def misorientationGrain(kocks, angs, frames, kor, gr_mis=False):
'''
It takes in the mesh, the grain number of interest, the angles output from
FePX and then the number of frames.
It outputs the misorientations angles calculated for that specific grain
by using the built in misorientation function within the ODFPF library.
Input: kocks - the kocks angle of the the grain being examined
grNum - an integer of the grain that you want to find the
misorientation for each element
angs - a numpy array 3xnxnframes of the angles output from FePX
frames - list of frames your interested in examining
Output: misAngs - a numpy array of nxframes that contains the angle of
misorientation for each element with respect to the
original orientation of the grain
misQuat - a numpy array of 4xnxnframes that contains the
misorientation quaternion for each element with respect to
the original orientation of the grain
'''
angs = np.atleast_3d(angs)
if angs.shape[0] == 1:
angs = angs.T
lenQuat = angs.shape[1]
deg = 'degrees'
misAngs = np.zeros((lenQuat, len(frames)))
misQuat = np.zeros((4, lenQuat, len(frames)))
misQuat[0, :, :] = 1
if (gr_mis):
origQuat = rot.OrientConvert(kocks, 'rod', 'quat', deg, deg)
else:
origQuat = rot.OrientConvert(kocks, 'kocks', 'quat', deg, deg)
csym = rot.CubSymmetries()
j = 0
for i in frames:
if kor == 'axis' or kor == 'axisangle':
tQuat = rot.QuatOfAngleAxis(np.squeeze(angs[0, :, i]),
np.squeeze(angs[1:4, :, i]))
else:
tQuat = rot.OrientConvert(np.squeeze(angs[:, :, i]), kor, 'quat',
deg, deg)
misAngs[:, j], misQuat[:, :,
j] = rot.Misorientation(origQuat, tQuat, csym)
j += 1
return (misAngs, misQuat)
#A list holding our deformation stats for the discrete and lofem methods
deflist = []
ldeflist = []
#el_angs is a temporary variable that will hold the grain values that go into misoriD
el_angs = np.zeros((3,nel,nsteps))
#Our difference quats, lofem quaternion at nodes, lofem quaternion at the centroid of the element, and discrete method quats
diff_misQuats = np.zeros((4,nel,nsteps))
lQuats = np.zeros((4, npts, nsteps))
leQuats = np.zeros((4, nel, nsteps))
dQuats = np.zeros((4, nel, nsteps))
#Just converting from our inputted orientation data to quaternions
for j in range(nsteps):
el_angs[:,:,j] = fe.elem_fe_cen_val(ldata['angs'][:,indlog2,j], lcon2)
lQuats[:,:,j] = rot.QuatOfRod(np.squeeze(ldata['angs'][:,indlog2,j]))
leQuats[:,:,j] = rot.QuatOfRod(np.squeeze(el_angs[:,:,j]))
dQuats[:,:,j] = rot.OrientConvert(np.squeeze(data['angs'][:,indlog,j]), 'kocks', 'quat', 'degrees', 'radians')
#Here we're getting the misorientation angle and quaternion for our angles when taken with respect the original orientation
#for the lofem method
lemisAngs, lemisQuats = mis.misorientationGrain(mesh['kocks'][:,i-1], el_angs, frames, kor)
for j in range(nsteps):
#Getting misorientation between the lofem and disc elements
temp2, tempQ = mis.misorientationGrain(data['angs'][:,indlog, j], el_angs[:,:,j], [0], kor)
diff_misQuats[:,:,j] = np.squeeze(tempQ)
misoriD[indlog, j] = np.squeeze(temp2)
crd = np.squeeze(data['coord'][:,ucon, j])
#Getting strain data
epsVec = np.squeeze(ldata['strain'][:, indlog, j])
#Taking the strain data and putting it into the tensorial view
#FEpX saves strain data off as 11, 21, 31, 22, 32, 33 so we also have to do some other
