Rescale velocities

This module rescales particle velocities to satisfy a selected constraint, depending on the mode of operation, such that a given target energy \(E_\text{target}\) matches either

1. the total energy (micro-canonical, nve) or

2. the kinetic energy (isokinetic)

of either (a) the whole system or (b) each particle separately.

The rescale operation conserves the direction of velocities, it adjusts only their magnitude. The scaling factor \(\lambda\) is calculated as:

\[\lambda = \sqrt{\frac{E_\text{target} - \alpha E_\text{pot}}{E_\text{kin}}} \,,\]

where \(\alpha = 1\) in the micro-canonical mode (1) and \(\alpha = 0\) in the iso-kinetic mode (2). In case (a), the same factor \(\lambda\) is applied to the whole system (all particles) and the potential and kinetic energies, \(E_\text{pot}\) and \(E_\text{kin}\), are averages over all particles, respectively (before rescaling). In case (b), \(\lambda\) is calculated for each particle separately, using the individual energy values.

class halmd.mdsim.velocities.rescale(args)

Construct rescale module.

Parameters:

• args (table) – keyword arguments

• args.particle – instance of halmd.mdsim.particle

• args.target_energy (number) – desired energy value (either total or kinetic energy)

• args.mode (string) – mode of operation (nve or isokinetic)

• args.per_particle (boolean) – perform rescaling per particle (default: false)

If the mode of operation is nve, the target energy refers to the total energy. If the mode is isokinetic, the target energy refers to the kinetic energy.

If the switch per_particle is set to true, the rescaling is performed for each particle separately, otherwise the same factor is applied to all particles.

set()

Rescale particle velocities.

target_energy

Target energy value (assignable)

In nve mode, it refers to the total energy (kinetic plus potential parts) whereas it refers to the kinetic energy in isokinetic mode.