#!/usr/bin/env python # -*- coding: UTF-8 no BOM -*- import os,sys,math import numpy as np import scipy.ndimage from optparse import OptionParser import damask scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptID = ' '.join([scriptName,damask.version]) #-------------------------------------------------------------------------------------------------- def cell2node(cellData,grid): nodeData = 0.0 datalen = np.array(cellData.shape[3:]).prod() for i in xrange(datalen): node = scipy.ndimage.convolve(cellData.reshape(tuple(grid)+(datalen,))[...,i], np.ones((2,2,2))/8., # 2x2x2 neighborhood of cells mode = 'wrap', origin = -1, # offset to have cell origin as center ) # now averaged at cell origins node = np.append(node,node[np.newaxis,0,:,:,...],axis=0) # wrap along z node = np.append(node,node[:,0,np.newaxis,:,...],axis=1) # wrap along y node = np.append(node,node[:,:,0,np.newaxis,...],axis=2) # wrap along x nodeData = node[...,np.newaxis] if i==0 else np.concatenate((nodeData,node[...,np.newaxis]),axis=-1) return nodeData #-------------------------------------------------------------------------------------------------- def displacementAvgFFT(F,grid,size,nodal=False,transformed=False): """calculate average cell center (or nodal) displacement for deformation gradient field specified in each grid cell""" if nodal: x, y, z = np.meshgrid(np.linspace(0,size[0],1+grid[0]), np.linspace(0,size[1],1+grid[1]), np.linspace(0,size[2],1+grid[2]), indexing = 'ij') else: x, y, z = np.meshgrid(np.linspace(0,size[0],grid[0],endpoint=False), np.linspace(0,size[1],grid[1],endpoint=False), np.linspace(0,size[2],grid[2],endpoint=False), indexing = 'ij') origCoords = np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3) F_fourier = F if transformed else np.fft.rfftn(F,axes=(0,1,2)) # transform or use provided data Favg = np.real(F_fourier[0,0,0,:,:])/grid.prod() # take zero freq for average avgDisplacement = np.einsum('ml,ijkl->ijkm',Favg-np.eye(3),origCoords) # dX = Favg.X return avgDisplacement #-------------------------------------------------------------------------------------------------- def displacementFluctFFT(F,grid,size,nodal=False,transformed=False): """calculate cell center (or nodal) displacement for deformation gradient field specified in each grid cell""" integrator = 0.5j * size / math.pi kk, kj, ki = np.meshgrid(np.where(np.arange(grid[2])>grid[2]//2,np.arange(grid[2])-grid[2],np.arange(grid[2])), np.where(np.arange(grid[1])>grid[1]//2,np.arange(grid[1])-grid[1],np.arange(grid[1])), np.arange(grid[0]//2+1), indexing = 'ij') k_s = np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3) k_sSquared = np.einsum('...l,...l',k_s,k_s) k_sSquared[0,0,0] = 1.0 # ignore global average frequency #-------------------------------------------------------------------------------------------------- # integration in Fourier space displacement_fourier = -np.einsum('ijkml,ijkl,l->ijkm', F if transformed else np.fft.rfftn(F,axes=(0,1,2)), k_s, integrator, ) / k_sSquared[...,np.newaxis] #-------------------------------------------------------------------------------------------------- # backtransformation to real space displacement = np.fft.irfftn(displacement_fourier,grid,axes=(0,1,2)) return cell2node(displacement,grid) if nodal else displacement # -------------------------------------------------------------------- # MAIN # -------------------------------------------------------------------- parser = OptionParser(option_class=damask.extendableOption, usage='%prog options file[s]', description = """ Add deformed configuration of given initial coordinates. Operates on periodic three-dimensional x,y,z-ordered data sets. """, version = scriptID) parser.add_option('-f', '--defgrad', dest = 'defgrad', metavar = 'string', help = 'column label of deformation gradient [%default]') parser.add_option('-c', '--coordinates', dest = 'coords', metavar = 'string', help = 'column label of coordinates [%default]') parser.add_option('--nodal', dest = 'nodal', action = 'store_true', help = 'output nodal (not cell-centered) displacements') parser.set_defaults(defgrad = 'f', coords = 'ipinitialcoord', nodal = False, ) (options,filenames) = parser.parse_args() # --- loop over input files ------------------------------------------------------------------------- if filenames == []: filenames = [None] for name in filenames: try: table = damask.ASCIItable(name = name, outname = (os.path.splitext(name)[0]+ '_nodal'+ os.path.splitext(name)[1]) if (options.nodal and name) else None, buffered = False) except: continue damask.util.report(scriptName,name) # ------------------------------------------ read header ------------------------------------------ table.head_read() # ------------------------------------------ sanity checks ---------------------------------------- errors = [] remarks = [] if table.label_dimension(options.defgrad) != 9: errors.append('deformation gradient "{}" is not a 3x3 tensor.'.format(options.defgrad)) coordDim = table.label_dimension(options.coords) if not 3 >= coordDim >= 1: errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.coords)) elif coordDim < 3: remarks.append('appending {} dimension{} to coordinates "{}"...'.format(3-coordDim, 's' if coordDim < 2 else '', options.coords)) if remarks != []: damask.util.croak(remarks) if errors != []: damask.util.croak(errors) table.close(dismiss=True) continue # --------------- figure out size and grid --------------------------------------------------------- table.data_readArray([options.defgrad,options.coords]) table.data_rewind() if len(table.data.shape) < 2: table.data.shape += (1,) # expand to 2D shape if table.data[:,9:].shape[1] < 3: table.data = np.hstack((table.data, np.zeros((table.data.shape[0], 3-table.data[:,9:].shape[1]),dtype='f'))) # fill coords up to 3D with zeros if remarks != []: damask.util.croak(remarks) if errors != []: damask.util.croak(errors) table.close(dismiss = True) continue # --------------- figure out size and grid --------------------------------------------------------- coords = [np.unique(table.data[:,9+i]) for i in xrange(3)] mincorner = np.array(map(min,coords)) maxcorner = np.array(map(max,coords)) grid = np.array(map(len,coords),'i') size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1) size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set to smallest among other spacings N = grid.prod() if N != len(table.data): errors.append('data count {} does not match grid {}x{}x{}.'.format(N,*grid)) if errors != []: damask.util.croak(errors) table.close(dismiss = True) continue # ------------------------------------------ process data ------------------------------------------ F_fourier = np.fft.rfftn(table.data[:,:9].reshape(grid[2],grid[1],grid[0],3,3),axes=(0,1,2)) # perform transform only once... displacement = displacementFluctFFT(F_fourier,grid,size,options.nodal,transformed=True) avgDisplacement = displacementAvgFFT (F_fourier,grid,size,options.nodal,transformed=True) # ------------------------------------------ assemble header --------------------------------------- if options.nodal: table.info_clear() table.labels_clear() table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:])) table.labels_append((['{}_pos' .format(i+1) for i in xrange(3)] if options.nodal else []) + ['{}_avg({}).{}' .format(i+1,options.defgrad,options.coords) for i in xrange(3)] + ['{}_fluct({}).{}'.format(i+1,options.defgrad,options.coords) for i in xrange(3)] ) table.head_write() # ------------------------------------------ output data ------------------------------------------- zrange = np.linspace(0,size[2],1+grid[2]) if options.nodal else xrange(grid[2]) yrange = np.linspace(0,size[1],1+grid[1]) if options.nodal else xrange(grid[1]) xrange = np.linspace(0,size[0],1+grid[0]) if options.nodal else xrange(grid[0]) for i,z in enumerate(zrange): for j,y in enumerate(yrange): for k,x in enumerate(xrange): if options.nodal: table.data_clear() else: table.data_read() table.data_append([x,y,z] if options.nodal else []) table.data_append(list(avgDisplacement[i,j,k,:])) table.data_append(list( displacement[i,j,k,:])) table.data_write() # ------------------------------------------ output finalization ----------------------------------- table.close() # close ASCII tables