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
