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Fix calculation of interfaceEnergy

This commit is contained in:
Brendan Robert Vande Kieft 2016-09-15 17:36:43 -04:00
parent 3b0b677dc9
commit 1180c8bb88
1 changed files with 7 additions and 2 deletions
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9
processing/pre/geom_grainGrowth.py
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@ -81,17 +81,20 @@ for name in filenames:
periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]/2:-grid[0]/2, periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]/2:-grid[0]/2,
grid[1]/2:-grid[1]/2, grid[1]/2:-grid[1]/2,
grid[2]/2:-grid[2]/2] # periodically extend the microstructure grid[2]/2:-grid[2]/2] # periodically extend the microstructure
# store a copy the initial microstructure to find locations of immutable indices # store a copy the initial microstructure to find locations of immutable indices
microstructure_original = np.copy(microstructure) microstructure_original = np.copy(microstructure)
X,Y,Z = np.mgrid[0:grid[0],0:grid[1],0:grid[2]] X,Y,Z = np.mgrid[0:grid[0],0:grid[1],0:grid[2]]
# Calculates gaussian weights for simulating 3d diffusion
gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d))/math.pow(2.0*np.pi*options.d*options.d,1.5) gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d))/math.pow(2.0*np.pi*options.d*options.d,1.5)
gauss[:,:,grid[2]/2::] = gauss[:,:,round(grid[2]/2.)-1::-1] # trying to cope with uneven (odd) grid size gauss[:,:,grid[2]/2::] = gauss[:,:,round(grid[2]/2.)-1::-1] # trying to cope with uneven (odd) grid size
gauss[:,grid[1]/2::,:] = gauss[:,round(grid[1]/2.)-1::-1,:] gauss[:,grid[1]/2::,:] = gauss[:,round(grid[1]/2.)-1::-1,:]
gauss[grid[0]/2::,:,:] = gauss[round(grid[0]/2.)-1::-1,:,:] gauss[grid[0]/2::,:,:] = gauss[round(grid[0]/2.)-1::-1,:,:]
gauss = np.fft.rfftn(gauss) gauss = np.fft.rfftn(gauss)
interfacialEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0 interfacialEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0 #1.0 if A & B are distinct & nonzero, 0.0 otherwise
struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
@ -101,9 +104,11 @@ for name in filenames:
for j in (-1,0,1): for j in (-1,0,1):
for k in (-1,0,1): for k in (-1,0,1):
# assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood) # assign interfacial energy to all voxels that have a differing neighbor (in Moore neighborhood)
interfaceEnergy = np.maximum(boundary, boundary = np.maximum(boundary,
interfacialEnergy(microstructure,np.roll(np.roll(np.roll( interfacialEnergy(microstructure,np.roll(np.roll(np.roll(
microstructure,i,axis=0), j,axis=1), k,axis=2))) microstructure,i,axis=0), j,axis=1), k,axis=2)))
interfaceEnergy = boundary
# periodically extend interfacial energy array by half a grid size in positive and negative directions # periodically extend interfacial energy array by half a grid size in positive and negative directions
periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]/2:-grid[0]/2, periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]/2:-grid[0]/2,
grid[1]/2:-grid[1]/2, grid[1]/2:-grid[1]/2,