Velocity Verlet

This NVE-ensemble integrator implements the velocity-Verlet algorithm in J. Chem. Phys. 76, 637 (1982).

The algorithm consists of a first half-step

\[\begin{split}\vec{v}\Bigl(t + \frac{\tau}{2}\Bigr) &= \vec{v}\Bigl(t\Bigr) + \frac{\tau}{2} \frac{\vec{F}\left(t\right)}{m} \\ \vec{r}\Bigl(t + \tau\Bigr) &= \vec{r}\Bigl(t\Bigr) + \tau \vec{v}\Bigl(t + \frac{\tau}{2}\Bigr)\end{split}\]

and a second half-step

\[\vec{v}\Bigl(t + \tau\Bigr) = \vec{v}\Bigl(t + \frac{\tau}{2}\Bigr) + \frac{\tau}{2} \frac{\vec{F}\left(t + \tau\right)}{m}\]

class halmd.mdsim.integrators.verlet(args)

Construct velocity-Verlet integrator for given system of particles.

Parameters:

• args (table) – keyword arguments

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

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

• args.timestep (number) – integration time step (defaults to halmd.mdsim.clock.timestep)

set_timestep(timestep)

Set integration time step in MD units.

Parameters:

timestep (number) – integration timestep

This method forwards to halmd.mdsim.clock.set_timestep(), to ensure that all integrators use an identical time step.

timestep

Integration time step in MD units.

disconnect()

Disconnect integrator from core and profiler.

integrate()

Calculate first half-step.

By default this function is connected to halmd.mdsim.core.on_integrate().

finalize()

Calculate second half-step.

By default this function is connected to halmd.mdsim.core.on_finalize().