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fixing bug in Find_overlapping_atoms + some pep8 modifications
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@oekosheri
oekosheri committed Aug 8, 2019
1 parent 4a41879 commit b1fca9b
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Showing 2 changed files with 95 additions and 66 deletions.
63 changes: 38 additions & 25 deletions gb_code/csl_generator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,8 @@

def get_cubic_sigma(uvw, m, n=1):
"""
CSL analytical formula based on the book: 'Interfaces in crystalline materials',
CSL analytical formula based on the book:
'Interfaces in crystalline materials',
Sutton and Balluffi, clarendon press, 1996.
generates possible sigma values.
arguments:
Expand Down Expand Up @@ -81,17 +82,19 @@ def get_theta_m_n_list(uvw, sigma):
thetas.sort(key=lambda x: x[0])
return thetas


def print_list(uvw, limit):
"""
prints a list of smallest sigmas/angles for a given axis(uvw).
"""
for i in range(limit):
tt = get_theta_m_n_list(uvw, i)
if len(tt) > 0:
theta, m, n = tt[0]
theta, _, _ = tt[0]
print("Sigma: {0:3d} Theta: {1:5.2f} "
.format(i, degrees(theta)))


def rot(a, Theta):
"""
produces a rotation matrix.
Expand All @@ -112,28 +115,31 @@ def rot(a, Theta):


# Helpful Functions:
#-------------------#
# -------------------#

def integer_array(A, tol=1e-7):
"""
returns True if an array is ineteger.
"""
return np.all(abs(np.round(A) - A) < tol)


def angv(a, b):
"""
returns the angle between two vectors.
"""
ang = acos(np.round(dot(a, b)/norm(a)/norm(b), 8))
return round(degrees(ang), 7)


def ang(a, b):
"""
returns the cos(angle) between two vectors.
"""
ang = np.round(dot(a, b)/norm(a)/norm(b), 7)
return abs(ang)


def CommonDivisor(a):
"""
returns the common factor of vector a and the reduced vector.
Expand All @@ -146,6 +152,7 @@ def CommonDivisor(a):
CommFac.append(i)
return(a.astype(int), (abs(np.prod(CommFac))))


def SmallestInteger(a):
"""
returns the smallest multiple integer to make an integer array.
Expand All @@ -157,12 +164,13 @@ def SmallestInteger(a):
break
return (testV, i) if integer_array(testV) else None


def integerMatrix(a):
"""
returns an integer matrix from row vectors.
"""
Found = True
b = np.zeros((3,3))
b = np.zeros((3, 3))
a = np.array(a)
for i in range(3):
for j in range(1, 2000):
Expand All @@ -175,6 +183,7 @@ def integerMatrix(a):
print("Can not make integer matrix!")
return (b) if Found else None


def SymmEquivalent(arr):
"""
returns cubic symmetric eqivalents of the given 2 dimensional vector.
Expand Down Expand Up @@ -213,6 +222,7 @@ def SymmEquivalent(arr):
Result = np.array(Result)
return np.unique(Result, axis=0)


def Tilt_Twist_comp(v1, uvw, m, n):
"""
returns the tilt and twist components of a given GB plane.
Expand Down Expand Up @@ -270,7 +280,7 @@ def Create_Possible_GB_Plane_List(uvw, m=5, n=1, lim=5):
[1, 1, 0],
[0, 1, 1],
[1, 0, 1],
], dtype='float')
], dtype='float')
# Find GB plane coordinates:
for i in range(len(indice_0)):
if CommonDivisor(indice_0[i])[1] <= 1:
Expand Down Expand Up @@ -302,6 +312,7 @@ def Create_Possible_GB_Plane_List(uvw, m=5, n=1, lim=5):

return (V1, V2, MeanPlanes, GBtype)


def Create_minimal_cell_Method_1(sigma, uvw, R):
"""
finds Minimal cell by means of a numerical search.
Expand Down Expand Up @@ -376,6 +387,7 @@ def MiniCell_search(indices, MiniCell_1, R, sigma):
else:
return Found


def Basis(basis):
"""
defines the basis.
Expand Down Expand Up @@ -407,6 +419,7 @@ def Basis(basis):

return basis


def Find_Orthogonal_cell(basis, uvw, m, n, GB1):
"""
finds Orthogonal cells from the CSL minimal cells.
Expand Down Expand Up @@ -473,7 +486,7 @@ def Find_Orthogonal_cell(basis, uvw, m, n, GB1):
OrthoCell_1 = OrthoCell_1.astype(float)
OrthoCell_2 = OrthoCell_2.astype(float)

if basis == 'sc' or basis == 'diamond' :
if basis == 'sc' or basis == 'diamond':

return ((OrthoCell_1.astype(float),
OrthoCell_2.astype(float), Num.astype(int)))
Expand All @@ -487,17 +500,18 @@ def Find_Orthogonal_cell(basis, uvw, m, n, GB1):
else:
return None


def print_list_GB_Planes(uvw, basis, m, n, lim=3):
"""
prints lists of GB planes given an axis, basis, m and n.
"""
uvw = np.array(uvw)
V1, V2, Mean, Type = Create_Possible_GB_Plane_List(uvw, m, n, lim)
V1, V2, _, Type = Create_Possible_GB_Plane_List(uvw, m, n, lim)
for i in range(len(V1)):
Or = Find_Orthogonal_cell(basis, uvw, m, n, V1[i])
if Or:
print ("{0:<20s} {1:<20s} {2:<20s} {3:<10s}"
.format(str(V1[i]), str(V2[i]), Type[i], str(Or[2])))
print("{0:<20s} {1:<20s} {2:<20s} {3:<10s}"
.format(str(V1[i]), str(V2[i]), Type[i], str(Or[2])))


# ___CSL/DSC vector construction___#
Expand Down Expand Up @@ -608,6 +622,7 @@ def face_centering(a):

return z_f if det(z_f) == 0.25 else None


def DSC_vec(basis, sigma, minicell):
"""
a discrete shift complete (DSC)
Expand All @@ -626,6 +641,7 @@ def DSC_vec(basis, sigma, minicell):
D = dot(D_sc, face_centering(D_sc))
return D


def CSL_vec(basis, minicell):
"""
CSL minimal cell for sc, fcc and bcc.
Expand All @@ -642,6 +658,7 @@ def CSL_vec(basis, minicell):
C = dot(C_sc, face_centering(C_sc))
return C


def DSC_on_plane(D, Pnormal):
"""
projects the given DSC network on a given plane.
Expand All @@ -668,8 +685,10 @@ def CSL_density(basis, minicell, plane):
density = 1/(hnorm * det(C))
return (abs(density), 1/hnorm)

# An auxilary function to help reduce the size of the small orthogonal cell that
# is decided otherwise based on Sc for fcc and bcc
# An auxilary function to help reduce the size of the small orthogonal cell
# that is decided otherwise based on Sc for fcc and bcc


def Ortho_fcc_bcc(basis, O1, O2):
ortho1 = np.zeros((3, 3))
ortho2 = np.zeros((3, 3))
Expand All @@ -685,15 +704,17 @@ def Ortho_fcc_bcc(basis, O1, O2):
ortho1[:, i] = O1[:, i] / Min_d
ortho2[:, i] = O2[:, i] / Min_d
return (ortho1, ortho2)

# Writing to a yaml file that will be read by gb_generator


def Write_to_io(axis, m, n, basis):
"""
an input file for gb_generator.py that can be customized.
It also contains the output from the usage of csl_generator.py.
"""

my_dict = {'GB_plane': str([axis[0], axis[1], axis[2]]), 'lattice_parameter': '4',
my_dict = {'GB_plane': str([axis[0], axis[1], axis[2]]),
'lattice_parameter': '4',
'overlap_distance': '0.0', 'which_g': 'g1',
'rigid_trans': 'no', 'a': '10', 'b': '5',
'dimensions': '[1,1,1]',
Expand Down Expand Up @@ -743,8 +764,8 @@ def Write_to_io(axis, m, n, basis):
f.write('# File type, either VASP or LAMMPS input \n')
f.write(list(my_dict.keys())[8] + ': ' + list(my_dict.values())[8] +
'\n\n\n')
f.write('# The following is your csl_generator output. YOU DO NOT NEED '
'TO CHANGE THEM! \n\n')
f.write('# The following is your csl_generator output.'
' YOU DO NOT NEED TO CHANGE THEM! \n\n')
f.write('axis'+': ' + str([axis[0], axis[1], axis[2]]) + '\n')
f.write('m' + ': ' + str(m) + '\n')
f.write('n' + ': ' + str(n) + '\n')
Expand All @@ -763,7 +784,6 @@ def main():
uvw = np.array([int(sys.argv[1]), int(sys.argv[2]), int(sys.argv[3])])
uvw = CommonDivisor(uvw)[0]


if len(sys.argv) == 4:
limit = 100
print(" List of possible CSLs for {} axis sorted by Sigma "
Expand Down Expand Up @@ -792,7 +812,7 @@ def main():
sigma = int(sys.argv[5])

try:
t, m, n = get_theta_m_n_list(uvw, sigma)[0]
_, m, n = get_theta_m_n_list(uvw, sigma)[0]
Write_to_io(uvw, m, n, basis)

print("----------List of possible CSL planes for Sigma {}---------"
Expand All @@ -814,7 +834,7 @@ def main():

try:

t, m, n = get_theta_m_n_list(uvw, sigma)[0]
_, m, n = get_theta_m_n_list(uvw, sigma)[0]
lim = int(sys.argv[6])

if lim > 10:
Expand All @@ -839,10 +859,3 @@ def main():

if __name__ == '__main__':
main()







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