jayponder/tinker — pull request #5 by dmargul (2014-02-20 19:30:33+00:00)
Title: Isokinetic and Stochastic Isokinetic Thermostats/Integrators

The isokinetic thermostat scheme from Phys Rev Lett. 2004 93(15):150201 and the stochastic isokinetic thermostat scheme from Mol. Phys. 2013 111(22-23):3579 are included for single and multiple time steps.

One required keyword: integrator can take the values "ISOKINETIC" or "STOCH-ISOK"

For the above schemes, the keyword "nrespa" can take an integer value and defines the number of small time steps per large time step. By default, nrespa = 1. Regardless of the value chosen for nrespa, the large/only time step is specified by the user in the usual place.

By default, the length of the thermostat chains in the two isokinetic schemes is 4. The optional keyword "nhc-length" can take integer values 1-4, and the upper limit can be relaxed by changing the value of "isok_chain" in bath.i.

The RESPA integrator from the original repository has been tweaked so that any large or small time step can be used. Note that this requires the use of the keyword "nrespa" as described above.