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DAMASK_EICMD
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now assuming periodic microstructures (was not fully correct before, assuming non-periodicity)

This commit is contained in:
Martin Diehl 2014-04-01 16:43:39 +00:00
parent 436fa63912
commit c254f87814
1 changed files with 26 additions and 21 deletions
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47
processing/pre/geom_grainGrowth.py
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@ -154,46 +154,51 @@ for file in files:
i += s i += s
#--- reshape, if 2D make copy --------------------------------------------------------------------- #--- reshape, if 2D make copy ---------------------------------------------------------------------
nMicrostuctures = numpy.prod([2 if i == 1 else i for i in info['grid']]) expandedGrid = numpy.array([2 if i == 1 else i for i in info['grid']],'i')
nMicrostuctures = numpy.prod(expandedGrid)
if nMicrostuctures > info['grid'].prod(): if nMicrostuctures > info['grid'].prod():
microstructure[info['grid'].prod():nMicrostuctures] = microstructure[0:info['grid'].prod()] microstructure[info['grid'].prod():nMicrostuctures] = microstructure[0:info['grid'].prod()]
microstructure = microstructure.reshape([2 if i == 1 else i for i in info['grid']],order='F') microstructure = microstructure.reshape([2 if i == 1 else i for i in info['grid']],order='F')
grid = numpy.array([2 if i == 1 else i for i in info['grid']],'i')
#--- domain decomposition -------------------------------------------------------------------------
stride = numpy.array([2 if i == 1 else i for i in info['grid']],'i')
if numpy.any(numpy.floor(stride) != stride):
file['croak'].write('invalid domain decomposition.\n')
continue
#--- initialize helper data ----------------------------------------------------------------------- #--- initialize helper data -----------------------------------------------------------------------
window = 0 X,Y,Z = numpy.mgrid[0:expandedGrid[0],0:expandedGrid[1],0:expandedGrid[2]]
X,Y,Z = numpy.mgrid[0:stride[0]+2*window,0:stride[1]+2*window,0:stride[2]+2*window]
gauss = numpy.exp(-(X*X+Y*Y+Z*Z)/(2.0*options.d*options.d))/math.pow(2.0*numpy.pi*options.d*options.d,1.5) gauss = numpy.exp(-(X*X+Y*Y+Z*Z)/(2.0*options.d*options.d))/math.pow(2.0*numpy.pi*options.d*options.d,1.5)
gauss[:,:,(stride[2]+2*window)/2::] = gauss[:,:,(stride[2]+2*window)/2-1::-1] gauss[:,:,(expandedGrid[2])/2::] = gauss[:,:,(expandedGrid[2])/2-1::-1]
gauss[:,(stride[1]+2*window)/2::,:] = gauss[:,(stride[1]+2*window)/2-1::-1,:] gauss[:,(expandedGrid[1])/2::,:] = gauss[:,(expandedGrid[1])/2-1::-1,:]
gauss[(stride[0]+2*window)/2::,:,:] = gauss[(stride[0]+2*window)/2-1::-1,:,:] gauss[(expandedGrid[0])/2::,:,:] = gauss[(expandedGrid[0])/2-1::-1,:,:]
gauss = numpy.fft.rfftn(gauss) gauss = numpy.fft.rfftn(gauss)
interfacialEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0
struc = ndimage.generate_binary_structure(3,1)
for smoothIter in xrange(options.N): for smoothIter in xrange(options.N):
interfacialEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0
struc = ndimage.generate_binary_structure(3,1)
microExt = numpy.zeros([microstructure.shape[0]+2,microstructure.shape[1]+2,microstructure.shape[2]+2])
microExt[1:-1,1:-1,1:-1] = microstructure
boundary = numpy.zeros(microstructure.shape) boundary = numpy.zeros(microstructure.shape)
for i in range(3): for i in range(3):
for j in range(3): for j in range(3):
for k in range(3): for k in range(3):
boundary = numpy.maximum(boundary, boundary = numpy.maximum(boundary,
interfacialEnergy(microstructure,microExt[i:microstructure.shape[0]+i, interfacialEnergy(microstructure,numpy.roll(numpy.roll(numpy.roll(
j:microstructure.shape[1]+j, microstructure,i-1,axis=0),j-1,axis=1),k-1,axis=2)))
k:microstructure.shape[2]+k]))
index = ndimage.morphology.distance_transform_edt(boundary == 0.,return_distances = False,return_indices = True) index = ndimage.morphology.distance_transform_edt(boundary == 0.,return_distances = False,return_indices = True)
boundary = numpy.fft.irfftn(numpy.fft.rfftn(numpy.where(ndimage.morphology.binary_dilation(boundary != 0., boundary = numpy.fft.irfftn(numpy.fft.rfftn(numpy.where(ndimage.morphology.binary_dilation(boundary != 0.,
structure = struc, structure = struc,
iterations = 2*options.d-1), iterations = 2*options.d-1),
boundary[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(microstructure.shape), boundary[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(microstructure.shape),
0.))*gauss) 0.))*gauss)
index = ndimage.morphology.distance_transform_edt(boundary >= 0.5,return_distances=False,return_indices=True) boundaryExt = numpy.tile(boundary,(3,3,3))
microstructure = microstructure[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(microstructure.shape) boundaryExt = boundaryExt[(expandedGrid[0])/2:-(expandedGrid[0])/2,
(expandedGrid[1])/2:-(expandedGrid[1])/2,
(expandedGrid[2])/2:-(expandedGrid[2])/2]
microstructureExt = numpy.tile(microstructure,(3,3,3))
microstructureExt = microstructureExt[(expandedGrid[0])/2:-(expandedGrid[0])/2,
(expandedGrid[1])/2:-(expandedGrid[1])/2,
(expandedGrid[2])/2:-(expandedGrid[2])/2]
index = ndimage.morphology.distance_transform_edt(boundaryExt >= 0.5,return_distances=False,return_indices=True)
microstructureExt = microstructureExt[index[0].flatten(),index[1].flatten(),index[2].flatten()].reshape(microstructureExt.shape)
microstructure = microstructureExt[(expandedGrid[0])/2:-(expandedGrid[0])/2,
(expandedGrid[1])/2:-(expandedGrid[1])/2,
(expandedGrid[2])/2:-(expandedGrid[2])/2]
# --- renumber to sequence 1...Ngrains if requested ------------------------------------------------ # --- renumber to sequence 1...Ngrains if requested ------------------------------------------------
# http://stackoverflow.com/questions/10741346/numpy-frequency-counts-for-unique-values-in-an-array # http://stackoverflow.com/questions/10741346/numpy-frequency-counts-for-unique-values-in-an-array