Python RigidFragment Examples

Example #1

File: tip4p.py Project: js850/PyGMIN

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

Example #2

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

Example #3

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

Example #4

File: pap_example.py Project: js850/PyGMIN

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

Example #5

File: oxgui.py Project: js850/PyGMIN

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

Example #6

File: otp.py Project: yfyh2013/PyGMIN

 def get_rigid_fragment(self):
     return RigidFragment()

Example #7

File: pap_example.py Project: yfyh2013/PyGMIN

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