major changes in WriteGB, modifying Jupyter notebooks. (0fdc075d) · Commits · 郑智淋 / GB_code

.ipynb_checkpoints/Usage_of_GB_code-checkpoint.ipynb

0 → 100644

+1465 −0

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Usage_of_GB_code.ipynb

+140 −136

File changed.

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gb_generator.py

+46 −21

Original line number	Diff line number	Diff line
		@@ -77,13 +77,22 @@ class GB_character:

		def WriteGB(self, *args):

		if len(args) == 8:
		self.overD = float(args[0])
		if self.overD > 0:
		self.whichG = str(args[1])
		self.trans = args[2]
		if self.trans:
		if len(args) != 8:
		print('Make sure the input arguments are right!')
		sys.exit()
		a = int(args[3])
		b = int(args[4])
		self.dim = np.array([int(args[5]), int(args[6]), int(args[7])])
		else:
		if len(args) != 6:
		print('Make sure the input arguments are right!')
		sys.exit()
		self.dim = np.array([int(args[3]), int(args[4]), int(args[5])])
		xdel, ydel, x_indice, y_indice = self.Find_overlapping_Atoms()
		print ("<<------ {} atoms are being removed! ------>>"
		.format(len(xdel)))
		@@ -106,24 +115,34 @@ class GB_character:

		if not self.trans:
		count = 0
		print ("<<------ 1 GB structure is being created! ------>>")
		self.Write_to_Lammps(count)
		elif self.trans:
		self.Translate(a, b)

		elif len(args) == 6:

		self.trans = (args[0])
		a = int(args[1])
		b = int(args[2])
		self.dim = np.array([int(args[3]), int(args[4]), int(args[5])])
		elif self.overD == 0:
		self.trans = args[1]
		if self.trans:
		if len(args) != 7:
		print('Make sure the input arguments are right!')
		sys.exit()
		print ("<<------ 0 atoms are being removed! ------>>")
		a = int(args[2])
		b = int(args[3])
		self.dim = np.array([int(args[4]), int(args[5]), int(args[6])])
		self.Expand_Super_cell()

		if not self.trans:
		self.Translate(a, b)
		else:
		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])])
		count = 0
		print ("<<------ 1 GB structure is being created! ------>>")
		self.Write_to_Lammps(count)
		elif self.trans:

		self.Translate(a, b)
		else:
		print('Overlap distance is not inputted correctly!')
		sys.exit()

		def CSL_Ortho_unitcell_atom_generator(self):

		@@ -376,11 +395,17 @@ def main():
		gbI.ParseGB(axis, basis, LatP, m, n, gbplane)
		gbI.CSL_Bicrystal_Atom_generator()

		if overlap > 0:
		if overlap > 0 and rigid:
		gbI.WriteGB(overlap, whichG, rigid, a, b, dim1, dim2, dim3)

		elif overlap == 0:
		gbI.WriteGB(rigid, a, b, dim1, dim2, dim3)
		elif overlap > 0 and not rigid:
		gbI.WriteGB(overlap, whichG, rigid, dim1, dim2, dim3)

		elif overlap == 0 and rigid:
		gbI.WriteGB(overlap, rigid, a, b, dim1, dim2, dim3)

		elif overlap == 0 and not rigid:
		gbI.WriteGB(overlap, rigid, dim1, dim2, dim3)

		else:
		print(Usage)

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