ZeroVelocities¶

class ZeroVelocities¶: Utility for using zero velocities as the starting value in a MolecularDynamics() simulation.

Usage Examples¶

Perform a molecular dynamics run of a silicon crystal, with the initial velocities of all particles set to zero.

# Set up lattice
lattice = FaceCenteredCubic(5.4306*Angstrom)

# Define elements
elements = [Silicon, Silicon]

# Define coordinates
fractional_coordinates = [[-0.009580233862,  0.002314591627,  0.010466101485],
                          [ 0.259580233862,  0.247685408373,  0.239533898515]]

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

potentialSet = Tersoff_Si_1988b()
calculator = TremoloXCalculator(parameters=potentialSet)
bulk_configuration.setCalculator(calculator)

# The MD method will use initial velocities corresponding to zero.
method = NVEVelocityVerlet(initial_velocity=ZeroVelocities())

md_trajectory = MolecularDynamics(
    bulk_configuration,
    constraints=[],
    trajectory_filename='trajectory.nc',
    steps=500,
    log_interval=100,
    method=method
)

zero_velocities.py

Notes¶

Use this object as initial_velocity parameter in the MD method (e.g. NVEVelocityVerlet), when you want to run an MD simulation with zero initial velocities. This has the same effect as setting initial_velocity to None in the MD method.