Dear QuantumWise staffs:
Using a 'post-step-hook' hook function, as shown in
https://forum.quantumatk.com/index.php?topic=4696.msg20375#msg20375, the corresponding script as follows:
*********************************************************************
charges = PartialCharges(bulk_configuration).evaluate()
field = [0.01, 0.0, 0.0]*Volt/Ang
class ElectricFieldHook(object):
def __init__(self, charges, electric_field):
# Store the charges and the electric field.
charges = charges.reshape(-1, 1)
field = electric_field.reshape(1, 3)
self.efield_forces = (charges*field).convertTo(eV/Ang)
def __call__(self, step, time, configuration, forces, stress):
# Add the electric field forces to the forces vector.
forces += self.efield_forces
electric_field_hook = ElectricFieldHook(
charges=partial_charges,
electric_field=field
)
# -------------------------------------------------------------
# Molecular Dynamics
# -------------------------------------------------------------
initial_velocity = None
method = NVTBerendsen(
time_step=1*femtoSecond,
reservoir_temperature=300*Kelvin,
thermostat_timescale=100*femtoSecond,
initial_velocity=initial_velocity,
heating_rate=0*Kelvin/picoSecond,
)
rigid_indices_0 = [203, 204, 205, 206, 207, 208, 209, 210, 211, 212,
213, 214, 215, 216, 217, 218, 219, 220, 221, 222,
223, 224, 225, 226, 227, 228, 229, 230, 231, 232,
233, 234, 235, 236, 237, 238, 239, 240, 241, 242]
rigid_indices_1 = [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
39]
constraints = [RigidBody(rigid_indices_0),
RigidBody(rigid_indices_1)]
md_trajectory = MolecularDynamics(
bulk_configuration,
constraints=constraints,
trajectory_filename='trajectory.nc',
steps=200,
log_interval=1,
post_step_hook=electric_field_hook,
method=method
)
bulk_configuration = md_trajectory.lastImage()
nlsave('Device-AGNR-Tran1-MDopt.nc', md_trajectory)
*****************************************************************************
it doesn't work, the error message is "NL.ComputerScienceUtilities.Exceptions.NLTypeError: The LCAOCalculator does not
support calculation of PartialCharges."
how to deal with it? Thanks
