def LatticeViewer(lattice, atoms, isCartesian=True):
if not isCartesian:
atoms = atoms2cart(lattice, atoms)
lx, ly, lz = lattice
if doTranslate:
cx, cy, cz = 0.5 * (lx + ly + lz)
else:
cx, cy, cz = 0, 0, 0
o = array([-cx, -cy, -cz])
gray = (0.5, 0.5, 0.5)
red = (1, 0, 0)
lines = [
(tuple(o), tuple(o + lx), gray),
(tuple(o + lx), tuple(o + lx + ly), gray),
(tuple(o + lx + ly), tuple(o + ly), gray),
(tuple(o + ly), tuple(o), gray),
(tuple(o + lz), tuple(o + lx + lz), gray),
(tuple(o + lx + lz), tuple(o + lx + ly + lz), gray),
(tuple(o + lx + ly + lz), tuple(o + ly + lz), gray),
(tuple(o + ly + lz), tuple(o + lz), gray),
(tuple(o), tuple(o + lz), gray),
(tuple(o + lx), tuple(o + lx + lz), gray),
(tuple(o + lx + ly), tuple(o + lx + ly + lz), gray),
(tuple(o + ly), tuple(o + ly + lz), gray),
]
spheres = []
for sym, pos in atoms:
x, y, z = pos
x, y, z = x - cx, y - cy, z - cz
spheres.append(((x, y, z), 0.3, red, 20, 20))
cyls = []
bs = BSWindow(spheres, cyls, lines)
bs.run()
return
from Pistol.Util import distance
from Pistol.XYZ import read
for filename in sys.argv[1:]:
geos = read(filename,do_center=1)
geo = geos[-1]
spheres = []
for atno,(x,y,z) in geo:
r,g,b = color[atno]
rad = radius[atno]
rad *= 0.25
r /= 255.
g /= 255.
b /= 255.
spheres.append(((x,y,z),rad,(r,g,b),20,20))
cyls = []
nat = len(geo)
for i in range(nat):
atno1,(x1,y1,z1) = geo[i]
for j in range(i):
atno2,(x2,y2,z2) = geo[j]
r12 = distance((x1,y1,z1),(x2,y2,z2))
r12o = 0.6*(radius[atno1]+radius[atno2])
if 0.3 < r12 < r12o:
cyls.append(((x1,y1,z1),(x2,y2,z2),0.15,20,(0.5,0.5,0.5)))
bs = BSWindow(spheres,cyls)
bs.run()