handling two issues: 1- enforces low index axis in tilt/symmtilts 2- handles... (4a41879a) · Commits · 郑智淋 / GB_code

gb_code/csl_generator.py

+37 −14

Original line number	Diff line number	Diff line
		@@ -157,6 +157,24 @@ 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))
		a = np.array(a)
		for i in range(3):
		for j in range(1, 2000):
		testV = j * a[i]
		if integer_array(testV):
		b[i] = testV
		break
		if all(b[i] == 0):
		Found = False
		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.
		@@ -419,8 +437,13 @@ def Find_Orthogonal_cell(basis, uvw, m, n, GB1):
		Min_1, Min_2 = Create_minimal_cell_Method_1(Sigma, uvw, R)
		# Find Ortho vectors:
		tol = 0.001
		Found = False
		if ang(OrthoCell_1[:, 0], uvw) < tol:
		OrthoCell_1[:, 1] = uvw
		OrthoCell_2[:, 1] = uvw
		else:

		for i in range(len(indice_0)):

		v1 = (indice_0[i, 0] * Min_1[:, 0] +
		indice_0[i, 1] * Min_1[:, 1] +
		indice_0[i, 2] * Min_1[:, 2])
		@@ -430,7 +453,6 @@ def Find_Orthogonal_cell(basis, uvw, m, n, GB1):
		if ang(v1, OrthoCell_1[:, 0]) < tol:
		OrthoCell_1[:, 1] = v1
		OrthoCell_2[:, 1] = v2
		Found = True
		break
		OrthoCell_1[:, 2] = np.cross(OrthoCell_1[:, 0], OrthoCell_1[:, 1])
		OrthoCell_2[:, 2] = np.cross(OrthoCell_2[:, 0], OrthoCell_2[:, 1])
		@@ -452,6 +474,7 @@ def Find_Orthogonal_cell(basis, uvw, m, n, GB1):
		OrthoCell_2 = OrthoCell_2.astype(float)

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

		return ((OrthoCell_1.astype(float),
		OrthoCell_2.astype(float), Num.astype(int)))

+2 −1

Original line number	Diff line number	Diff line
		@@ -174,13 +174,14 @@ class GB_character:
		populates a unitcell from the orthogonal vectors.
		"""
		Or = self.ortho.T
		Orint = cslgen.integerMatrix(Or)
		LoopBound = np.zeros((3, 2), dtype=float)
		transformed = []
		CubeCoords = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1], [1, 1, 0],
		[0, 1, 1], [1, 0, 1], [1, 1, 1], [0, 0, 0]],
		dtype=float)
		for i in range(len(CubeCoords)):
		transformed.append(np.dot(Or.T, CubeCoords[i]))
		transformed.append(np.dot(Orint.T, CubeCoords[i]))

		# Finding bounds for atoms in a CSL unitcell: