def from_abc(klass, a, b, c, alpha, beta, gamma):
""" Create 3 vectors from six parameters
"""
sin_gamma = sin(gamma)
cos_gamma = cos(gamma)
tan_gamma = tan(gamma)
cos_beta = cos(beta)
cos_alpha = cos(alpha)
v1 = Vec(a, 0, 0)
v2 = Vec(b * cos_gamma, b * sin_gamma, 0)
v3 = Vec(
c * cos_beta, -(c * cos_beta / tan_gamma) + c * cos_alpha / sin_gamma,
sqrt(c**2 - (c * cos_beta)**2 -
(-(c * cos_beta / tan_gamma) + c * cos_alpha / sin_gamma)**2))
return Reper(v1, v2, v3)
def __init__( self, *args, **kargs ):
if len( args ) == 6:
a,b,c, alpha, beta, gamma = args
if kargs.get( 'indeg', False ):
self.rep = Reper.from_abc( a,b,c, alpha * math.pi / 180.0, beta * math.pi / 180.0, gamma * math.pi / 180.0 )
else:
self.rep = Reper.from_abc( a,b,c, alpha, beta, gamma )
elif len( args ) == 9:
self.rep = Reper( Vec( *args[0:3] ), Vec( *args[3:6] ), Vec( *args[6:9] ) )
else:
assert type( args[ 0 ] ) is Reper
self.rep = args[ 0 ]
self.atoms = {}
self.decart = kargs.get( 'decart', False ) ## by default assume that all coordinates of atoms in fractional coordinates
def norm(self):
""" Reduce & make all zelling args negative.
"""
vs = [self.v1, self.v2, self.v3, (self.v1 + self.v2 + self.v3) * -1]
f = True
while f:
f = False
for i, v1 in enumerate(vs):
for j, v2 in enumerate(vs):
if i != j and v1 * v2 > 0.0001:
for k in xrange(4):
if k != i and k != j:
vs[k] += v1 ## add v1 to all, except v1 and v2
vs[i] *= -1 ## v1 --> -v1
v1 *= -1 ## also correct cycle var
f = True
return Reper(vs[0], vs[1], vs[2])
def minimize(self):
""" Reduce reper to 3 minimal vector.
"""
vs = [self.v1, self.v2, self.v3]
f = True
while f:
f = False
vts = [t for t in vs]
abc = ( (i,j,k) for i in xrange( -1, 2 )\
for j in xrange( -1, 2 )\
for k in xrange( -1, 2 ) )
for a, b, c in abc:
vnew = a * vs[0] + b * vs[1] + c * vs[2]
for i, v in enumerate(vts):
if v.vlen2() > vnew.vlen2():
vo, vts[i] = vts[i], vnew
if abs(vts[0] * vts[1].vcross(vts[2])) > 0.0001:
f = True
else:
vts[i] = vo
#print vs, vts, f
vs = vts
return Reper(*vs)
