espressopp.integrator.BerendsenBarostat

This is the Berendsen barostat implementation according to the original paper [Berendsen84]. If Berendsen barostat is defined (as a property of integrator) then at the each run the system size and the particle coordinates will be scaled by scaling parameter \(\mu\) according to the formula:

\[\mu = [1 - \Delta t/\tau (P_{0} - P)]^{1/3}\]

where \(\Delta t\) - integration timestep, \(\tau\) - time parameter (coupling parameter), \(P_{0}\) - external pressure and \(P\) - instantaneous pressure.

Example:

>>> berendsenP = espressopp.integrator.BerendsenBarostat(system)
>>> berendsenP.tau = 0.1
>>> berendsenP.pressure = 1.0
>>> integrator.addExtension(berendsenP)

!IMPORTANT In order to run npt simulation one should separately define thermostat as well (e.g. BerendsenThermostat).

Definition:

In order to define the Berendsen barostat

>>> berendsenP = espressopp.integrator.BerendsenBarostat(system)

one should have the System defined.

Properties:

• berendsenP.tau

  The property ‘tau’ defines the time parameter \(\tau\).

• berendsenP.pressure

  The property ‘pressure’ defines the external pressure \(P_{0}\).

Setting the integration property:

>>> integrator.addExtension(berendsenP)

It will define Berendsen barostat as a property of integrator.

One more example:

>>> berendsen_barostat = espressopp.integrator.BerendsenBarostat(system)
>>> berendsen_barostat.tau = 10.0
>>> berendsen_barostat.pressure = 3.5
>>> integrator.addExtension(berendsen_barostat)

Canceling the barostat:

If one do not need the pressure regulation in system anymore or need to switch the ensamble or whatever :)

>>> # define barostat with parameters
>>> berendsen = espressopp.integrator.BerendsenBarostat(system)
>>> berendsen.tau = 0.8
>>> berendsen.pressure = 15.0
>>> integrator.addExtension(berendsen)
>>> ...
>>> # some runs
>>> ...
>>> # disconnect Berendsen barostat
>>> berendsen.disconnect()
>>> # the next runs will not include the system size and particle coordinates scaling

Connecting the barostat back after the disconnection

>>> berendsen.connect()

References:

[Berendsen84]

Berendsen et al., J. Chem. Phys., 81, 1984, p. 3684

espressopp.integrator.BerendsenBarostat(system)

Parameters:system –