From f040842ed4418bf5776747090548282906f9964e Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Fri, 15 Apr 2016 07:41:55 -0400 Subject: [PATCH] superseded by addDisplacements --- processing/post/addDeformedConfiguration.py | 164 -------------------- 1 file changed, 164 deletions(-) delete mode 100755 processing/post/addDeformedConfiguration.py diff --git a/processing/post/addDeformedConfiguration.py b/processing/post/addDeformedConfiguration.py deleted file mode 100755 index 3fb39ee0d..000000000 --- a/processing/post/addDeformedConfiguration.py +++ /dev/null @@ -1,164 +0,0 @@ -#!/usr/bin/env python -# -*- coding: UTF-8 no BOM -*- - -import os,sys,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]) - -#-------------------------------------------------------------------------------------------------- -def deformedCoordsFFT(F,undeformed=False): - - wgt = 1.0/grid.prod() - integrator = np.array([0.+1.j,0.+1.j,0.+1.j],'c16') * size/ 2.0 / math.pi - step = size/grid - - F_fourier = np.fft.rfftn(F,axes=(0,1,2)) - coords_fourier = np.zeros(F_fourier.shape[0:4],'c16') - - if undeformed: - Favg=np.eye(3) - else: - Favg=np.real(F_fourier[0,0,0,:,:])*wgt -#-------------------------------------------------------------------------------------------------- -# integration in Fourier space - k_s = np.zeros([3],'i') - for i in xrange(grid[2]): - k_s[2] = i - if(i > grid[2]//2 ): k_s[2] = k_s[2] - grid[2] - for j in xrange(grid[1]): - k_s[1] = j - if(j > grid[1]//2 ): k_s[1] = k_s[1] - grid[1] - for k in xrange(grid[0]//2+1): - k_s[0] = k - for m in xrange(3): - coords_fourier[i,j,k,m] = sum(F_fourier[i,j,k,m,0:3]*k_s*integrator) - if (any(k_s != 0)): - coords_fourier[i,j,k,0:3] /= -sum(k_s*k_s) - -#-------------------------------------------------------------------------------------------------- -# add average to scaled fluctuation and put (0,0,0) on (0,0,0) - coords = np.fft.irfftn(coords_fourier,F.shape[0:3],axes=(0,1,2)) - - offset_coords = np.dot(F[0,0,0,:,:],step/2.0) - scaling*coords[0,0,0,0:3] - for z in xrange(grid[2]): - for y in xrange(grid[1]): - for x in xrange(grid[0]): - coords[z,y,x,0:3] = scaling*coords[z,y,x,0:3] \ - + offset_coords \ - + np.dot(Favg,step*np.array([x,y,z])) - - return coords - -# -------------------------------------------------------------------- -# 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='heading of deformation gradient columns [%default]') -parser.add_option('--reference', dest='undeformed', action='store_true', - help='map results to reference (undeformed) average configuration [%default]') -parser.add_option('--scaling', dest='scaling', action='extend', metavar = '', - help='scaling of fluctuation') -parser.add_option('-u', '--unitlength', dest='unitlength', type='float', metavar = 'float', - help='set unit length for 2D model [%default]') -parser.add_option('--coordinates', dest='coords', metavar='string', - help='column heading for coordinates [%default]') - -parser.set_defaults(defgrad = 'f') -parser.set_defaults(coords = 'ipinitialcoord') -parser.set_defaults(scaling = []) -parser.set_defaults(undeformed = False) -parser.set_defaults(unitlength = 0.0) - -(options,filenames) = parser.parse_args() - -options.scaling += [1.0 for i in xrange(max(0,3-len(options.scaling)))] -scaling = map(float, options.scaling) - - -# --- loop over input files ------------------------------------------------------------------------- - -if filenames == []: filenames = [None] - -for name in filenames: - try: - table = damask.ASCIItable(name = name, - buffered = False) - except: continue - damask.util.report(scriptName,name) - -# ------------------------------------------ read header ------------------------------------------ - - table.head_read() - -# ------------------------------------------ sanity checks ---------------------------------------- - - errors = [] - remarks = [] - - if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords)) - else: colCoord = table.label_index(options.coords) - - if table.label_dimension(options.defgrad) != 9: errors.append('deformation gradient {} is not a tensor.'.format(options.defgrad)) - else: colF = table.label_index(options.defgrad) - - 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() - - coords = [np.unique(table.data[:,colCoord+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 - -# ------------------------------------------ assemble header --------------------------------------- - - table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:])) - for coord in xrange(3): - label = '{}_{}_{}'.format(coord+1,options.defgrad,options.coords) - if np.any(scaling) != 1.0: label+='_{}_{}_{}'.format(scaling) - if options.undeformed: label+='_undeformed' - table.labels_append([label]) # extend ASCII header with new labels - table.head_write() - -# ------------------------------------------ read deformation gradient field ----------------------- - centroids = deformedCoordsFFT(table.data[:,colF:colF+9].reshape(grid[2],grid[1],grid[0],3,3), - options.undeformed) -# ------------------------------------------ process data ------------------------------------------ - table.data_rewind() - for z in xrange(grid[2]): - for y in xrange(grid[1]): - for x in xrange(grid[0]): - table.data_read() - table.data_append(list(centroids[z,y,x,:])) - table.data_write() - -# ------------------------------------------ output finalization ----------------------------------- - - table.close() # close ASCII tables \ No newline at end of file