changes to docstrings and notebooks. (3a16ecb7) · Commits · 郑智淋 / GB_code

Dichromatic_pattern_CSL_.ipynb

+1 −0

Original line number	Diff line number	Diff line
		@@ -51,6 +51,7 @@
		}
		],
		"source": [
		"# for example: [1, 0, 0], [1, 1, 0] or [1, 1, 1]\n",
		"axis = np.array([1,1,1])\n",
		"\n",
		"# list Sigma boundaries < 50\n",

Usage_of_GB_code.ipynb

+13 −11

File changed.

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csl_generator.py

+25 −5

Original line number	Diff line number	Diff line
		@@ -106,7 +106,7 @@ def rot(a, Theta):

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

		@@ -118,6 +118,9 @@ def angv(a, b):
		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)

		@@ -291,6 +294,9 @@ def Create_minimal_cell_Method_1(sigma, uvw, R):


		def MiniCell_search(indices, MiniCell_1, R, sigma):
		"""
		a numerical search for the minimal cell.
		"""

		tol = 0.001
		# norm1 = norm(indices, axis=1)
		@@ -452,6 +458,9 @@ def print_list_GB_Planes(uvw, basis, m, n, lim=3):
		# DSC and CSL lattices for bcc and fcc were made from the Sc lattice
		# via body_centering and face_centering:
		def odd_even(M1):
		"""
		finds odd and even elements of a matrix.
		"""
		d_e = np.array([['a', 'a', 'a'],
		['a', 'a', 'a'],
		['a', 'a', 'a']], dtype=str)
		@@ -504,6 +513,9 @@ def tertiary_test_b(a):


		def body_centering(b):
		"""
		converting a single crystal minimal cell to a bcc one.
		"""
		z_b = np.eye(3, 3)
		while det(z_b) != 0.5:
		if det(self_test_b(b)) == 0.5:
		@@ -519,6 +531,9 @@ def body_centering(b):


		def face_centering(a):
		"""
		converting a single crystal minimal cell to an fcc one.
		"""
		z_f = np.eye(3, 3)
		M = a.copy()
		count = 0
		@@ -547,7 +562,8 @@ def face_centering(a):

		def DSC_vec(basis, sigma, minicell):
		"""
		a DSC network for the given sigma and minimal cell.
		a discrete shift complete (DSC)
		network for the given sigma and minimal cell.
		"""
		D_sc = np.round(sigma * (inv(minicell).T), 6).astype(int)
		if basis == 'sc':
		@@ -560,7 +576,7 @@ def DSC_vec(basis, sigma, minicell):

		def CSL_vec(basis, minicell):
		"""
		your CSL cell for sc, fcc and bcc.
		CSL minimal cell for sc, fcc and bcc.
		"""
		C_sc = minicell.copy()
		if basis == 'sc':
		@@ -573,7 +589,7 @@ def CSL_vec(basis, minicell):

		def DSC_on_plane(D, Pnormal):
		"""
		projects the given DSC network on the given plane.
		projects the given DSC network on a given plane.
		"""
		D_proj = np.zeros((3, 3))
		Pnormal = np.array(Pnormal)
		@@ -585,7 +601,7 @@ def DSC_on_plane(D, Pnormal):

		def CSL_density(basis, minicell, plane):
		"""
		returns the CSL density of the given plane and its d_spacing.
		returns the CSL density of a given plane and its d_spacing.
		"""
		plane = np.array(plane)
		C = CSL_vec(basis, minicell)
		@@ -617,6 +633,10 @@ def Ortho_fcc_bcc(basis, O1, O2):

		# 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',
		'overlap_distance': '0.3', 'which_g': 'g1',

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