save time of better fit damask.util.croak('Thread {:d}: Better match ({:d} bins, {:6.4f} --> {:6.4f})'\ .format(self.threadID,i+1,target[i]['error'],currentError[i])) damask.util.croak(' target: '+np.array_str(target[i]['histogram'])) damask.util.croak(' best: '+np.array_str(currentHist[i])) currentSeedsName = baseFile+'_'+str(bestSeedsUpdate).replace('.','-') # name of new seed file (use time as unique identifier) perturbedSeedsVFile.reset() bestSeedsVFile.close() bestSeedsVFile = StringIO() sys.stdout.flush() with open(currentSeedsName+'.seeds','w') as currentSeedsFile: # write to new file for line in perturbedSeedsVFile: currentSeedsFile.write(line) bestSeedsVFile.write(line) for j in range(nMicrostructures): # save new errors for all bins target[j]['error'] = currentError[j] if myMatch > match: # one or more new bins have no deviation damask.util.croak( 'Stage {:d} cleared'.format(myMatch)) match=myMatch sys.stdout.flush() break if i == min(nMicrostructures,myMatch+options.bins)-1: # same quality as before: take it to keep on moving bestSeedsUpdate = time.time() perturbedSeedsVFile.reset() bestSeedsVFile.close() bestSeedsVFile = StringIO() for line in perturbedSeedsVFile: bestSeedsVFile.write(line) for j in range(nMicrostructures): target[j]['error'] = currentError[j] randReset = True else: #--- not all grains are tessellated damask.util.croak('Thread {:d}: Microstructure mismatch ({:d} microstructures mapped)'\ .format(self.threadID,myNmicrostructures)) randReset = True s.release() # -------------------------------------------------------------------- # MAIN # -------------------------------------------------------------------- parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """ Monte Carlo simulation to produce seed file that gives same size distribution like given geometry file. """, version = scriptID) parser.add_option('-s','--seeds', dest='seedFile', metavar='string', help='name of the intial seed file. If not found, a new one is created [%default]') parser.add_option('-g','--grid', dest='grid', type='int', nargs=3, metavar='int int int', help='a,b,c grid of hexahedral box [%default]') parser.add_option('-t','--threads', dest='threads', type='int', metavar='int', help='number of parallel executions [%default]') parser.add_option('-r', '--rnd', dest='randomSeed', type='int', metavar='int', help='seed of random number generator [%default]') parser.add_option('--target', dest='target', metavar='string', help='name of the geom file with target distribution [%default]') parser.add_option('--tolerance', dest='threshold', type='int', metavar='int', help='stopping criterion (bin number) [%default]') parser.add_option('--scale', dest='scale',type='float', metavar='float', help='maximum moving distance of perturbed seed in pixel [%default]') parser.add_option('--bins', dest='bins', type='int', metavar='int', help='bins to sort beyond current best fit [%default]') parser.add_option('--maxseeds', dest='maxseeds', type='int', metavar='int', help='maximum number of seeds to move simulateneously [number of seeds]') parser.set_defaults(seedFile = 'seeds', grid = (64,64,64), threads = 2, randomSeed = None, target = 'geom', threshold = 20, bins = 15, scale = 1.0, maxseeds = 0) options = parser.parse_args()[0] damask.util.report(scriptName,options.seedFile) if options.randomSeed is None: options.randomSeed = int(os.urandom(4).encode('hex'), 16) damask.util.croak(options.randomSeed) delta = (options.scale/options.grid[0],options.scale/options.grid[1],options.scale/options.grid[2]) baseFile=os.path.splitext(os.path.basename(options.seedFile))[0] points = np.array(options.grid).prod().astype('float') # ----------- calculate target distribution and bin edges targetGeomFile = os.path.splitext(os.path.basename(options.target))[0]+'.geom' targetGeomTable = damask.ASCIItable(targetGeomFile,None,labeled=False,readonly=True) targetGeomTable.head_read() info,devNull = targetGeomTable.head_getGeom() nMicrostructures = info['microstructures'] targetVolFrac = np.bincount(targetGeomTable.microstructure_read(info['grid']))[1:nMicrostructures+1]/\ float(info['grid'].prod()) target=[] for i in range(1,nMicrostructures+1): targetHist,targetBins = np.histogram(targetVolFrac,bins=i) #bin boundaries target.append({'histogram':targetHist,'bins':targetBins}) # ----------- create initial seed file or open existing one bestSeedsVFile = StringIO() if os.path.isfile(os.path.splitext(options.seedFile)[0]+'.seeds'): with open(os.path.splitext(options.seedFile)[0]+'.seeds') as initialSeedFile: for line in initialSeedFile: bestSeedsVFile.write(line) else: bestSeedsVFile.write(damask.util.execute('seeds_fromRandom'+\ ' -g '+' '.join(map(str, options.grid))+\ ' -r {:d}'.format(options.randomSeed)+\ ' -N '+str(nMicrostructures))[0]) bestSeedsUpdate = time.time() # ----------- tessellate initial seed file to get and evaluate geom file bestSeedsVFile.reset() initialGeomVFile = StringIO() initialGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+ ' -g '+' '.join(map(str, options.grid)),bestSeedsVFile)[0]) initialGeomVFile.reset() initialGeomTable = damask.ASCIItable(initialGeomVFile,None,labeled=False,readonly=True) initialGeomTable.head_read() info,devNull = initialGeomTable.head_getGeom() if info['microstructures'] != nMicrostructures: damask.util.croak('error. Microstructure count mismatch') initialData = np.bincount(initialGeomTable.microstructure_read(info['grid']))/points for i in range(nMicrostructures): initialHist = np.histogram(initialData,bins=target[i]['bins'])[0] target[i]['error']=np.sqrt(np.square(np.array(target[i]['histogram']-initialHist)).sum()) # as long as not all grain sizes are within the range, the error is the deviation to left and right if target[0]['error'] > 0.0: target[0]['error'] *=((target[0]['bins'][0]-np.min(initialData))**2.0+ (target[0]['bins'][1]-np.max(initialData))**2.0)**0.5 match=0 for i in range(nMicrostructures): if target[i]['error'] > 0.0: break match = i+1 if options.maxseeds < 1: maxSeeds = info['microstructures'] else: maxSeeds = options.maxseeds if match >0: damask.util.croak('Stage {:d} cleared'.format(match)) sys.stdout.flush() initialGeomVFile.close() # start mulithreaded monte carlo simulation threads=[] s=threading.Semaphore(1) for i in range(options.threads): threads.append(myThread(i)) threads[i].start() for i in range(options.threads): threads[i].join()