Velocity Verlet with Nosé-Hoover thermostat¶

This NVT-ensemble integrator implements the Verlet algorithm algorithm with Nosé-Hoover chain thermostat with a chain length $M = 2$ .

For reference and detailed description of the algorithm see the original papers by S. Nosé, W.G. Hoover and Martyna et al.:

class halmd.mdsim.integrators.verlet_nvt_hoover(args)¶

Construct velocity-Verlet integrator with Nosé-Hoover chain thermostat.

Parameters:

args (table) – keyword arguments
args.particle – instance of halmd.mdsim.particle
args.force – instance of halmd.mdsim.forces
args.box – instance of halmd.mdsim.box
args.timestep (number) – integration time step (defaults to halmd.mdsim.clock.timestep)
args.temperature (number) – temperature of heat bath
args.resonance_frequency (number) – Coupling rate of the thermostat
args.every (number) – Number of time steps between writing of theromostat chain values

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.

set_temperature(temperature)¶

Set temperature of heat bath.

Parameters:	temperature (number) – temperature of heat bath

resonance_frequency¶: Resonance frequency of the Nosé-Hoover thermostat, this is connected to the mass of the thermostat via $m_1 = d T / \Omega^2$ and $m_2 = T/\Omega^2$ , where $\Omega$ is $2\pi\times\textrm{Coupling frequency}$ and $d$ the dimension.