def surfscreen(structure, MI_lib, r=5):
MI_List = []
for site in structure:
nearbysites = structure.get_neighbors(site, r)
perm = combinations(nearbysites, 2)
for two_sites in perm:
three_coords = [site.coords]
for X in two_sites:
three_coords.append(X[0].coords)
MI = miller_index_from_sites(structure.lattice.matrix,
three_coords)
if any(np.abs(MI) > 4):
continue
if np.isnan(MI).any():
continue
MI_rounded = np.round(MI)
if npl.norm(MI_rounded - MI) > 0.01:
continue
MI_List.append(MI_rounded)
PlotDict = {}
for index in MI_List:
for key in MI_lib.keys():
if any((index == x).all() for x in MI_lib[key]):
if key not in PlotDict.keys():
PlotDict[key] = 0
PlotDict[key] += 1
print(index, MI_lib[key])
import matplotlib.pyplot as plt
plt.bar(PlotDict.keys(), PlotDict.values(), color='g')
plt.show()
def test_miller_index_from_sites(self):
"""Test surface miller index convenience function"""
# test on a cubic system
m = Lattice.cubic(1)
s1 = np.array([0.5, -1.5, 3])
s2 = np.array([0.5, 3.0, -1.5])
s3 = np.array([2.5, 1.5, -4.0])
self.assertEqual(miller_index_from_sites(m, [s1, s2, s3]), (2, 1, 1))
# test casting from matrix to Lattice
m = [[2.319, -4.01662582, 0.0], [2.319, 4.01662582, 0.0], [0.0, 0.0, 7.252]]
s1 = np.array([2.319, 1.33887527, 6.3455])
s2 = np.array([1.1595, 0.66943764, 4.5325])
s3 = np.array([1.1595, 0.66943764, 0.9065])
hkl = miller_index_from_sites(m, [s1, s2, s3])
self.assertEqual(hkl, (2, -1, 0))
def test_miller_index_from_sites(self):
"""Test surface miller index convenience function"""
# test on a cubic system
m = Lattice.cubic(1)
s1 = np.array([0.5, -1.5, 3])
s2 = np.array([0.5, 3., -1.5])
s3 = np.array([2.5, 1.5, -4.])
self.assertEqual(miller_index_from_sites(m, [s1, s2, s3]),
(2, 1, 1))
# test casting from matrix to Lattice
m = [[2.319, -4.01662582, 0.], [2.319, 4.01662582, 0.], [0., 0., 7.252]]
s1 = np.array([2.319, 1.33887527, 6.3455])
s2 = np.array([1.1595, 0.66943764, 4.5325])
s3 = np.array([1.1595, 0.66943764, 0.9065])
hkl = miller_index_from_sites(m, [s1, s2, s3])
self.assertEqual(hkl, (2, -1, 0))
def test_miller_index_from_sites(self):
# test on a cubic system
m = Lattice.cubic(1).matrix
s1 = np.array([0.5, -1.5, 3])
s2 = np.array([0.5, 3.,-1.5])
s3 = np.array([2.5, 1.5,-4.])
self.assertEqual(tuple(miller_index_from_sites(m, [s1, s2, s3])),
(-2,-1,-1))
# test on a hexagonal system
m = np.array([[2.319, -4.01662582, 0.],
[2.319, 4.01662582, 0.],
[0., 0., 7.252]])
s1 = np.array([2.319, 1.33887527, 6.3455])
s2 = np.array([1.1595, 0.66943764, 4.5325])
s3 = np.array([1.1595, 0.66943764, 0.9065])
hkl = [np.round(i, 6) for i in miller_index_from_sites(m, [s1, s2, s3])]
self.assertEqual(tuple(hkl), (2, -1, 0))
def test_miller_index_from_sites(self):
# test on a cubic system
m = Lattice.cubic(1).matrix
s1 = np.array([0.5, -1.5, 3])
s2 = np.array([0.5, 3.,-1.5])
s3 = np.array([2.5, 1.5,-4.])
self.assertEqual(tuple(miller_index_from_sites(m, [s1, s2, s3])),
(-2,-1,-1))
# test on a hexagonal system
m = np.array([[2.319, -4.01662582, 0.],
[2.319, 4.01662582, 0.],
[0., 0., 7.252]])
s1 = np.array([2.319, 1.33887527, 6.3455])
s2 = np.array([1.1595, 0.66943764, 4.5325])
s3 = np.array([1.1595, 0.66943764, 0.9065])
hkl = [np.round(i, 6) for i in miller_index_from_sites(m, [s1, s2, s3])]
self.assertEqual(tuple(hkl), (2, -1, 0))