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polishing and introduction of locally derived grid in FFT subroutine

This commit is contained in:
Aritra Chakraborty 2016-03-16 14:55:56 -04:00
parent 93466273ff
commit ce26ad06da
2 changed files with 31 additions and 44 deletions
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39
processing/post/addCurl.py
View File

@ -10,40 +10,35 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version]) scriptID = ' '.join([scriptName,damask.version])
def curlFFT(geomdim,field): def curlFFT(geomdim,field):
grid = np.array(np.shape(field)[2::-1])
N = grid.prod() # field size N = grid.prod() # field size
n = np.array(np.shape(field)[3:]).prod() # data size n = np.array(np.shape(field)[3:]).prod() # data size
if n == 3: if n == 3: dataType = 'vector'
dataType = 'vector' elif n == 9: dataType = 'tensor'
elif n == 9:
dataType = 'tensor'
field_fourier = np.fft.fftpack.rfftn(field,axes=(0,1,2)) field_fourier = np.fft.fftpack.rfftn(field,axes=(0,1,2))
curl_fourier = np.zeros(field_fourier.shape,'c16') curl_fourier = np.zeros(field_fourier.shape,'c16')
# differentiation in Fourier space # differentiation in Fourier space
k_s = np.zeros([3],'i') k_s = np.zeros([3],'i')
TWOPIIMG = (0.0+2.0j*math.pi) TWOPIIMG = 2.0j*math.pi
for i in xrange(grid[2]): for i in xrange(grid[2]):
k_s[0] = i k_s[0] = i
if(grid[2]%2==0 and i == grid[2]//2): # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011) if grid[2]%2 == 0 and i == grid[2]//2: k_s[0] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
k_s[0]=0 elif i > grid[2]//2: k_s[0] -= grid[2]
elif (i > grid[2]//2):
k_s[0] = k_s[0] - grid[2]
for j in xrange(grid[1]): for j in xrange(grid[1]):
k_s[1] = j k_s[1] = j
if(grid[1]%2==0 and j == grid[1]//2): # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011) if grid[1]%2 == 0 and j == grid[1]//2: k_s[1] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
k_s[1]=0 elif j > grid[1]//2: k_s[1] -= grid[1]
elif (j > grid[1]//2):
k_s[1] = k_s[1] - grid[1]
for k in xrange(grid[0]//2+1): for k in xrange(grid[0]//2+1):
k_s[2] = k k_s[2] = k
if(grid[0]%2==0 and k == grid[0]//2): # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011) if grid[0]%2 == 0 and k == grid[0]//2: k_s[2] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
k_s[2]=0
xi = (k_s/geomdim)[2::-1].astype('c16') # reversing the field input order
xi = np.array([k_s[2]/geomdim[2]+0.0j,k_s[1]/geomdim[1]+0.j,k_s[0]/geomdim[0]+0.j],'c16')
if dataType == 'tensor': if dataType == 'tensor':
for l in xrange(3): for l in xrange(3):
curl_fourier[i,j,k,0,l] = ( field_fourier[i,j,k,l,2]*xi[1]\ curl_fourier[i,j,k,0,l] = ( field_fourier[i,j,k,l,2]*xi[1]\
@ -100,10 +95,8 @@ if options.vector is None and options.tensor is None:
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
try: try: table = damask.ASCIItable(name = name,buffered = False)
table = damask.ASCIItable(name = name,buffered = False) except: continue
except:
continue
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------ # ------------------------------------------ read header ------------------------------------------
@ -161,9 +154,9 @@ for name in filenames:
stack = [table.data] stack = [table.data]
for type, data in items.iteritems(): for type, data in items.iteritems():
for i,label in enumerate(data['active']): for i,label in enumerate(data['active']):
stack.append(curlFFT(size[::-1], # we need to reverse order here, because x stack.append(curlFFT(size[::-1], # we need to reverse order here, because x is fastest,ie rightmost, but leftmost in our x,y,z notation
table.data[:,data['column'][i]:data['column'][i]+data['dim']]. # is fastest,ie rightmost, but leftmost in table.data[:,data['column'][i]:data['column'][i]+data['dim']].
reshape([grid[2],grid[1],grid[0]]+data['shape']))) # our x,y,z notation reshape([grid[2],grid[1],grid[0]]+data['shape'])))
# ------------------------------------------ output result ----------------------------------------- # ------------------------------------------ output result -----------------------------------------

36
processing/post/addDivergence.py
View File

@ -10,6 +10,7 @@ scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version]) scriptID = ' '.join([scriptName,damask.version])
def divFFT(geomdim,field): def divFFT(geomdim,field):
grid = np.array(np.shape(field)[2::-1])
N = grid.prod() # field size N = grid.prod() # field size
n = np.array(np.shape(field)[3:]).prod() # data size n = np.array(np.shape(field)[3:]).prod() # data size
@ -18,27 +19,22 @@ def divFFT(geomdim,field):
# differentiation in Fourier space # differentiation in Fourier space
k_s=np.zeros([3],'i') k_s=np.zeros([3],'i')
TWOPIIMG = (0.0+2.0j*math.pi) TWOPIIMG = 2.0j*math.pi
for i in xrange(grid[2]): for i in xrange(grid[2]):
k_s[0] = i k_s[0] = i
if(grid[2]%2==0 and i == grid[2]//2): # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011) if grid[2]%2 == 0 and i == grid[2]//2: k_s[0] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
k_s[0]=0 elif i > grid[2]//2: k_s[0] -= grid[2]
elif (i > grid[2]//2):
k_s[0] = k_s[0] - grid[2]
for j in xrange(grid[1]): for j in xrange(grid[1]):
k_s[1] = j k_s[1] = j
if(grid[1]%2==0 and j == grid[1]//2): # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011) if grid[1]%2 == 0 and j == grid[1]//2: k_s[1] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
k_s[1]=0 elif j > grid[1]//2: k_s[1] -= grid[1]
elif (j > grid[1]//2):
k_s[1] = k_s[1] - grid[1]
for k in xrange(grid[0]//2+1): for k in xrange(grid[0]//2+1):
k_s[2] = k k_s[2] = k
if(grid[0]%2==0 and k == grid[0]//2): # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011) if grid[0]%2 == 0 and k == grid[0]//2: k_s[2] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
k_s[2]=0
xi=np.array([k_s[2]/geomdim[2]+0.0j,k_s[1]/geomdim[1]+0.j,k_s[0]/geomdim[0]+0.j],'c16') xi = (k_s/geomdim)[2::-1].astype('c16') # reversing the field input order
if n == 9: # tensor, 3x3 -> 3 if n == 9: # tensor, 3x3 -> 3
for l in xrange(3): for l in xrange(3):
div_fourier[i,j,k,l] = sum(field_fourier[i,j,k,l,0:3]*xi) *TWOPIIMG div_fourier[i,j,k,l] = sum(field_fourier[i,j,k,l,0:3]*xi) *TWOPIIMG
@ -85,10 +81,8 @@ if options.vector is None and options.tensor is None:
if filenames == []: filenames = [None] if filenames == []: filenames = [None]
for name in filenames: for name in filenames:
try: try: table = damask.ASCIItable(name = name,buffered = False)
table = damask.ASCIItable(name = name,buffered = False) except: continue
except:
continue
damask.util.report(scriptName,name) damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------ # ------------------------------------------ read header ------------------------------------------
@ -140,16 +134,16 @@ for name in filenames:
maxcorner = np.array(map(max,coords)) maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i') 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 = 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 size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 equal to smallest among other spacings
# ------------------------------------------ process value field ----------------------------------- # ------------------------------------------ process value field -----------------------------------
stack = [table.data] stack = [table.data]
for type, data in items.iteritems(): for type, data in items.iteritems():
for i,label in enumerate(data['active']): for i,label in enumerate(data['active']):
stack.append(divFFT(size[::-1], # we need to reverse order here, because x stack.append(divFFT(size[::-1], # we need to reverse order here, because x is fastest,ie rightmost, but leftmost in our x,y,z notation
table.data[:,data['column'][i]:data['column'][i]+data['dim']]. # is fastest,ie rightmost, but leftmost in table.data[:,data['column'][i]:data['column'][i]+data['dim']].
reshape([grid[2],grid[1],grid[0]]+data['shape']))) # our x,y,z notation reshape([grid[2],grid[1],grid[0]]+data['shape'])))
# ------------------------------------------ output result ----------------------------------------- # ------------------------------------------ output result -----------------------------------------
@ -158,4 +152,4 @@ for name in filenames:
# ------------------------------------------ output finalization ----------------------------------- # ------------------------------------------ output finalization -----------------------------------
table.close() # close input ASCII table (works for stdin) table.close() # close input ASCII table (works for stdin)