def water():
water = RigidFragment()
rho = 0.9572
theta = 104.52/180.0*pi
water.add_atom("O", np.array([0., 0., 0.]), 16.)
water.add_atom("H", rho*np.array([0.0, sin(0.5*theta), cos(0.5*theta)]), 1.)
water.add_atom("H", rho*np.array([0.0, -sin(0.5*theta), cos(0.5*theta)]), 1.)
water.finalize_setup()
return water
def water():
water = RigidFragment()
rho = 0.9572
theta = 104.52 / 180.0 * pi
water.add_atom("O", np.array([0., 0., 0.]), 16.)
water.add_atom("H",
rho *
np.array([0.0, sin(0.5 * theta),
cos(0.5 * theta)]), 1.)
water.add_atom("H",
rho * np.array([0.0, -sin(0.5 * theta),
cos(0.5 * theta)]), 1.)
water.finalize_setup()
return water
def create_base():
base = RigidFragment()
base.add_atom("O", np.array([-0.4, 0., 0.]), 1.)
base.add_atom("H", np.array([0.4, 0., 0.]), 1.)
base.finalize_setup(shift_com=False)
print "inversion:\n", base.inversion
print "symmetry:\n", base.symmetries
base.inversion = None
return base
def create_pap():
pap = RigidFragment()
rho = 0.3572
theta = 104.52/180.0*pi
pap.add_atom("O", np.array([0., 0., 0.]), 1.)
pap.add_atom("H", np.array([-0.038490, 0.1204928, 0.3794728]), 1.)
pap.add_atom("C", np.array([-0.038490, -0.1204928, -0.3794728]), 1.)
pap.finalize_setup(shift_com=False)
print "inversion:\n", pap.inversion
print "symmetry:\n", pap.symmetries
pap.inversion=None
#print pap.S
#pap.S = 0.3*np.identity(3)
return pap
def create_base():
base = RigidFragment()
base.add_atom("O", np.array([-0.4, 0., 0.]), 1.)
base.add_atom("H", np.array([0.4, 0., 0.]), 1.)
base.finalize_setup(shift_com=False)
print "inversion:\n", base.inversion
print "symmetry:\n", base.symmetries
base.inversion=None
return base
def get_rigid_fragment(self):
return RigidFragment()
def create_pap():
pap = RigidFragment()
rho = 0.3572
theta = 104.52 / 180.0 * pi
pap.add_atom("O", np.array([0., 0., 0.]), 1.)
pap.add_atom("H", np.array([-0.038490, 0.1204928, 0.3794728]), 1.)
pap.add_atom("C", np.array([-0.038490, -0.1204928, -0.3794728]), 1.)
pap.finalize_setup(shift_com=False)
print "inversion:\n", pap.inversion
print "symmetry:\n", pap.symmetries
pap.inversion = None
#print pap.S
#pap.S = 0.3*np.identity(3)
return pap