Velocity Verlet with Nosé-Hoover thermostat¶
This NVT-ensemble integrator implements the Verlet algorithm algorithm
with Nosé-Hoover chain thermostat with a chain length .
For reference and detailed description of the algorithm see the original papers by S. Nosé, W.G. Hoover and Martyna et al.:
- S. Nosé, J. Chem. Phys. 81, 511 (1984)
- W. G. Hoover, Phys. Rev. A 31, 1695 (1985)
- J. Martyna et al., J. Chem. Phys. 97, 2635 (1992)
- 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.
- timestep¶
Integration time step in MD units.
- set_temperature(temperature)¶
Set temperature of heat bath.
Parameters: temperature (number) – temperature of heat bath
- temperature¶
Temperature of heat bath.
- resonance_frequency¶
Resonance frequency of the Nosé-Hoover thermostat, this is connected to the mass of the thermostat via
and
, where
is
and
the dimension.
- set_mass(mass)¶
Set mass of heat bath.
Parameters: mass (table) – Sequence of masses for the heat bath coupling.
- mass¶
Array of masses
of heat bath, connected to the coupling strength of the thermostat.
- 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().