TimeStampedForceBiasMonteCarlo

TimeStampedForceBiasMonteCarlo(configuration, constraints=None, trajectory_filename=None, steps=None, log_interval=None, method=None, pre_step_hook=None, post_step_hook=None, write_velocities=False, write_forces=True, write_stresses=False)

Function for performing a time-stamped force-bias Monte Carlo simulation.

Parameters:
  • configuration (MoleculeConfiguration | BulkConfiguration | DeviceConfiguration | SurfaceConfiguration) – The initial configuration.
  • constraints (list of int | list of FixAtomConstraints) – The list of atomic indices, denoting fixed atoms, or constraint objects.
    Default: []
  • trajectory_filename (str | None) – The filename of the file to be used for storing the trajectory, or None if no trajectory should be written.
    Default: None
  • steps (int) – The number of steps to take in the simulation.
    Default: 50
  • log_interval (int) – The resolution used in saving steps to a trajectory file ad writing the log file, where a value of 1 results in all steps being saved, and e.g. a value of 2 resulting in every other step being discarded.
    Default: 1
  • method (ForceBiasMontCarlo) – The Monte Carlo method used for the simulation.
    Default: ForceBiasMonteCarlo
  • pre_step_hook (function | list of functions | None) – An optional user-defined function or a list of functions which will be called just before the forces evaluation. The signature of the function requires the arguments (step, time, configuration, forces, stress). The return status is ignored. Unhandled exceptions will abort the simulation. If a list is given the functions will be called in the given order.
    Default: None
  • post_step_hook (function | list of functions | None) – An optional user-defined function or a list of functions which will be called just after the forces evaluation. The signature of the function requires the arguments (step, time, configuration, forces, stress). The return status is ignored. Unhandled exceptions will abort the simulation. If a list is given the functions will be called in the given order.
    Default: None
  • write_velocities (bool) – Write the velocities to the trajectory file every log_interval steps. Since, the time-stamped force-bias Monte Carlo algorithm does not use velocities explicity, zero velocities will be written.
    Default: False
  • write_forces (bool) – Write the forces to the trajectory file every log_interval steps.
    Default: True
  • write_stresses (bool) – Write the stress to the trajectory file every log_interval steps.
    Default: False
Returns:

The Monte Carlo trajectory.

Return type:

MDTrajectory

Usage Examples

Perform a time-stamped force-bias Monte Carlo run of 500 steps of a bulk silicon crystal, using the Stillinger-Weber potential:

# -------------------------------------------------------------
# Bulk configuration
# -------------------------------------------------------------

# Set up lattice
vector_a = [5.4306, 0.0, 0.0]*Angstrom
vector_b = [0.0, 5.4306, 0.0]*Angstrom
vector_c = [0.0, 0.0, 5.4306]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon,
            Silicon]

# Define coordinates
fractional_coordinates = [[0.0 ,  0.0 ,  0.0 ],
                          [0.25,  0.25,  0.25],
                          [0.5 ,  0.5 ,  0.0 ],
                          [0.75,  0.75,  0.25],
                          [0.5 ,  0.0 ,  0.5 ],
                          [0.75,  0.25,  0.75],
                          [0.0 ,  0.5 ,  0.5 ],
                          [0.25,  0.75,  0.75]]

# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------

potentialSet = StillingerWeber_Si_1985()
calculator = TremoloXCalculator(parameters=potentialSet)

bulk_configuration.setCalculator(calculator)
bulk_configuration.update()

# -------------------------------------------------------------
# Time-Stamped Force-Bias Monte Carlo
# -------------------------------------------------------------

method = ForceBiasMonteCarlo(
    reservoir_temperature=500.0*Kelvin,
    max_atom_displacement=0.3*Ang,
)

mc_trajectory = TimeStampedForceBiasMonteCarlo(
    bulk_configuration,
    constraints=[],
    trajectory_filename='tfmc_trajectory.hdf5',
    steps=500,
    log_interval=50,
    method=method
)

bulk_configuration = mc_trajectory.lastImage()


tfmc_example.py

Notes

This function performs a time-stamped force-bias MonteCarlo (TFMC) simulation on the given configuration (see [NB12] for a summary on the TFMC method). The TFMC algorithm essentially consists of a Monte Carlo sampling of the energy landscape at a given temperature.

For details about the Monte Carlo algorithm and how the simulation parameters are specified see ForceBiasMonteCarlo.

Each Monte Carlo step in the TFMC algorithm is a possible realization of how the atoms might move in the potential energy landscape, starting from a given configuration. Therefore the simulation bears some similarity to Molecular Dynamics, and it is even possible to estimate a time step by which subsequent images are separated on average [MPN+12]. The time step in TFMC is typically a factor of 2-50 larger than in Molecular Dynamics simulations, however, one must keep in mind that it is not very rigorously defined and primarily suitable for long-timescale-kinetics.

The TimeStampedForceBiasMonteCarlo function returns an MDTrajectory object. After the simulation has completed, you can extract various properties of the stored snapshots, such as coordinates, or forces, by using the MDTrajectory class methods.

Similar to MolecularDynamics, you can perform custom operations on the configuration during the simulation by using the pre_step_hook or post_step_hook functionality.

The pre-step-hook one is invoked immediately before the force and stress calculations, which allows you to modify atomic positions or the cell vectors.

The post-step-hook is invoked after the force and stress calculation, which means that you can modify the forces and stress, e.g. by adding a bias potential.

Suitable functions must have the signature (step, time, configuration, forces, stress) where step denotes the integration step number, time is the current simulation time, and configuration is the current configuration, forces is the PhysicalQuantity array holding the current forces, and stress is the stress tensor. Note, that you need to modify these two arrays in-place, as the return status of the function is ignored. You can use the class methods of the configuration object (see e.g. BulkConfiguration) to perform operations on the atoms.

Moreover, it is possible to give a list of hook functions, which will be called sequentially at each TFMC step.

Only FixAtomConstraints are supported in TFMC simulations.

[MPN+12]Maarten J. Mees, Geoffrey Pourtois, Erik C. Neyts, Barend J. Thijsse, and André Stesmans. Uniform-acceptance force-bias monte carlo method with time scale to study solid-state diffusion. Phys. Rev. B, 85:134301, 2012. doi:10.1103/PhysRevB.85.134301.
[NB12]Erik C. Neyts and Annemie Bogaerts. Combining molecular dynamics with monte carlo simulations: implementations and applications. Theor. Chem. Acc., 132(2):1320, 2012. doi:10.1007/s00214-012-1320-x.