Loading .gitignore +1 −3 Original line number Diff line number Diff line test .idea GB_* input* __pycache__ .vscode log.file io_file Draft_code.py .ipynb* Readme Loading gb_generator.py 0 → 100644 +391 −0 Original line number Diff line number Diff line #!/usr/bin/env python import sys import numpy as np from numpy import dot, cross from numpy.linalg import det, norm import csl_generator as cslgen Usage = """ The code runs in one mode only and takes all necessary options to write a final GB structure from the input io_file, which is written after you run csl_generator.py. Add the GB_plane of interest from the CS planes list (GB1) after running csl_generator.py in second mode. "python gb_generator.py io_file" """ class GB_character: def __init__(self): self.axis = np.array([1, 0, 0]) self.sigma = 1 self.theta = 0 self.m = 1 self.n = 1 self.R = np.eye(1) self.basis = 'fcc' self.LatP = 4.05 self.gbplane = np.array([1, 1, 1]) self.ortho1 = np.eye(3) self.ortho2 = np.eye(3) self.ortho = np.eye(3) self.atoms = np.eye(3) self.atoms1 = np.eye(3) self.atoms2 = np.eye(3) self.rot1 = np.eye(3) self.rot2 = np.eye(3) self.Num = 0 self.dim = np.array([1, 1, 1]) self.overD = 0 self.whichG = 'g1' self.trans = False def ParseGB(self, axis, basis, LatP, m, n, gb): self.axis = np.array(axis) self.m = int(m) self.n = int(n) self.sigma = cslgen.get_cubic_sigma(self.axis, self.m, self.n) self.theta = cslgen.get_cubic_theta(self.axis, self.m, self.n) self.R = cslgen.rot(self.axis, self.theta) if (str(basis) == 'fcc' or str(basis) == 'bcc' or str(basis) == 'sc' or str(basis) == 'diamond'): self.basis = str(basis) self.LatP = float(LatP) self.gbplane = np.array(gb) try: self.ortho1, self.ortho2, self.Num = cslgen.Find_Orthogonal_cell( self.basis, self.axis, self.m, self.n, self.gbplane) except: print(""" Could not find the orthogonal cells.... Most likely the input GB_plane is "NOT" a CSL plane. Go back to the first script and double check! """) sys.exit() else: print("Sorry! For now only works for cubic lattices ... ") sys.exit() def WriteGB(self, *args): if len(args) == 8: self.overD = float(args[0]) self.whichG = str(args[1]) self.trans = args[2] a = int(args[3]) b = int(args[4]) self.dim = np.array([int(args[5]), int(args[6]), int(args[7])]) xdel, ydel, x_indice, y_indice = self.Find_overlapping_Atoms() print ("<<------ {} atoms are being removed! ------>>" .format(len(xdel))) if self.whichG == "G1" or self.whichG == "g1": self.atoms1 = np.delete(self.atoms1, x_indice, axis=0) xdel[:, 0] = xdel[:, 0] + norm(self.ortho1[:, 0]) self.atoms1 = np.vstack((self.atoms1, xdel)) elif self.whichG == "G2" or self.whichG == "g2": self.atoms2 = np.delete(self.atoms2, y_indice, axis=0) ydel[:, 0] = ydel[:, 0] - norm(self.ortho1[:, 0]) self.atoms2 = np.vstack((self.atoms2, ydel)) else: print("You must choose either 'g1', 'g2' ") sys.exit() self.Expand_Super_cell() if not self.trans: count = 0 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])]) self.Expand_Super_cell() if not self.trans: count = 0 self.Write_to_Lammps(count) elif self.trans: self.Translate(a, b) def CSL_Ortho_unitcell_atom_generator(self): # The fastest way of building unitcells: Or = self.ortho.T 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])) # Finding bounds for atoms in a CSL unitcell: LoopBound[0, :] = [min(np.array(transformed)[:, 0]), max(np.array(transformed)[:, 0])] LoopBound[1, :] = [min(np.array(transformed)[:, 1]), max(np.array(transformed)[:, 1])] LoopBound[2, :] = [min(np.array(transformed)[:, 2]), max(np.array(transformed)[:, 2])] # Filling up the unitcell: Tol = 1 x = np.arange(LoopBound[0, 0] - Tol, LoopBound[0, 1] + Tol + 1, 1) y = np.arange(LoopBound[1, 0] - Tol, LoopBound[1, 1] + Tol + 1, 1) z = np.arange(LoopBound[2, 0] - Tol, LoopBound[2, 1] + Tol + 1, 1) V = len(x) * len(y) * len(z) indice = (np.stack(np.meshgrid(x, y, z)).T).reshape(V, 3) Base = cslgen.Basis(str(self.basis)) Atoms = [] tol = 0.001 # produce Atoms: for i in range(V): for j in range(len(Base)): Atoms.append(indice[i, 0:3] + Base[j, 0:3]) Atoms = np.array(Atoms) # Cell conditions Con1 = dot(Atoms, Or[0]) / norm(Or[0]) + tol Con2 = dot(Atoms, Or[1]) / norm(Or[1]) + tol Con3 = dot(Atoms, Or[2]) / norm(Or[2]) + tol # Application of the conditions: Atoms = (Atoms[(Con1 >= 0) & (Con1 <= norm(Or[0])) & (Con2 >= 0) & (Con2 <= norm(Or[1])) & (Con3 >= 0) & (Con3 <= norm(Or[2]))]) if len(Atoms) == (round(det(Or) * len(Base), 7)).astype(int): self.Atoms = Atoms else: self.Atoms = None return def CSL_Bicrystal_Atom_generator(self): Or_1 = self.ortho1.T Or_2 = self.ortho2.T self.rot1 = np.array([Or_1[0, :] / norm(Or_1[0, :]), Or_1[1, :] / norm(Or_1[1, :]), Or_1[2, :] / norm(Or_1[2, :])]) self.rot2 = np.array([Or_2[0, :] / norm(Or_2[0, :]), Or_2[1, :] / norm(Or_2[1, :]), Or_2[2, :] / norm(Or_2[2, :])]) self.ortho = self.ortho1.copy() self.CSL_Ortho_unitcell_atom_generator() self.atoms1 = self.Atoms self.ortho = self.ortho2.copy() self.CSL_Ortho_unitcell_atom_generator() self.atoms2 = self.Atoms self.atoms1 = dot(self.rot1, self.atoms1.T).T self.atoms2 = dot(self.rot2, self.atoms2.T).T self.atoms2[:, 0] = self.atoms2[:, 0] - norm(Or_2[0, :]) # print(self.atoms2, norm(Or_2[0, :]) ) return def Expand_Super_cell(self): a = norm(self.ortho1[:, 0]) b = norm(self.ortho1[:, 1]) c = norm(self.ortho1[:, 2]) dimX, dimY, dimZ = self.dim X = self.atoms1.copy() Y = self.atoms2.copy() X_new = [] Y_new = [] for i in range(dimX): for j in range(dimY): for k in range(dimZ): Position1 = [i * a, j * b, k * c] Position2 = [-i * a, j * b, k * c] for l in range(len(X)): X_new.append(Position1[0:3] + X[l, 0:3]) for m in range(len(Y)): Y_new.append(Position2[0:3] + Y[m, 0:3]) self.atoms1 = np.array(X_new) self.atoms2 = np.array(Y_new) return def Find_overlapping_Atoms(self): IndX = np.where([self.atoms1[:, 0] < 1])[1] IndY = np.where([self.atoms2[:, 0] > -1])[1] X_new = self.atoms1[self.atoms1[:, 0] < 1] Y_new = self.atoms2[self.atoms2[:, 0] > -1] x = np.arange(0, len(X_new), 1) y = np.arange(0, len(Y_new), 1) indice = (np.stack(np.meshgrid(x, y)).T).reshape(len(x) * len(y), 2) norms = norm(X_new[indice[:, 0]] - Y_new[indice[:, 1]], axis=1) indice_x = indice[norms < self.overD][:, 0] indice_y = indice[norms < self.overD][:, 1] X_del = X_new[indice_x] Y_del = Y_new[indice_y] return (X_del, Y_del, IndX[indice_x], IndY[indice_y]) def Translate(self, a, b): tol = 0.001 if (1 - cslgen.ang(self.gbplane, self.axis) < tol): M1, M2 = cslgen.Create_minimal_cell_Method_1( self.sigma, self.axis, self.R) D = (1 / self.sigma * cslgen.DSC_vec(self.basis, self.sigma, M1)) Dvecs = cslgen.DSC_on_plane(D, self.gbplane) TransDvecs = np.round(dot(self.rot1, Dvecs), 7) shift1 = TransDvecs[:, 0] / 2 shift2 = TransDvecs[:, 1] / 2 a = b = 3 else: #a = 10 #b = 5 if norm(self.ortho1[:, 1]) > norm(self.ortho1[:, 2]): shift1 = (1 / a) * (norm(self.ortho1[:, 1]) * np.array([0, 1, 0])) shift2 = (1 / b) * (norm(self.ortho1[:, 2]) * np.array([0, 0, 1])) else: shift1 = (1 / a) * (norm(self.ortho1[:, 2]) * np.array([0, 0, 1])) shift2 = (1 / b) * (norm(self.ortho1[:, 1]) * np.array([0, 1, 0])) print("<<------ {} GB structures are being created! ------>>" .format(int(a*b))) XX = self.atoms1 count = 0 for i in range(a): for j in range(b): count += 1 shift = i * shift1 + j * shift2 atoms1_new = XX.copy() + shift self.atoms1 = atoms1_new self.Write_to_Lammps(count) def Write_to_Lammps(self, trans): name = 'input_G' plane = str(self.gbplane[0])+str(self.gbplane[1])+str(self.gbplane[2]) if self.overD > 0: overD = str(self.overD) else: overD = str(None) Trans = str(trans) # tol = 0.001 X = self.atoms1.copy() Y = self.atoms2.copy() NumberAt = len(X) + len(Y) X_new = X * self.LatP Y_new = Y * self.LatP dimx, dimy, dimz = self.dim xlo = -1 * np.round(norm(self.ortho1[:, 0]) * dimx * self.LatP, 8) xhi = np.round(norm(self.ortho1[:, 0]) * dimx * self.LatP, 8) ylo = 0.0 yhi = np.round(norm(self.ortho1[:, 1]) * dimy * self.LatP, 8) zlo = 0.0 zhi = np.round(norm(self.ortho1[:, 2]) * dimz * self.LatP, 8) Type1 = np.ones(len(X_new), int).reshape(1, -1) Type2 = 2 * np.ones(len(Y_new), int).reshape(1, -1) # Type = np.concatenate((Type1, Type2), axis=1) Counter = np.arange(1, NumberAt + 1).reshape(1, -1) # data = np.concatenate((X_new, Y_new)) W1 = np.concatenate((Type1.T, X_new), axis=1) W2 = np.concatenate((Type2.T, Y_new), axis=1) Wf = np.concatenate((W1, W2)) FinalMat = np.concatenate((Counter.T, Wf), axis=1) with open(name + plane + '_' + overD + '_' +Trans, 'w') as f: f.write('#Header \n \n') f.write('{} atoms \n \n'.format(NumberAt)) f.write('2 atom types \n \n') f.write('{0:.8f} {1:.8f} xlo xhi \n'.format(xlo, xhi)) f.write('{0:.8f} {1:.8f} ylo yhi \n'.format(ylo, yhi)) f.write('{0:.8f} {1:.8f} zlo zhi \n\n'.format(zlo, zhi)) f.write('Atoms \n \n') np.savetxt(f, FinalMat, fmt='%i %i %.8f %.8f %.8f') f.close() def __str__(self): return "GB_character" def main(): import yaml if len(sys.argv) == 2: io_file = sys.argv[1] file = open(io_file, 'r') in_params = yaml.load(file) try: axis = np.array(in_params['axis']) m = int(in_params['m']) n = int(in_params['n']) basis = str(in_params['basis']) gbplane = np.array(in_params['GB_plane']) LatP = in_params['lattice_parameter'] overlap = in_params['overlap_distance'] whichG = in_params['which_g'] rigid = in_params['rigid_trans'] a = in_params['a'] b = in_params['b'] dim1, dim2, dim3 = in_params['dimensions'] except: print('Make sure the input argumnets in io_file are' 'put in correctly!') sys.exit() ################### gbI = GB_character() gbI.ParseGB(axis, basis, LatP, m, n, gbplane) gbI.CSL_Bicrystal_Atom_generator() if overlap > 0: gbI.WriteGB(overlap, whichG, rigid, a, b, dim1, dim2, dim3) elif overlap == 0: gbI.WriteGB(rigid, a, b, dim1, dim2, dim3) else: print(Usage) return if __name__ == '__main__': main() Loading
.gitignore +1 −3 Original line number Diff line number Diff line test .idea GB_* input* __pycache__ .vscode log.file io_file Draft_code.py .ipynb* Readme Loading
gb_generator.py 0 → 100644 +391 −0 Original line number Diff line number Diff line #!/usr/bin/env python import sys import numpy as np from numpy import dot, cross from numpy.linalg import det, norm import csl_generator as cslgen Usage = """ The code runs in one mode only and takes all necessary options to write a final GB structure from the input io_file, which is written after you run csl_generator.py. Add the GB_plane of interest from the CS planes list (GB1) after running csl_generator.py in second mode. "python gb_generator.py io_file" """ class GB_character: def __init__(self): self.axis = np.array([1, 0, 0]) self.sigma = 1 self.theta = 0 self.m = 1 self.n = 1 self.R = np.eye(1) self.basis = 'fcc' self.LatP = 4.05 self.gbplane = np.array([1, 1, 1]) self.ortho1 = np.eye(3) self.ortho2 = np.eye(3) self.ortho = np.eye(3) self.atoms = np.eye(3) self.atoms1 = np.eye(3) self.atoms2 = np.eye(3) self.rot1 = np.eye(3) self.rot2 = np.eye(3) self.Num = 0 self.dim = np.array([1, 1, 1]) self.overD = 0 self.whichG = 'g1' self.trans = False def ParseGB(self, axis, basis, LatP, m, n, gb): self.axis = np.array(axis) self.m = int(m) self.n = int(n) self.sigma = cslgen.get_cubic_sigma(self.axis, self.m, self.n) self.theta = cslgen.get_cubic_theta(self.axis, self.m, self.n) self.R = cslgen.rot(self.axis, self.theta) if (str(basis) == 'fcc' or str(basis) == 'bcc' or str(basis) == 'sc' or str(basis) == 'diamond'): self.basis = str(basis) self.LatP = float(LatP) self.gbplane = np.array(gb) try: self.ortho1, self.ortho2, self.Num = cslgen.Find_Orthogonal_cell( self.basis, self.axis, self.m, self.n, self.gbplane) except: print(""" Could not find the orthogonal cells.... Most likely the input GB_plane is "NOT" a CSL plane. Go back to the first script and double check! """) sys.exit() else: print("Sorry! For now only works for cubic lattices ... ") sys.exit() def WriteGB(self, *args): if len(args) == 8: self.overD = float(args[0]) self.whichG = str(args[1]) self.trans = args[2] a = int(args[3]) b = int(args[4]) self.dim = np.array([int(args[5]), int(args[6]), int(args[7])]) xdel, ydel, x_indice, y_indice = self.Find_overlapping_Atoms() print ("<<------ {} atoms are being removed! ------>>" .format(len(xdel))) if self.whichG == "G1" or self.whichG == "g1": self.atoms1 = np.delete(self.atoms1, x_indice, axis=0) xdel[:, 0] = xdel[:, 0] + norm(self.ortho1[:, 0]) self.atoms1 = np.vstack((self.atoms1, xdel)) elif self.whichG == "G2" or self.whichG == "g2": self.atoms2 = np.delete(self.atoms2, y_indice, axis=0) ydel[:, 0] = ydel[:, 0] - norm(self.ortho1[:, 0]) self.atoms2 = np.vstack((self.atoms2, ydel)) else: print("You must choose either 'g1', 'g2' ") sys.exit() self.Expand_Super_cell() if not self.trans: count = 0 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])]) self.Expand_Super_cell() if not self.trans: count = 0 self.Write_to_Lammps(count) elif self.trans: self.Translate(a, b) def CSL_Ortho_unitcell_atom_generator(self): # The fastest way of building unitcells: Or = self.ortho.T 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])) # Finding bounds for atoms in a CSL unitcell: LoopBound[0, :] = [min(np.array(transformed)[:, 0]), max(np.array(transformed)[:, 0])] LoopBound[1, :] = [min(np.array(transformed)[:, 1]), max(np.array(transformed)[:, 1])] LoopBound[2, :] = [min(np.array(transformed)[:, 2]), max(np.array(transformed)[:, 2])] # Filling up the unitcell: Tol = 1 x = np.arange(LoopBound[0, 0] - Tol, LoopBound[0, 1] + Tol + 1, 1) y = np.arange(LoopBound[1, 0] - Tol, LoopBound[1, 1] + Tol + 1, 1) z = np.arange(LoopBound[2, 0] - Tol, LoopBound[2, 1] + Tol + 1, 1) V = len(x) * len(y) * len(z) indice = (np.stack(np.meshgrid(x, y, z)).T).reshape(V, 3) Base = cslgen.Basis(str(self.basis)) Atoms = [] tol = 0.001 # produce Atoms: for i in range(V): for j in range(len(Base)): Atoms.append(indice[i, 0:3] + Base[j, 0:3]) Atoms = np.array(Atoms) # Cell conditions Con1 = dot(Atoms, Or[0]) / norm(Or[0]) + tol Con2 = dot(Atoms, Or[1]) / norm(Or[1]) + tol Con3 = dot(Atoms, Or[2]) / norm(Or[2]) + tol # Application of the conditions: Atoms = (Atoms[(Con1 >= 0) & (Con1 <= norm(Or[0])) & (Con2 >= 0) & (Con2 <= norm(Or[1])) & (Con3 >= 0) & (Con3 <= norm(Or[2]))]) if len(Atoms) == (round(det(Or) * len(Base), 7)).astype(int): self.Atoms = Atoms else: self.Atoms = None return def CSL_Bicrystal_Atom_generator(self): Or_1 = self.ortho1.T Or_2 = self.ortho2.T self.rot1 = np.array([Or_1[0, :] / norm(Or_1[0, :]), Or_1[1, :] / norm(Or_1[1, :]), Or_1[2, :] / norm(Or_1[2, :])]) self.rot2 = np.array([Or_2[0, :] / norm(Or_2[0, :]), Or_2[1, :] / norm(Or_2[1, :]), Or_2[2, :] / norm(Or_2[2, :])]) self.ortho = self.ortho1.copy() self.CSL_Ortho_unitcell_atom_generator() self.atoms1 = self.Atoms self.ortho = self.ortho2.copy() self.CSL_Ortho_unitcell_atom_generator() self.atoms2 = self.Atoms self.atoms1 = dot(self.rot1, self.atoms1.T).T self.atoms2 = dot(self.rot2, self.atoms2.T).T self.atoms2[:, 0] = self.atoms2[:, 0] - norm(Or_2[0, :]) # print(self.atoms2, norm(Or_2[0, :]) ) return def Expand_Super_cell(self): a = norm(self.ortho1[:, 0]) b = norm(self.ortho1[:, 1]) c = norm(self.ortho1[:, 2]) dimX, dimY, dimZ = self.dim X = self.atoms1.copy() Y = self.atoms2.copy() X_new = [] Y_new = [] for i in range(dimX): for j in range(dimY): for k in range(dimZ): Position1 = [i * a, j * b, k * c] Position2 = [-i * a, j * b, k * c] for l in range(len(X)): X_new.append(Position1[0:3] + X[l, 0:3]) for m in range(len(Y)): Y_new.append(Position2[0:3] + Y[m, 0:3]) self.atoms1 = np.array(X_new) self.atoms2 = np.array(Y_new) return def Find_overlapping_Atoms(self): IndX = np.where([self.atoms1[:, 0] < 1])[1] IndY = np.where([self.atoms2[:, 0] > -1])[1] X_new = self.atoms1[self.atoms1[:, 0] < 1] Y_new = self.atoms2[self.atoms2[:, 0] > -1] x = np.arange(0, len(X_new), 1) y = np.arange(0, len(Y_new), 1) indice = (np.stack(np.meshgrid(x, y)).T).reshape(len(x) * len(y), 2) norms = norm(X_new[indice[:, 0]] - Y_new[indice[:, 1]], axis=1) indice_x = indice[norms < self.overD][:, 0] indice_y = indice[norms < self.overD][:, 1] X_del = X_new[indice_x] Y_del = Y_new[indice_y] return (X_del, Y_del, IndX[indice_x], IndY[indice_y]) def Translate(self, a, b): tol = 0.001 if (1 - cslgen.ang(self.gbplane, self.axis) < tol): M1, M2 = cslgen.Create_minimal_cell_Method_1( self.sigma, self.axis, self.R) D = (1 / self.sigma * cslgen.DSC_vec(self.basis, self.sigma, M1)) Dvecs = cslgen.DSC_on_plane(D, self.gbplane) TransDvecs = np.round(dot(self.rot1, Dvecs), 7) shift1 = TransDvecs[:, 0] / 2 shift2 = TransDvecs[:, 1] / 2 a = b = 3 else: #a = 10 #b = 5 if norm(self.ortho1[:, 1]) > norm(self.ortho1[:, 2]): shift1 = (1 / a) * (norm(self.ortho1[:, 1]) * np.array([0, 1, 0])) shift2 = (1 / b) * (norm(self.ortho1[:, 2]) * np.array([0, 0, 1])) else: shift1 = (1 / a) * (norm(self.ortho1[:, 2]) * np.array([0, 0, 1])) shift2 = (1 / b) * (norm(self.ortho1[:, 1]) * np.array([0, 1, 0])) print("<<------ {} GB structures are being created! ------>>" .format(int(a*b))) XX = self.atoms1 count = 0 for i in range(a): for j in range(b): count += 1 shift = i * shift1 + j * shift2 atoms1_new = XX.copy() + shift self.atoms1 = atoms1_new self.Write_to_Lammps(count) def Write_to_Lammps(self, trans): name = 'input_G' plane = str(self.gbplane[0])+str(self.gbplane[1])+str(self.gbplane[2]) if self.overD > 0: overD = str(self.overD) else: overD = str(None) Trans = str(trans) # tol = 0.001 X = self.atoms1.copy() Y = self.atoms2.copy() NumberAt = len(X) + len(Y) X_new = X * self.LatP Y_new = Y * self.LatP dimx, dimy, dimz = self.dim xlo = -1 * np.round(norm(self.ortho1[:, 0]) * dimx * self.LatP, 8) xhi = np.round(norm(self.ortho1[:, 0]) * dimx * self.LatP, 8) ylo = 0.0 yhi = np.round(norm(self.ortho1[:, 1]) * dimy * self.LatP, 8) zlo = 0.0 zhi = np.round(norm(self.ortho1[:, 2]) * dimz * self.LatP, 8) Type1 = np.ones(len(X_new), int).reshape(1, -1) Type2 = 2 * np.ones(len(Y_new), int).reshape(1, -1) # Type = np.concatenate((Type1, Type2), axis=1) Counter = np.arange(1, NumberAt + 1).reshape(1, -1) # data = np.concatenate((X_new, Y_new)) W1 = np.concatenate((Type1.T, X_new), axis=1) W2 = np.concatenate((Type2.T, Y_new), axis=1) Wf = np.concatenate((W1, W2)) FinalMat = np.concatenate((Counter.T, Wf), axis=1) with open(name + plane + '_' + overD + '_' +Trans, 'w') as f: f.write('#Header \n \n') f.write('{} atoms \n \n'.format(NumberAt)) f.write('2 atom types \n \n') f.write('{0:.8f} {1:.8f} xlo xhi \n'.format(xlo, xhi)) f.write('{0:.8f} {1:.8f} ylo yhi \n'.format(ylo, yhi)) f.write('{0:.8f} {1:.8f} zlo zhi \n\n'.format(zlo, zhi)) f.write('Atoms \n \n') np.savetxt(f, FinalMat, fmt='%i %i %.8f %.8f %.8f') f.close() def __str__(self): return "GB_character" def main(): import yaml if len(sys.argv) == 2: io_file = sys.argv[1] file = open(io_file, 'r') in_params = yaml.load(file) try: axis = np.array(in_params['axis']) m = int(in_params['m']) n = int(in_params['n']) basis = str(in_params['basis']) gbplane = np.array(in_params['GB_plane']) LatP = in_params['lattice_parameter'] overlap = in_params['overlap_distance'] whichG = in_params['which_g'] rigid = in_params['rigid_trans'] a = in_params['a'] b = in_params['b'] dim1, dim2, dim3 = in_params['dimensions'] except: print('Make sure the input argumnets in io_file are' 'put in correctly!') sys.exit() ################### gbI = GB_character() gbI.ParseGB(axis, basis, LatP, m, n, gbplane) gbI.CSL_Bicrystal_Atom_generator() if overlap > 0: gbI.WriteGB(overlap, whichG, rigid, a, b, dim1, dim2, dim3) elif overlap == 0: gbI.WriteGB(rigid, a, b, dim1, dim2, dim3) else: print(Usage) return if __name__ == '__main__': main()
