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_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_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