fully adopted code from addDisplacement
This commit is contained in:
parent
c949f407e5
commit
745c012088
|
@ -1,9 +1,9 @@
|
|||
#!/usr/bin/env python2
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,sys
|
||||
import numpy as np
|
||||
import os
|
||||
import math
|
||||
import numpy as np
|
||||
import scipy.ndimage
|
||||
from optparse import OptionParser
|
||||
import damask
|
||||
|
@ -18,7 +18,7 @@ def cell2node(cellData,grid):
|
|||
datalen = np.array(cellData.shape[3:]).prod()
|
||||
|
||||
for i in xrange(datalen):
|
||||
node = scipy.ndimage.convolve(cellData.reshape(tuple(grid)+(datalen,))[...,i],
|
||||
node = scipy.ndimage.convolve(cellData.reshape(tuple(grid[::-1])+(datalen,))[...,i],
|
||||
np.ones((2,2,2))/8., # 2x2x2 neighborhood of cells
|
||||
mode = 'wrap',
|
||||
origin = -1, # offset to have cell origin as center
|
||||
|
@ -32,26 +32,26 @@ def cell2node(cellData,grid):
|
|||
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"""
|
||||
def deformationAvgFFT(F,grid,size,nodal=False,transformed=False):
|
||||
"""calculate average cell center (or nodal) deformation for deformation gradient field specified in each grid cell"""
|
||||
if nodal:
|
||||
x, y, z = np.meshgrid(np.linspace(0,size[0],1+grid[0]),
|
||||
x, y, z = np.meshgrid(np.linspace(0,size[2],1+grid[2]),
|
||||
np.linspace(0,size[1],1+grid[1]),
|
||||
np.linspace(0,size[2],1+grid[2]),
|
||||
np.linspace(0,size[0],1+grid[0]),
|
||||
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),
|
||||
x, y, z = np.meshgrid(np.linspace(size[2]/grid[2]/2.,size[2]-size[2]/grid[2]/2.,grid[2]),
|
||||
np.linspace(size[1]/grid[1]/2.,size[1]-size[1]/grid[1]/2.,grid[1]),
|
||||
np.linspace(size[0]/grid[0]/2.,size[0]-size[0]/grid[0]/2.,grid[0]),
|
||||
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
|
||||
avgDeformation = np.einsum('ml,ijkl->ijkm',Favg,origCoords) # dX = Favg.X
|
||||
|
||||
return avgDisplacement
|
||||
return avgDeformation
|
||||
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
def displacementFluctFFT(F,grid,size,nodal=False,transformed=False):
|
||||
|
@ -69,7 +69,7 @@ def displacementFluctFFT(F,grid,size,nodal=False,transformed=False):
|
|||
#--------------------------------------------------------------------------------------------------
|
||||
# integration in Fourier space
|
||||
|
||||
displacement_fourier = +np.einsum('ijkml,ijkl,l->ijkm',
|
||||
displacement_fourier = -np.einsum('ijkml,ijkl,l->ijkm',
|
||||
F if transformed else np.fft.rfftn(F,axes=(0,1,2)),
|
||||
k_s,
|
||||
integrator,
|
||||
|
@ -78,7 +78,7 @@ def displacementFluctFFT(F,grid,size,nodal=False,transformed=False):
|
|||
#--------------------------------------------------------------------------------------------------
|
||||
# backtransformation to real space
|
||||
|
||||
displacement = np.fft.irfftn(displacement_fourier,grid,axes=(0,1,2))
|
||||
displacement = np.fft.irfftn(displacement_fourier,grid[::-1],axes=(0,1,2))
|
||||
|
||||
return cell2node(displacement,grid) if nodal else displacement
|
||||
|
||||
|
@ -137,7 +137,7 @@ def volumeMismatch(size,F,nodes):
|
|||
(compatible) cube and determinant of defgrad at the FP
|
||||
"""
|
||||
coords = np.empty([8,3])
|
||||
vMismatch = np.empty(grid)
|
||||
vMismatch = np.empty(grid[::-1])
|
||||
volInitial = size.prod()/grid.prod()
|
||||
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
|
@ -145,23 +145,22 @@ def volumeMismatch(size,F,nodes):
|
|||
for k in xrange(grid[2]):
|
||||
for j in xrange(grid[1]):
|
||||
for i in xrange(grid[0]):
|
||||
coords[0,0:3] = nodes[i, j, k ,0:3]
|
||||
coords[1,0:3] = nodes[i+1,j, k ,0:3]
|
||||
coords[2,0:3] = nodes[i+1,j+1,k ,0:3]
|
||||
coords[3,0:3] = nodes[i, j+1,k ,0:3]
|
||||
coords[4,0:3] = nodes[i, j, k+1,0:3]
|
||||
coords[5,0:3] = nodes[i+1,j, k+1,0:3]
|
||||
coords[6,0:3] = nodes[i+1,j+1,k+1,0:3]
|
||||
coords[7,0:3] = nodes[i, j+1,k+1,0:3]
|
||||
vMismatch[i,j,k] = \
|
||||
abs(volTetrahedron([coords[6,0:3],coords[0,0:3],coords[7,0:3],coords[3,0:3]])) \
|
||||
coords[0,0:3] = nodes[k, j, i ,0:3]
|
||||
coords[1,0:3] = nodes[k ,j, i+1,0:3]
|
||||
coords[2,0:3] = nodes[k ,j+1,i+1,0:3]
|
||||
coords[3,0:3] = nodes[k, j+1,i ,0:3]
|
||||
coords[4,0:3] = nodes[k+1,j, i ,0:3]
|
||||
coords[5,0:3] = nodes[k+1,j, i+1,0:3]
|
||||
coords[6,0:3] = nodes[k+1,j+1,i+1,0:3]
|
||||
coords[7,0:3] = nodes[k+1,j+1,i ,0:3]
|
||||
vMismatch[k,j,i] = \
|
||||
( abs(volTetrahedron([coords[6,0:3],coords[0,0:3],coords[7,0:3],coords[3,0:3]])) \
|
||||
+ abs(volTetrahedron([coords[6,0:3],coords[0,0:3],coords[7,0:3],coords[4,0:3]])) \
|
||||
+ abs(volTetrahedron([coords[6,0:3],coords[0,0:3],coords[2,0:3],coords[3,0:3]])) \
|
||||
+ abs(volTetrahedron([coords[6,0:3],coords[0,0:3],coords[2,0:3],coords[1,0:3]])) \
|
||||
+ abs(volTetrahedron([coords[6,0:3],coords[4,0:3],coords[1,0:3],coords[5,0:3]])) \
|
||||
+ abs(volTetrahedron([coords[6,0:3],coords[4,0:3],coords[1,0:3],coords[0,0:3]]))
|
||||
vMismatch[i,j,k] = vMismatch[i,j,k]/np.linalg.det(F[i,j,k,0:3,0:3])
|
||||
|
||||
+ abs(volTetrahedron([coords[6,0:3],coords[4,0:3],coords[1,0:3],coords[0,0:3]]))) \
|
||||
/np.linalg.det(F[k,j,i,0:3,0:3])
|
||||
return vMismatch/volInitial
|
||||
|
||||
|
||||
|
@ -175,7 +174,7 @@ def shapeMismatch(size,F,nodes,centres):
|
|||
the initial volume element with the current deformation gradient
|
||||
"""
|
||||
coordsInitial = np.empty([8,3])
|
||||
sMismatch = np.empty(grid)
|
||||
sMismatch = np.empty(grid[::-1])
|
||||
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
# initial positions
|
||||
|
@ -194,15 +193,15 @@ def shapeMismatch(size,F,nodes,centres):
|
|||
for k in xrange(grid[2]):
|
||||
for j in xrange(grid[1]):
|
||||
for i in xrange(grid[0]):
|
||||
sMismatch[i,j,k] = \
|
||||
+ np.linalg.norm(nodes[i, j, k,0:3] - centres[i,j,k,0:3] - np.dot(F[i,j,k,:,:], coordsInitial[0,0:3]))\
|
||||
+ np.linalg.norm(nodes[i+1,j, k,0:3] - centres[i,j,k,0:3] - np.dot(F[i,j,k,:,:], coordsInitial[1,0:3]))\
|
||||
+ np.linalg.norm(nodes[i+1,j+1,k ,0:3] - centres[i,j,k,0:3] - np.dot(F[i,j,k,:,:], coordsInitial[2,0:3]))\
|
||||
+ np.linalg.norm(nodes[i, j+1,k ,0:3] - centres[i,j,k,0:3] - np.dot(F[i,j,k,:,:], coordsInitial[3,0:3]))\
|
||||
+ np.linalg.norm(nodes[i, j, k+1,0:3] - centres[i,j,k,0:3] - np.dot(F[i,j,k,:,:], coordsInitial[4,0:3]))\
|
||||
+ np.linalg.norm(nodes[i+1,j, k+1,0:3] - centres[i,j,k,0:3] - np.dot(F[i,j,k,:,:], coordsInitial[5,0:3]))\
|
||||
+ np.linalg.norm(nodes[i+1,j+1,k+1,0:3] - centres[i,j,k,0:3] - np.dot(F[i,j,k,:,:], coordsInitial[6,0:3]))\
|
||||
+ np.linalg.norm(nodes[i, j+1,k+1,0:3] - centres[i,j,k,0:3] - np.dot(F[i,j,k,:,:], coordsInitial[7,0:3]))
|
||||
sMismatch[k,j,i] = \
|
||||
+ np.linalg.norm(nodes[k, j, i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[0,0:3]))\
|
||||
+ np.linalg.norm(nodes[k, j, i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[1,0:3]))\
|
||||
+ np.linalg.norm(nodes[k, j+1,i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[2,0:3]))\
|
||||
+ np.linalg.norm(nodes[k, j+1,i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[3,0:3]))\
|
||||
+ np.linalg.norm(nodes[k+1,j, i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[4,0:3]))\
|
||||
+ np.linalg.norm(nodes[k+1,j, i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[5,0:3]))\
|
||||
+ np.linalg.norm(nodes[k+1,j+1,i+1,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[6,0:3]))\
|
||||
+ np.linalg.norm(nodes[k+1,j+1,i ,0:3] - centres[k,j,i,0:3] - np.dot(F[k,j,i,:,:], coordsInitial[7,0:3]))
|
||||
return sMismatch
|
||||
|
||||
|
||||
|
@ -307,38 +306,32 @@ for name in filenames:
|
|||
# -----------------------------process data and assemble header -------------------------------------
|
||||
|
||||
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...
|
||||
nodes = np.vstack(np.meshgrid(np.linspace(0.0,size[0],grid[0]+1),
|
||||
np.linspace(0.0,size[1],grid[1]+1),
|
||||
np.linspace(0.0,size[2],grid[2]+1))).reshape([3,17,17,17]).T\
|
||||
+ displacementFluctFFT(F_fourier,grid,size,True,transformed=True)\
|
||||
+ displacementAvgFFT (F_fourier,grid,size,True,transformed=True)
|
||||
nodes = displacementFluctFFT(F_fourier,grid,size,True,transformed=True)\
|
||||
+ deformationAvgFFT (F_fourier,grid,size,True,transformed=True)
|
||||
|
||||
if options.shape:
|
||||
table.labels_append(['shapeMismatch({})'.format(options.defgrad)])
|
||||
centres = np.vstack(np.meshgrid(np.linspace(size[0]/grid[0]*.5,size[0]-size[0]/grid[0]*.5,grid[0]),
|
||||
np.linspace(size[1]/grid[1]*.5,size[1]-size[1]/grid[1]*.5,grid[1]),
|
||||
np.linspace(size[2]/grid[2]*.5,size[2]-size[2]/grid[2]*.5,grid[2]))).reshape([3,16,16,16]).T\
|
||||
+ displacementFluctFFT(F_fourier,grid,size,False,transformed=True)\
|
||||
+ displacementAvgFFT (F_fourier,grid,size,False,transformed=True)
|
||||
centres = displacementFluctFFT(F_fourier,grid,size,False,transformed=True)\
|
||||
+ deformationAvgFFT (F_fourier,grid,size,False,transformed=True)
|
||||
|
||||
if options.volume:
|
||||
table.labels_append(['volMismatch({})'.format(options.defgrad)])
|
||||
|
||||
table.head_write()
|
||||
if options.shape: shapeMismatch = shapeMismatch( size,table.data[:,:9].reshape(grid[2],grid[1],grid[0],3,3),nodes,centres)
|
||||
if options.volume: volumeMismatch = volumeMismatch(size,table.data[:,:9].reshape(grid[2],grid[1],grid[0],3,3),nodes)
|
||||
if options.shape:
|
||||
shapeMismatch = shapeMismatch( size,table.data[:,:9].reshape(grid[2],grid[1],grid[0],3,3),nodes,centres)
|
||||
if options.volume:
|
||||
volumeMismatch = volumeMismatch(size,table.data[:,:9].reshape(grid[2],grid[1],grid[0],3,3),nodes)
|
||||
|
||||
# ------------------------------------------ process data ------------------------------------------
|
||||
table.data_rewind()
|
||||
idx = 0
|
||||
outputAlive = True
|
||||
while outputAlive and table.data_read(): # read next data line of ASCII table
|
||||
(x,y,z) = damask.util.gridLocation(idx,grid) # figure out (x,y,z) position from line count
|
||||
idx += 1
|
||||
if options.shape: table.data_append( shapeMismatch[x,y,z])
|
||||
if options.volume: table.data_append(volumeMismatch[x,y,z])
|
||||
outputAlive = table.data_write()
|
||||
# ------------------------------------------ output data -------------------------------------------
|
||||
for i in xrange(grid[2]):
|
||||
for j in xrange(grid[1]):
|
||||
for k in xrange(grid[0]):
|
||||
table.data_read()
|
||||
if options.shape: table.data_append(shapeMismatch[i,j,k])
|
||||
if options.volume: table.data_append(volumeMismatch[i,j,k])
|
||||
table.data_write()
|
||||
|
||||
# ------------------------------------------ output finalization -----------------------------------
|
||||
|
||||
table.close()
|
||||
|
||||
table.close() # close ASCII tables
|
||||
|
|
Loading…
Reference in New Issue