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DAMASK_EICMD
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Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development

This commit is contained in:
Martin Diehl 2016-06-29 12:39:14 +02:00
parent b759a79f9a 2c8427eb2a
commit fbf67de37a
6 changed files with 42 additions and 44 deletions
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2
VERSION
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@ -1 +1 @@
v2.0.0-292-g2ebc5ec
v2.0.0-297-ga27aba1

8
processing/post/addCalculation.py
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@ -74,7 +74,7 @@ for name in filenames:
}
# ------------------------------------------ Evaluate condition ---------------------------------------
if options.condition:
if options.condition is not None:
interpolator = []
condition = options.condition # copy per file, since might be altered inline
breaker = False
@ -89,7 +89,7 @@ for name in filenames:
try:
interpolator += ['%s(table.data[%i])'%({ '':'float',
's#':'str'}[operand[1]],
table.label_index(operand[2]))] # ccould be generalized to indexrange as array lookup
table.label_index(operand[2]))] # could be generalized to indexrange as array lookup
except:
damask.util.croak('column "{}" not found.'.format(operand[2]))
breaker = True
@ -98,8 +98,6 @@ for name in filenames:
evaluator_condition = "'" + condition + "'.format(" + ','.join(interpolator) + ")"
else: condition = ''
# ------------------------------------------ build formulae ----------------------------------------
evaluator = {}
@ -168,7 +166,7 @@ for name in filenames:
Nold = max(1,len(oldIndices)) # Nold could be zero for new columns
Nnew = len(output.label_indexrange(label))
output.data_append(eval(evaluator[label]) if label in options.labels and
(condition == '' or eval(eval(evaluator_condition)))
(options.condition is None or eval(eval(evaluator_condition)))
else np.tile([table.data[i] for i in oldIndices]
if label in tabLabels
else np.nan,

6
processing/post/addCurl.py
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@ -18,7 +18,7 @@ def curlFFT(geomdim,field):
if n == 3: dataType = 'vector'
elif n == 9: dataType = 'tensor'
field_fourier = np.fft.fftpack.rfftn(field,axes=(0,1,2),s=shapeFFT)
field_fourier = np.fft.rfftn(field,axes=(0,1,2),s=shapeFFT)
curl_fourier = np.empty(field_fourier.shape,'c16')
# differentiation in Fourier space
@ -56,7 +56,7 @@ def curlFFT(geomdim,field):
curl_fourier[i,j,k,2] = ( field_fourier[i,j,k,1]*xi[0]\
-field_fourier[i,j,k,0]*xi[1]) *TWOPIIMG
return np.fft.fftpack.irfftn(curl_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,n])
return np.fft.irfftn(curl_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,n])
# --------------------------------------------------------------------
@ -158,7 +158,7 @@ for name in filenames:
# we need to reverse order here, because x is fastest,ie rightmost, but leftmost in our x,y,z notation
stack.append(curlFFT(size[::-1],
table.data[:,data['column'][i]:data['column'][i]+data['dim']].
reshape([grid[2],grid[1],grid[0]]+data['shape'])))
reshape(grid[::-1].tolist()+data['shape'])))
# ------------------------------------------ output result -----------------------------------------

32
processing/post/addDisplacement.py
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@ -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
@ -35,14 +35,14 @@ def cell2node(cellData,grid):
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"""
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),
x, y, z = np.meshgrid(np.linspace(0,size[2],grid[2],endpoint=False),
np.linspace(0,size[1],grid[1],endpoint=False),
np.linspace(0,size[2],grid[2],endpoint=False),
np.linspace(0,size[0],grid[0],endpoint=False),
indexing = 'ij')
origCoords = np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
@ -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
@ -186,7 +186,7 @@ for name in filenames:
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...
displacement = displacementFluctFFT(F_fourier,grid,size,options.nodal,transformed=True)
fluctDisplacement = displacementFluctFFT(F_fourier,grid,size,options.nodal,transformed=True)
avgDisplacement = displacementAvgFFT (F_fourier,grid,size,options.nodal,transformed=True)
# ------------------------------------------ assemble header ---------------------------------------
@ -203,18 +203,18 @@ for name in filenames:
# ------------------------------------------ output data -------------------------------------------
zrange = np.linspace(0,size[2],1+grid[2]) if options.nodal else xrange(grid[2])
yrange = np.linspace(0,size[1],1+grid[1]) if options.nodal else xrange(grid[1])
xrange = np.linspace(0,size[0],1+grid[0]) if options.nodal else xrange(grid[0])
Zrange = np.linspace(0,size[2],1+grid[2]) if options.nodal else xrange(grid[2])
Yrange = np.linspace(0,size[1],1+grid[1]) if options.nodal else xrange(grid[1])
Xrange = np.linspace(0,size[0],1+grid[0]) if options.nodal else xrange(grid[0])
for i,z in enumerate(zrange):
for j,y in enumerate(yrange):
for k,x in enumerate(xrange):
for i,z in enumerate(Zrange):
for j,y in enumerate(Yrange):
for k,x in enumerate(Xrange):
if options.nodal: table.data_clear()
else: table.data_read()
table.data_append([x,y,z] if options.nodal else [])
table.data_append(list(avgDisplacement[i,j,k,:]))
table.data_append(list( displacement[i,j,k,:]))
table.data_append(list( avgDisplacement[i,j,k,:]))
table.data_append(list(fluctDisplacement[i,j,k,:]))
table.data_write()
# ------------------------------------------ output finalization -----------------------------------

6
processing/post/addDivergence.py
View File

@ -15,7 +15,7 @@ def divFFT(geomdim,field):
N = grid.prod() # field size
n = np.array(np.shape(field)[3:]).prod() # data size
field_fourier = np.fft.fftpack.rfftn(field,axes=(0,1,2),s=shapeFFT)
field_fourier = np.fft.rfftn(field,axes=(0,1,2),s=shapeFFT)
div_fourier = np.empty(field_fourier.shape[0:len(np.shape(field))-1],'c16') # size depents on whether tensor or vector
# differentiation in Fourier space
@ -42,7 +42,7 @@ def divFFT(geomdim,field):
elif n == 3: # vector, 3 -> 1
div_fourier[i,j,k] = sum(field_fourier[i,j,k,0:3]*xi) *TWOPIIMG
return np.fft.fftpack.irfftn(div_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,n/3])
return np.fft.irfftn(div_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,n/3])
# --------------------------------------------------------------------
@ -145,7 +145,7 @@ for name in filenames:
# we need to reverse order here, because x is fastest,ie rightmost, but leftmost in our x,y,z notation
stack.append(divFFT(size[::-1],
table.data[:,data['column'][i]:data['column'][i]+data['dim']].
reshape([grid[2],grid[1],grid[0]]+data['shape'])))
reshape(grid[::-1].tolist()+data['shape'])))
# ------------------------------------------ output result -----------------------------------------

6
processing/post/addGradient.py
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@ -18,7 +18,7 @@ def gradFFT(geomdim,field):
if n == 3: dataType = 'vector'
elif n == 1: dataType = 'scalar'
field_fourier = np.fft.fftpack.rfftn(field,axes=(0,1,2),s=shapeFFT)
field_fourier = np.fft.rfftn(field,axes=(0,1,2),s=shapeFFT)
grad_fourier = np.empty(field_fourier.shape+(3,),'c16')
# differentiation in Fourier space
@ -46,7 +46,7 @@ def gradFFT(geomdim,field):
grad_fourier[i,j,k,1,:] = field_fourier[i,j,k,1]*xi *TWOPIIMG # tensor field from vector data
grad_fourier[i,j,k,2,:] = field_fourier[i,j,k,2]*xi *TWOPIIMG
return np.fft.fftpack.irfftn(grad_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,3*n])
return np.fft.irfftn(grad_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,3*n])
# --------------------------------------------------------------------
@ -148,7 +148,7 @@ for name in filenames:
# we need to reverse order here, because x is fastest,ie rightmost, but leftmost in our x,y,z notation
stack.append(gradFFT(size[::-1],
table.data[:,data['column'][i]:data['column'][i]+data['dim']].
reshape([grid[2],grid[1],grid[0]]+data['shape'])))
reshape(grid[::-1].tolist()+data['shape'])))
# ------------------------------------------ output result -----------------------------------------