addDeformedConfiguration without core module
This commit is contained in:
Martin Diehl
parent
26b2a36cae
commit
f49091c952
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@ -1,7 +1,7 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string
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import os,sys,string,math
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import numpy as np
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from optparse import OptionParser
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import damask
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@ -9,6 +9,49 @@ import damask
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scriptID = string.replace('$Id$','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
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#--------------------------------------------------------------------------------------------------
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def deformedCoordsFFT(F,undeformed=False):
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#--------------------------------------------------------------------------------------------------
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wgt = 1.0/grid.prod()
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integrator = grid[::-1] / 2.0 / math.pi
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step = size[::-1]/grid[::-1]
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F_fourier = np.fft.fftpack.rfftn(F,axes=(0,1,2))
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if undeformed:
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Favg=np.eye(3)
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else:
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Favg=np.real(F_fourier[0,0,0,:,:])*wgt
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coords_fourier = np.zeros(F_fourier.shape[:-1],'c16')
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#--------------------------------------------------------------------------------------------------
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# integration in Fourier space
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k_s = np.zeros([3],'i')
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for k in xrange(grid[2]):
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k_s[2] = k
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if(k > grid[0]/2 ): k_s[2] = k_s[2] - grid[2]
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for j in xrange(grid[1]):
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k_s[1] = j
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if(j > grid[1]/2 ): k_s[1] = k_s[1] - grid[1]
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for i in xrange(grid[0]/2+1):
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k_s[0] = i
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for m in xrange(3):
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coords_fourier[k,j,i,m] = sum(F_fourier[k,j,i,0:3,m]*k_s*\
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np.array([0.+1.j,0.+1.j,0.+1.j],'c16')*integrator)
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if (any(k_s != 0)):
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coords_fourier[k,j,i,0:3] /= -sum(k_s*k_s)
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#--------------------------------------------------------------------------------------------------
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# add average to scaled fluctuation and put (0,0,0) on (0,0,0)
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coords = np.fft.fftpack.irfftn(coords_fourier,axes=(0,1,2))
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offset_coords = np.dot(F[0,0,0,0:3,0:3],step/2.0) - scaling*coords[0,0,0,0:3]
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for k in xrange(grid[2]):
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for j in xrange(grid[1]):
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for i in xrange(grid[0]):
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coords[k,j,i,0:3] = scaling*coords[k,j,i,0:3] \
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+ offset_coords \
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+ np.dot(Favg,step*np.array([i,j,k]))
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return coords
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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@ -19,26 +62,29 @@ Operates on periodic three-dimensional x,y,z-ordered data sets.
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""", version = scriptID)
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parser.add_option('-c','--coordinates',
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dest = 'coords',
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type = 'string', metavar = 'string',
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help = 'column label of coordinates [%default]')
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parser.add_option('-f','--defgrad',
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dest = 'defgrad',
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type = 'string', metavar = 'string',
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help = 'column label of deformation gradient [%default]')
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parser.add_option('--scaling',
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dest = 'scaling',
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type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
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help = 'x/y/z scaling of displacement fluctuation')
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parser.add_option('-f', '--defgrad',dest='defgrad', metavar = 'string',
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help='heading of deformation gradient columns [%default]')
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parser.add_option('--reference', dest='undeformed', action='store_true',
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help='map results to reference (undeformed) average configuration [%default]')
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parser.add_option('--scaling', dest='scaling', action='extend', metavar = '<float LIST>',
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help='scaling of fluctuation')
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parser.add_option('-u', '--unitlength', dest='unitlength', type='float', metavar = 'float',
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help='set unit length for 2D model [%default]')
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parser.add_option('--coordinates', dest='coords', metavar='string',
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help='column heading for coordinates [%default]')
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parser.set_defaults(coords = 'ipinitialcoord',
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defgrad = 'f',
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scaling = [1.,1.,1.],
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)
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parser.set_defaults(defgrad = 'f')
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parser.set_defaults(coords = 'ipinitialcoord')
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parser.set_defaults(scaling = [])
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parser.set_defaults(undeformed = False)
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parser.set_defaults(unitlength = 0.0)
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(options,filenames) = parser.parse_args()
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options.scaling += [1.0 for i in xrange(max(0,3-len(options.scaling)))]
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scaling = map(float, options.scaling)
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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@ -83,7 +129,7 @@ for name in filenames:
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size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 equal to smallest among other spacings
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N = grid.prod()
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if N != len(table.data): errors.append('data count {} does not match grid {}x{}x{}.'.format(N,*grid))
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if errors != []:
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damask.util.croak(errors)
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@ -94,23 +140,16 @@ for name in filenames:
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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for coord in xrange(3):
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table.labels_append(['{}_{}.{}'.format(coord+1,options.defgrad,options.coords) ]) # extend ASCII header with new labels
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label = '{}_{}_{}'.format(coord+1,options.defgrad,options.coords)
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if np.any(scaling) != 1.0: label+='_{}_{}_{}'.format(scaling)
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if options.undeformed: label+='_undeformed'
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table.labels_append([label]) # extend ASCII header with new labels
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table.head_write()
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# ------------------------------------------ read deformation gradient field -----------------------
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table.data_rewind()
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F = np.array([0.0 for i in xrange(N*9)]).reshape([3,3]+grid.tolist())
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idx = 0
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while table.data_read():
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(x,y,z) = damask.util.gridLocation(idx,grid) # figure out (x,y,z) position from line count
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idx += 1
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F[0:3,0:3,x,y,z] = np.array(map(float,table.data[table.label_index(options.defgrad):\
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table.label_index(options.defgrad)+9]),'d').reshape(3,3)
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centroids = deformedCoordsFFT(table.data[:,colF:colF+9].reshape(grid[0],grid[1],grid[2],3,3),
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options.undeformed)
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# ------------------------------------------ calculate coordinates ---------------------------------
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Favg = damask.core.math.tensorAvg(F)
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centroids = damask.core.mesh.deformedCoordsFFT(size,F,Favg)
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# ------------------------------------------ process data ------------------------------------------
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table.data_rewind()
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idx = 0
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@ -118,7 +157,7 @@ for name in filenames:
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while outputAlive and table.data_read(): # read next data line of ASCII table
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(x,y,z) = damask.util.gridLocation(idx,grid) # figure out (x,y,z) position from line count
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idx += 1
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table.data_append(list(centroids[:,x,y,z]))
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table.data_append(list(centroids[z,y,x,:]))
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outputAlive = table.data_write()
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# ------------------------------------------ output finalization -----------------------------------
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