jaxdem.integrators.velocity_verlet_rescaling#

Velocity Verlet integrator with periodic velocity-rescaling thermostat.

Classes

VelocityVerletRescaling(k_B, temperature, ...)

Velocity Verlet with periodic velocity-rescaling thermostat.
class jaxdem.integrators.velocity_verlet_rescaling.VelocityVerletRescaling(k_B: Array, temperature: Array, rescale_every: Array, can_rotate: Array, subtract_drift: Array)#

Bases: VelocityVerlet

Velocity Verlet with periodic velocity-rescaling thermostat.

Every rescale_every steps, the integrator uniformly rescales the translational (and optionally rotational) velocities so the instantaneous kinetic temperature matches temperature. Between rescalings the dynamics are purely Newtonian (standard Velocity Verlet, inherited from VelocityVerlet).

The integrator applies the rescaling at the end of step_after_force, after the second Verlet half-kick. The terminal velocities on rescaling steps are then exactly at the target temperature.

The thermostat statistics (kinetic energy sums and drift mean) exclude fixed particles. The rescaling never modifies their prescribed velocities.

Parameters:

  • k_B (jax.Array) – Boltzmann constant (set to 1.0 for reduced units).

  • temperature (jax.Array) – Target temperature \(T\).

  • rescale_every (jax.Array) – Rescale velocities every this many steps (scalar integer).

  • can_rotate (jax.Array) – Whether to include rotational DOF in the thermostat (0 or 1). When 1, the thermostat also rescales the angular velocities and counts rotational kinetic energy toward the temperature.

  • subtract_drift (jax.Array) – Whether to remove center-of-mass drift before rescaling (0 or 1). When 1, the integrator subtracts the center-of-mass velocity on rescaling steps before it measures the temperature. Mainly relevant for small systems.

k_B: Array#
temperature: Array#
rescale_every: Array#
can_rotate: Array#
subtract_drift: Array#
classmethod Create(temperature: float = 1.0, k_B: float = 1.0, rescale_every: int = 1, can_rotate: bool = False, subtract_drift: bool = False) → VelocityVerletRescaling[source]#

Create the thermostat from plain Python values.

Parameters:

  • temperature (float, default 1.0) – Target temperature.

  • k_B (float, default 1.0) – Boltzmann constant (1.0 for reduced units).

  • rescale_every (int, default 1) – Rescale velocities every this many steps.

  • can_rotate (bool, default False) – Include rotational DOF in the thermostat.

  • subtract_drift (bool, default False) – Remove center-of-mass drift before rescaling.

static step_after_force(state: State, system: System) → tuple[State, System][source]#