Python OTPCluster.get_orthogonalize_to_zero_eigenvectors示例

示例#1

文件： profile_otp.py 项目： Mahdisadjadi/pele

def do_ts_search(nmol=20):
    from pele.transition_states import findTransitionState
    system = OTPCluster(nmol)
    db = system.create_database("test.sqlte")
    orthogopt = system.get_orthogonalize_to_zero_eigenvectors()
    for ts in db.transition_states():
        coords = db.transition_states()[0].coords.copy() 
        coords += np.random.uniform(-.5,.5, coords.size)
    
        print system.params.double_ended_connect.local_connect_params.tsSearchParams
        findTransitionState(coords, system.get_potential(), orthogZeroEigs=orthogopt, 
                            **system.params.double_ended_connect.local_connect_params.tsSearchParams)

示例#2

def do_ts_search(nmol=20):
    from pele.transition_states import findTransitionState
    system = OTPCluster(nmol)
    db = system.create_database("test.sqlte")
    orthogopt = system.get_orthogonalize_to_zero_eigenvectors()
    for ts in db.transition_states():
        coords = db.transition_states()[0].coords.copy()
        coords += np.random.uniform(-.5, .5, coords.size)

        print system.params.double_ended_connect.local_connect_params.tsSearchParams
        findTransitionState(coords,
                            system.get_potential(),
                            orthogZeroEigs=orthogopt,
                            **system.params.double_ended_connect.
                            local_connect_params.tsSearchParams)