def dodecahedron(b,save=False,filename=None): # http://en.wikipedia.org/wiki/Dodecahedron#Regular_dodecahedron # b is the nearest-neighbor interatomic bond distance p = 1.61803398875 # golden ratio b = b * 0.5 * p coords = [[0,0,0]] coords.append([p,0,1./p]) coords.append([-p,0,1./p]) coords.append([-p,0,-1./p]) coords.append([p,0,-1./p]) coords.append([1./p, p, 0]) coords.append([1./p, -p, 0]) coords.append([-1./p, -p, 0]) coords.append([-1./p, p, 0]) coords.append([0, 1./p, p]) coords.append([0, 1./p, -p]) coords.append([0, -1./p, -p]) coords.append([0, -1./p, p]) coords.append([1,1,1]) coords.append([1,-1,1]) coords.append([-1,-1,1]) coords.append([-1,1,1]) coords.append([-1,1,-1]) coords.append([1,1,-1]) coords.append([1,-1,-1]) coords.append([-1,-1,-1]) coords = [ [b*x for x in c] for c in coords] m = 0 for coord in coords: for x in coord: if(abs(x) > m): m = abs(x) atoms = [Atom(i,14,c[0],c[1],c[2]) for i,c in enumerate(coords)] model = Model(comment='dodecahedron', xsize=m, ysize=m, zsize=m, atoms=atoms) if(save): model.write_real_xyz(model.filename) if(filename == None): filename = 'dodecahedron.xyz' else: model.filename = filename #f = open(filename,'w') #f.write(str(len(coords))+'\n') #f.write('{0} {0} {0} comment\n'.format(m)) #for c in coords: # f.write('Si ' + ' '.join([str(x) for x in c]) + '\n') #f.close() return model
def icosahedron(b,save=False,filename=None): # http://en.wikipedia.org/wiki/Regular_icosahedron # b is the nearest-neighbor interatomic bond distance b = b * sqrt(2)* 1.113516364 / 1.84375 coords = [atom.coord for atom in dodecahedron(b).atoms] vertices = range(1,21) faces = [ [15, 2, 12, 16, 9], [11, 19, 10, 4, 18], [6, 7, 14, 15, 12], [10, 18, 17, 5, 8], [9, 16, 13, 8, 5], [7, 6, 20, 19, 11], [5, 1, 13, 4, 18], [4, 19, 6, 14, 1], [1, 9, 13, 12, 14], [2, 3, 20, 7, 15], [2, 16, 8, 17, 3], [3, 20, 11, 10, 17]] face_coords = [(0,0,0)] for f in faces: center = (sum(coords[i][0] for i in f)/5., sum(coords[i][1] for i in f)/5., sum(coords[i][2] for i in f)/5.) face_coords.append(center) m = 0 for coord in face_coords: for x in coord: if(abs(x) > m): m = abs(x) atoms = [Atom(i,14,c[0],c[1],c[2]) for i,c in enumerate(face_coords)] model = Model(comment='icosahedron', xsize=m, ysize=m, zsize=m, atoms=atoms) if(save): model.write_real_xyz(model.filename) if(filename == None): filename = 'icosahedron.xyz' else: model.filename = filename #f = open(filename,'w') #f.write(str(len(face_coords))+'\n') #f.write('{0} {0} {0} comment\n'.format(m)) #for c in face_coords: # f.write('Si ' + ' '.join([str(x) for x in c]) + '\n') #f.close() return model