Add deformed configuration of given initial coordinates.
Operates on periodic three-dimensional x,y,z-ordered data sets. Replaces 3Dvisualize..!
This commit is contained in:
Philip Eisenlohr
parent
170d377092
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dbfd107b48
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
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import numpy as np
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import scipy.ndimage
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from optparse import OptionParser
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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#--------------------------------------------------------------------------------------------------
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def cell2node(cellData,grid):
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nodeData = 0.0
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datalen = np.array(cellData.shape[3:]).prod()
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for i in xrange(datalen):
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node = scipy.ndimage.convolve(cellData.reshape(tuple(grid)+(datalen,))[...,i],
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np.ones((2,2,2))/8., # 2x2x2 neighborhood of cells
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mode = 'wrap',
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origin = -1, # offset to have cell origin as center
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) # now averaged at cell origins
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node = np.append(node,node[np.newaxis,0,:,:,...],axis=0) # wrap along z
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node = np.append(node,node[:,0,np.newaxis,:,...],axis=1) # wrap along y
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node = np.append(node,node[:,:,0,np.newaxis,...],axis=2) # wrap along x
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nodeData = node[...,np.newaxis] if i==0 else np.concatenate((nodeData,node[...,np.newaxis]),axis=-1)
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return nodeData
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#--------------------------------------------------------------------------------------------------
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def displacementAvgFFT(F,grid,size,nodal=False,transformed=False):
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"""calculate average cell center (or nodal) displacement for deformation gradient field specified in each grid cell"""
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if nodal:
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x, y, z = np.meshgrid(np.linspace(0,size[0],1+grid[0]),
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np.linspace(0,size[1],1+grid[1]),
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np.linspace(0,size[2],1+grid[2]),
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indexing = 'ij')
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else:
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x, y, z = np.meshgrid(np.linspace(0,size[0],grid[0],endpoint=False),
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np.linspace(0,size[1],grid[1],endpoint=False),
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np.linspace(0,size[2],grid[2],endpoint=False),
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indexing = 'ij')
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origCoords = np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
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F_fourier = F if transformed else np.fft.rfftn(F,axes=(0,1,2)) # transform or use provided data
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Favg = np.real(F_fourier[0,0,0,:,:])/grid.prod() # take zero freq for average
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avgDisplacement = np.einsum('ml,ijkl->ijkm',Favg-np.eye(3),origCoords) # dX = Favg.X
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return avgDisplacement
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#--------------------------------------------------------------------------------------------------
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def displacementFluctFFT(F,grid,size,nodal=False,transformed=False):
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"""calculate cell center (or nodal) displacement for deformation gradient field specified in each grid cell"""
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integrator = 0.5j * size / math.pi
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kk, kj, ki = np.meshgrid(np.where(np.arange(grid[2])>grid[2]//2,np.arange(grid[2])-grid[2],np.arange(grid[2])),
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np.where(np.arange(grid[1])>grid[1]//2,np.arange(grid[1])-grid[1],np.arange(grid[1])),
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np.arange(grid[0]//2+1),
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indexing = 'ij')
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k_s = np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3)
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k_sSquared = np.einsum('...l,...l',k_s,k_s)
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k_sSquared[0,0,0] = 1.0 # ignore global average frequency
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#--------------------------------------------------------------------------------------------------
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# integration in Fourier space
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displacement_fourier = -np.einsum('ijkml,ijkl,l->ijkm',
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F if transformed else np.fft.rfftn(F,axes=(0,1,2)),
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k_s,
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integrator,
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) / k_sSquared[...,np.newaxis]
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#--------------------------------------------------------------------------------------------------
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# backtransformation to real space
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displacement = np.fft.irfftn(displacement_fourier,grid,axes=(0,1,2))
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return cell2node(displacement,grid) if nodal else displacement
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options file[s]', description = """
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Add deformed configuration of given initial coordinates.
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Operates on periodic three-dimensional x,y,z-ordered data sets.
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""", version = scriptID)
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parser.add_option('-f', '--defgrad',
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dest = 'defgrad',
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metavar = 'string',
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help = 'column label of deformation gradient [%default]')
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parser.add_option('-c', '--coordinates',
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dest = 'coords',
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metavar = 'string',
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help = 'column label of coordinates [%default]')
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parser.add_option('--nodal',
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dest = 'nodal',
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action = 'store_true',
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help = 'output nodal (not cell-centered) displacements')
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parser.set_defaults(defgrad = 'f',
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coords = 'ipinitialcoord',
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nodal = False,
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)
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(options,filenames) = parser.parse_args()
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try: table = damask.ASCIItable(name = name,
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outname = (os.path.splitext(name)[0]+
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'_nodal'+
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os.path.splitext(name)[1]) if (options.nodal and name) else None,
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buffered = False)
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except: continue
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damask.util.report(scriptName,name)
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# ------------------------------------------ read header ------------------------------------------
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table.head_read()
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# ------------------------------------------ sanity checks ----------------------------------------
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errors = []
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remarks = []
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if table.label_dimension(options.defgrad) != 9:
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errors.append('deformation gradient "{}" is not a 3x3 tensor.'.format(options.defgrad))
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coordDim = table.label_dimension(options.coords)
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if not 3 >= coordDim >= 1: errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.coords))
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elif coordDim < 3: remarks.append('appending {} dimensions to coordinates "{}"...'.format(3-coordDim,options.coords))
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if remarks != []: damask.util.croak(remarks)
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss=True)
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continue
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# --------------- figure out size and grid ---------------------------------------------------------
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table.data_readArray([options.defgrad,options.coords])
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table.data_rewind()
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if len(table.data.shape) < 2: table.data.shape += (1,) # expand to 2D shape
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if table.data[:,9:].shape[1] < 3:
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table.data = np.hstack((table.data,
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np.zeros((table.data.shape[0],
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3-table.data[:,9:].shape[1]),dtype='f'))) # fill coords up to 3D with zeros
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if remarks != []: damask.util.croak(remarks)
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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# --------------- figure out size and grid ---------------------------------------------------------
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coords = [np.unique(table.data[:,9+i]) for i in xrange(3)]
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mincorner = np.array(map(min,coords))
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maxcorner = np.array(map(max,coords))
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grid = np.array(map(len,coords),'i')
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size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
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size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set 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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table.close(dismiss = True)
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continue
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# ------------------------------------------ process data ------------------------------------------
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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...
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displacement = displacementFluctFFT(F_fourier,grid,size,options.nodal,transformed=True)
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avgDisplacement = displacementAvgFFT (F_fourier,grid,size,options.nodal,transformed=True)
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# ------------------------------------------ assemble header ---------------------------------------
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if options.nodal:
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table.info_clear()
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table.labels_clear()
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table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
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table.labels_append((['{}_pos' .format(i+1) for i in xrange(3)] if options.nodal else []) +
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['{}_avg({}).{}' .format(i+1,options.defgrad,options.coords) for i in xrange(3)] +
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['{}_fluct({}).{}'.format(i+1,options.defgrad,options.coords) for i in xrange(3)] )
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table.head_write()
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# ------------------------------------------ output data -------------------------------------------
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zrange = np.linspace(0,size[2],1+grid[2]) if options.nodal else xrange(grid[2])
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yrange = np.linspace(0,size[1],1+grid[1]) if options.nodal else xrange(grid[1])
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xrange = np.linspace(0,size[0],1+grid[0]) if options.nodal else xrange(grid[0])
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for i,z in enumerate(zrange):
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for j,y in enumerate(yrange):
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for k,x in enumerate(xrange):
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if options.nodal: table.data_clear()
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else: table.data_read()
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table.data_append([x,y,z] if options.nodal else [])
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table.data_append(list(avgDisplacement[i,j,k,:]))
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table.data_append(list( displacement[i,j,k,:]))
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table.data_write()
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# ------------------------------------------ output finalization -----------------------------------
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table.close() # close ASCII tables
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