changes to gb scripts (8bf3a491) · Commits · 郑智淋 / GB_code

csl_generator.py

+0 −22

Original line number	Diff line number	Diff line
		@@ -5,21 +5,13 @@ This module is a collection of functions that produce CSL properties.
		When run from the terminal, the code runs in two modes.

		First mode:
		<<<<<<< HEAD
		'python CSLgenerator.py axis(u v w) [limit]' -----> Where the u v w are the
		=======
		'python CSLgenerator.py u v w [limit]' -----> Where the u v w are the
		>>>>>>> development
		indices of the rotation axis such as 1 0 0, 1 1 1, 1 1 0 and so on. The limit
		is the maximum Sigma of interest.
		(the limit by default: 100)

		Second mode:
		<<<<<<< HEAD
		'python CSLgenerator.py axis(u v w) basis sigma [limit]' -----> Where basis is
		=======
		'python CSLgenerator.py u v w basis sigma [limit]' -----> Where basis is
		>>>>>>> development
		either fcc, bcc, diamond or sc. You read the sigma of interest from the first
		mode run. The limit here refers to CSL GB inclinations. The bigger the limit,
		the higher the indices of CSL planes.
		@@ -134,11 +126,7 @@ def ang(a, b):

		def CommonDivisor(a):
		"""
		<<<<<<< HEAD
		returns the reduced vector and the common factor of vector a.
		=======
		returns the common factor of vector a and the reduced vector.
		>>>>>>> development
		"""
		CommFac = []
		a = np.array(a)
		@@ -212,13 +200,8 @@ def Tilt_Twist_comp(v1, uvw, m, n):
		twist = 2 * acos(cos(theta / 2) / cos(radians(tilt / 2)))
		print("Tilt component: {0:<6.2f} Twist component: {1:6.2f}"
		.format(tilt, twist))
		<<<<<<< HEAD


		=======


		>>>>>>> development
		def Create_Possible_GB_Plane_List(uvw, m=5, n=1, lim=5):
		"""
		generate GB planes and specifies the character.
		@@ -666,13 +649,8 @@ def Write_to_io(axis, m, n, basis):
		f.write('# CSL plane of interest that you read from the output of '
		'csl_generator as GB1 \n')
		f.write(list(my_dict.keys())[0] + ': ' + list(my_dict.values())[0] +
		<<<<<<< HEAD
		'\n')
		f.write('# lattice parameter in Angstrom \n \n')
		=======
		'\n\n')
		f.write('# lattice parameter in Angstrom \n')
		>>>>>>> development
		f.write(list(my_dict.keys())[1] + ': ' + list(my_dict.values())[1] +
		'\n\n')
		f.write('# atoms that are closer than this fraction of the lattice '

gb_generator.py

+0 −22

Original line number	Diff line number	Diff line
		@@ -83,13 +83,6 @@ class GB_character:
		print("Sorry! For now only works for cubic lattices ... ")
		sys.exit()

		<<<<<<< HEAD
		def WriteGB(self, *args):
		"""
		parses the arguments and writes the final structure to the file.
		"""
		self.overD = float(args[0])
		=======
		def WriteGB(self, overlap=0.0, rigid=False,
		dim1=1, dim2=1, dim3=1, file='LAMMPS',
		**kwargs):
		@@ -102,7 +95,6 @@ class GB_character:
		self.trans = rigid
		self.dim = np.array([int(dim1), int(dim2), int(dim3)])
		self.File = file
		>>>>>>> development
		if self.overD > 0:
		try:
		self.whichG = kwargs['whichG']
		@@ -160,13 +152,6 @@ class GB_character:
		self.Translate(a, b)

		else:
		<<<<<<< HEAD
		if len(args) != 5:
		print('Make sure the input arguments are right!')
		sys.exit()
		self.dim = np.array([int(args[2]), int(args[3]), int(args[4])])
		=======
		>>>>>>> development
		self.Expand_Super_cell()
		count = 0
		print ("<<------ 1 GB structure is being created! ------>>")
		@@ -315,12 +300,8 @@ class GB_character:
		def Translate(self, a, b ):

		"""
		<<<<<<< HEAD
		translates the GB on a mesh created by a, b integers and writes to LAMMPS.
		=======
		translates the GB on a mesh created by a, b integers and writes
		to LAMMPS or VASP.
		>>>>>>> development
		"""
		tol = 0.001
		if (1 - cslgen.ang(self.gbplane, self.axis) < tol):
		@@ -373,8 +354,6 @@ class GB_character:
		else:
		print("The output file must be either LAMMPS or VASP!")

		<<<<<<< HEAD
		=======
		def Write_to_Vasp(self, trans):
		"""
		write a single GB without translations to POSCAR.
		@@ -416,7 +395,6 @@ class GB_character:
		np.savetxt(f, Wf, fmt='%.8f %.8f %.8f')
		f.close()

		>>>>>>> development
		def Write_to_Lammps(self, trans):
		"""
		write a single GB without translations to LAMMPS.

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