#!/usr/bin/env python # -*- coding: UTF-8 no BOM -*- # This script is used for the post processing of the results achieved by the spectral method. # As it reads in the data coming from "materialpoint_results", it can be adopted to the data # computed using the FEM solvers. Until now, its capable to handle elements with one IP in a regular order # written by M. Diehl, m.diehl@mpie.de import os,sys,threading,re,numpy,time from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP # ----------------------------- class extendedOption(Option): # ----------------------------- # used for definition of new option parser action 'extend', which enables to take multiple option arguments # taken from online tutorial http://docs.python.org/library/optparse.html ACTIONS = Option.ACTIONS + ("extend",) STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",) TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",) ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",) def take_action(self, action, dest, opt, value, values, parser): if action == "extend": lvalue = value.split(",") values.ensure_value(dest, []).extend(lvalue) else: Option.take_action(self, action, dest, opt, value, values, parser) # ----------------------------- class backgroundMessage(threading.Thread): # ----------------------------- def __init__(self): threading.Thread.__init__(self) self.message = '' self.new_message = '' self.counter = 0 self.symbols = ['- ', '\ ', '| ', '/ '] self.waittime = 0.5 def __quit__(self): length = len(self.message) + len(self.symbols[self.counter]) sys.stderr.write(chr(8)*length + ' '*length + chr(8)*length) sys.stderr.write('') def run(self): while not threading.enumerate()[0]._Thread__stopped: time.sleep(self.waittime) self.update_message() self.__quit__() def set_message(self, new_message): self.new_message = new_message self.print_message() def print_message(self): length = len(self.message) + len(self.symbols[self.counter]) sys.stderr.write(chr(8)*length + ' '*length + chr(8)*length) # delete former message sys.stderr.write(self.symbols[self.counter] + self.new_message) # print new message self.message = self.new_message def update_message(self): self.counter = (self.counter + 1)%len(self.symbols) self.print_message() def outStdout(cmd,locals): if cmd[0:3] == '(!)': exec(cmd[3:]) elif cmd[0:3] == '(?)': cmd = eval(cmd[3:]) print cmd else: print cmd return def outFile(cmd,locals): if cmd[0:3] == '(!)': exec(cmd[3:]) elif cmd[0:3] == '(?)': cmd = eval(cmd[3:]) locals['filepointer'].write(cmd+'\n') else: locals['filepointer'].write(cmd+'\n') return def output(cmds,locals,dest): for cmd in cmds: if isinstance(cmd,list): output(cmd,locals,dest) else: {\ 'File': outFile,\ 'Stdout': outStdout,\ }[dest](str(cmd),locals) return def transliterateToFloat(x): try: return float(x) except: return 0.0 #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ def mesh(res,geomdim,defgrad_av,centroids): #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ neighbor = numpy.array([[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0], [0, 0, 1], [1, 0, 1], [1, 1, 1], [0, 1, 1]]) wrappedCentroids = numpy.zeros([res[0]+2,res[1]+2,res[2]+2,3],'d') nodes = numpy.zeros([res[0]+1,res[1]+1,res[2]+1,3],'d') wrappedCentroids[1:-1,1:-1,1:-1] = centroids diag = numpy.ones(3,'i') shift = numpy.zeros(3,'i') lookup = numpy.zeros(3,'i') for k in range(res[2]+2): for j in range(res[1]+2): for i in range(res[0]+2): if (k==0 or k==res[2]+1 or \ j==0 or j==res[1]+1 or \ i==0 or i==res[0]+1 ): me = numpy.array([i,j,k],'i') shift = numpy.sign(res+diag-2*me)*(numpy.abs(res+diag-2*me)/(res+diag)) lookup = me-diag+shift*res wrappedCentroids[i,j,k] = centroids[lookup[0],lookup[1],lookup[2]]- \ numpy.dot(defgrad_av, shift*geomdim) for k in range(res[2]+1): for j in range(res[1]+1): for i in range(res[0]+1): for n in range(8): nodes[i,j,k] += wrappedCentroids[i+neighbor[n,0],j+neighbor[n,1],k+neighbor[n,2]] nodes[:,:,:] /= 8.0 return nodes # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ def deformed(res,geomdimension,defgrad): # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ corner = numpy.array([[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0], [1, 1, 1], [0, 1, 1], [0, 0, 1], [1, 0, 1]]) step = numpy.array([[ 1, 1, 1], [-1, 1, 1], [-1,-1, 1], [ 1,-1, 1], [-1,-1,-1], [ 1,-1,-1], [ 1, 1,-1], [-1, 1,-1]]) order = numpy.array([[0, 1, 2], [0, 2, 1], [1, 0, 2], [1, 2, 0], [2, 0, 1], [2, 1, 0]]) coord = numpy.zeros([8,6,res[0],res[1],res[2],3], 'd') coord_avgOrder = numpy.zeros([8,res[0],res[1],res[2],3], 'd') coord_avgCorner = numpy.zeros([res[0],res[1],res[2],3], 'd') myStep = numpy.zeros(3,'d') rear = numpy.zeros(3,'i') init = numpy.zeros(3,'i') oppo = numpy.zeros(3,'i') me = numpy.zeros(3,'i') ones = numpy.ones( 3,'i') fones = numpy.ones( 3,'d') defgrad_av=numpy.average(numpy.average(numpy.average(defgrad,0),0),0) for s in range(8): # corners init = corner[s]*(res-ones) oppo = corner[(s+4)%8]*(res-ones) sys.stdout.write('.'*(8-s)+' '*s+'\r') sys.stdout.flush() for o in range(6): # orders for k in range(init[order[o,2]],oppo[order[o,2]]+step[s,order[o,2]],step[s,order[o,2]]): rear[order[o,1]] = init[order[o,1]] for j in range(init[order[o,1]],oppo[order[o,1]]+step[s,order[o,1]],step[s,order[o,1]]): rear[order[o,0]] = init[order[o,0]] for i in range(init[order[o,0]],oppo[order[o,0]]+step[s,order[o,0]],step[s,order[o,0]]): me[order[o,0]] = i me[order[o,1]] = j me[order[o,2]] = k if (numpy.all(me == init)): coord[s,o,me[0],me[1],me[2]] = geomdimension * (numpy.dot(defgrad_av,corner[s]) + \ numpy.dot(defgrad[me[0],me[1],me[2]],0.5*step[s]/res)) else: myStep = (me-rear)*geomdimension/res coord[s,o,me[0],me[1],me[2]] = coord[s,o,rear[0],rear[1],rear[2]] + \ 0.5*numpy.dot(defgrad[me[0],me[1],me[2]] + \ defgrad[rear[0],rear[1],rear[2]],myStep) rear[:] = me[:] coord_avgOrder[s] = numpy.average(coord[s],0) for k in range(res[2]): for j in range(res[1]): for i in range(res[0]): parameter_coords = (2.0*numpy.array([i,j,k])-res+fones)/(res-fones) pos = fones + parameter_coords neg = fones - parameter_coords coord_avgCorner[i,j,k] = ( coord_avgOrder[0,i,j,k] *neg[0]*neg[1]*neg[2]\ + coord_avgOrder[1,i,j,k] *pos[0]*neg[1]*neg[2]\ + coord_avgOrder[2,i,j,k] *pos[0]*pos[1]*neg[2]\ + coord_avgOrder[3,i,j,k] *neg[0]*pos[1]*neg[2]\ + coord_avgOrder[4,i,j,k] *pos[0]*pos[1]*pos[2]\ + coord_avgOrder[5,i,j,k] *neg[0]*pos[1]*pos[2]\ + coord_avgOrder[6,i,j,k] *neg[0]*neg[1]*pos[2]\ + coord_avgOrder[7,i,j,k] *pos[0]*neg[1]*pos[2])*0.125 print ' ' return coord_avgCorner, defgrad_av # ++++++++++++++++++++++++++++++++++++++++++++++++++++ def vtk_writeASCII_mesh(mesh,data,res): # ++++++++++++++++++++++++++++++++++++++++++++++++++++ """ function writes data array defined on a hexahedral mesh (geometry) """ N1 = (res[0]+1)*(res[1]+1)*(res[2]+1) N = res[0]*res[1]*res[2] cmds = [\ '# vtk DataFile Version 3.1', 'powered by 3Dvisualize', 'ASCII', 'DATASET UNSTRUCTURED_GRID', 'POINTS %i float'%N1, [[['\t'.join(map(str,mesh[i,j,k])) for i in range(res[0]+1)] for j in range(res[1]+1)] for k in range(res[2]+1)], 'CELLS %i %i'%(N,N*9), ] # cells for i in range (res[2]): for j in range (res[1]): for k in range (res[0]): base = i*(res[1]+1)*(res[2]+1)+j*(res[1]+1)+k cmds.append('8 '+'\t'.join(map(str,[ \ base, base+1, base+res[1]+2, base+res[1]+1, base+(res[1]+1)*(res[2]+1), base+(res[1]+1)*(res[2]+1)+1, base+(res[1]+1)*(res[2]+1)+res[1]+2, base+(res[1]+1)*(res[2]+1)+res[1]+1, ]))) cmds += [\ 'CELL_TYPES %i'%N, ['12']*N, 'CELL_DATA %i'%N, ] for type in data: for item in data[type]: cmds += [\ '%s %s float'%(type.upper(),item), 'LOOKUP_TABLE default', [[['\t'.join(map(str,data[type][item][:,j,k]))] for j in range(res[1])] for k in range(res[2])], ] # vtk = open(filename, 'w') # output(cmd,{'filepointer':vtk},'File') # vtk.close() return cmds # ++++++++++++++++++++++++++++++++++++++++++++++++++++ def gmsh_writeASCII_mesh(mesh,data,res): # ++++++++++++++++++++++++++++++++++++++++++++++++++++ """ function writes data array defined on a hexahedral mesh (geometry) """ N1 = (res[0]+1)*(res[1]+1)*(res[2]+1) N = res[0]*res[1]*res[2] cmds = [\ '$MeshFormat', '2.1 0 8', '$EndMeshFormat', '$Nodes', '%i float'%N1, [[['\t'.join(map(str,l,mesh[i,j,k])) for l in range(1,N1+1) for i in range(res[0]+1)] for j in range(res[1]+1)] for k in range(res[2]+1)], '$EndNodes', '$Elements', '%i'%N, ] n_elem = 0 for i in range (res[2]): for j in range (res[1]): for k in range (res[0]): base = i*(res[1]+1)*(res[2]+1)+j*(res[1]+1)+k n_elem +=1 cmds.append('\t'.join(map(str,[ \ n_elem, '5', base, base+1, base+res[1]+2, base+res[1]+1, base+(res[1]+1)*(res[2]+1), base+(res[1]+1)*(res[2]+1)+1, base+(res[1]+1)*(res[2]+1)+res[1]+2, base+(res[1]+1)*(res[2]+1)+res[1]+1, ]))) cmds += [\ 'ElementData', '1', '%s'%item, # name of the view '0.0', # thats the time value '3', '0', # time step '1', '%i'%N ] for type in data: for item in data[type]: cmds += [\ '%s %s float'%(type.upper(),item), 'LOOKUP_TABLE default', [[['\t'.join(map(str,data[type][item][:,j,k]))] for j in range(res[1])] for k in range(res[2])], ] # vtk = open(filename, 'w') # output(cmd,{'filepointer':vtk},'File') # vtk.close() return cmds # +++++++++++++++++++++++++++++++++++++++++++++++++++ def vtk_writeASCII_points(coordinates,data,res): # +++++++++++++++++++++++++++++++++++++++++++++++++++ """ function writes data array defined on a point field """ N = res[0]*res[1]*res[2] cmds = [\ '# vtk DataFile Version 3.1', 'powered by 3Dvisualize', 'ASCII', 'DATASET UNSTRUCTURED_GRID', 'POINTS %i float'%N, [[['\t'.join(map(str,coordinates[i,j,k])) for i in range(res[0])] for j in range(res[1])] for k in range(res[2])], 'CELLS %i %i'%(N,N*2), ['1\t%i'%i for i in range(N)], 'CELL_TYPES %i'%N, ['1']*N, 'POINT_DATA %i'%N, ] for type in data: for item in data[type]: cmds += [\ '%s %s float'%(type.upper(),item), 'LOOKUP_TABLE default', [[['\t'.join(map(str,data[type][item][:,j,k]))] for j in range(res[1])] for k in range(res[2])] ] return cmds # +++++++++++++++++++++++++++++++++++++++++++++++++++++ def vtk_writeASCII_box(diag,defgrad): # +++++++++++++++++++++++++++++++++++++++++++++++++++++ """ corner box for the average defgrad """ points = numpy.array([\ [0.0,0.0,0.0,],\ [diag[0],0.0,0.0,],\ [diag[0],diag[1],0.0,],\ [0.0,diag[1],0.0,],\ [0.0,0.0,diag[2],],\ [diag[0],0.0,diag[2],],\ [diag[0],diag[1],diag[2],],\ [0.0,diag[1],diag[2],],\ ]) cmds = [\ '# vtk DataFile Version 3.1', 'powered by 3Dvisualize', 'ASCII', 'DATASET UNSTRUCTURED_GRID', 'POINTS 8 float', ['\t'.join(map(str,numpy.dot(defgrad_av,points[p]))) for p in range(8)], 'CELLS 8 16', ['1\t%i'%i for i in range(8)], 'CELL_TYPES 8', ['1']*8, ] return cmds # ----------------------- MAIN ------------------------------- parser = OptionParser(option_class=extendedOption, usage='%prog [options] datafile', description = """ Produce VTK file from data field. $Id$ """) parser.add_option('-s', '--scalar', action='extend', dest='scalar', type='string', \ help='list of scalars to visualize') parser.add_option('-d', '--deformation', dest='defgrad', type='string', \ help='heading of deformation gradient columns [%default]') parser.add_option('-g', '--grain', dest='grain', type='int', \ help='grain of interest [%default]') parser.set_defaults(defgrad = 'f') parser.set_defaults(grain = 1) parser.set_defaults(scalar = []) parser.set_defaults(vector = []) parser.set_defaults(tensor = []) (options, args) = parser.parse_args() for filename in args: if not os.path.exists(filename): continue file = open(filename) content = file.readlines() file.close() m = re.search('(\d+)\shead',content[0],re.I) if m == None: continue print filename headrow = int(m.group(1)) headings = content[headrow].split() column = {} maxcol = 0 for col,head in enumerate(headings): if head == 'ip.x': ipcol = col maxcol = max(maxcol,col+3) break if ipcol < 0: print 'missing ip coordinates..!' continue column['tensor'] = {} for label in [options.defgrad] + options.tensor: column['tensor'][label] = -1 for col,head in enumerate(headings): if head == label or head == '%i_1_%s'%(options.grain,label): column['tensor'][label] = col maxcol = max(maxcol,col+9) break if column['tensor'][options.defgrad] < 0: print 'missing deformation gradient..!' continue column['vector'] = {} for label in options.vector: column['vector'][label] = -1 for col,head in enumerate(headings): if head == label or head == '%i_1_%s'%(options.grain,label): column['vector'][label] = col maxcol = max(maxcol,col+3) break column['scalar'] = {} for label in options.scalar: column['scalar'][label] = -1 for col,head in enumerate(headings): if head == label or head == '%i_%s'%(options.grain,label): column['scalar'][label] = col maxcol = max(maxcol,col+1) break values = numpy.array([map(transliterateToFloat,line.split()[:maxcol]) for line in content[headrow+1:]],'d') N = len(values) grid = [{},{},{}] for i in range(N): grid[0][str(values[i,ipcol+0])] = True grid[1][str(values[i,ipcol+1])] = True grid[2][str(values[i,ipcol+2])] = True res = numpy.array([len(grid[0]),\ len(grid[1]),\ len(grid[2]),],'i') dim = numpy.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\ max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\ max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),]*res/(res-numpy.ones(3)), 'd') print 'resolution',res print 'dimension',dim (centroids, defgrad_av) = deformed(res,dim, numpy.reshape(values[:,column['tensor'][options.defgrad]: column['tensor'][options.defgrad]+9], (res[0],res[1],res[2],3,3))) ms = mesh(res,dim,defgrad_av,centroids) fields = {\ 'tensors': {},\ 'vectors': {},\ 'scalars': {},\ } for me in options.tensor: fields['tensors'][me] = numpy.reshape(values[:,column['tensor'][me]:column['tensor'][me]+9],(res[0],res[1],res[2],3,3)) for me in options.vector: fields['vectors'][me] = numpy.reshape(values[:,column['vector'][me]:column['vector'][me]+3],(res[0],res[1],res[2],3)) for me in options.scalar: fields['scalars'][me] = numpy.reshape(values[:,column['scalar'][me]],(res[0],res[1],res[2])) out = {} out['mesh'] = vtk_writeASCII_mesh(ms,fields,res) out['points'] = vtk_writeASCII_points(centroids,fields,res) out['box'] = vtk_writeASCII_box(dim,defgrad_av) for what in out.keys(): vtk = open(os.path.splitext(filename)[0]+'_%s.vtk'%what, 'w') output(out[what],{'filepointer':vtk},'File') vtk.close()