Nose-Hoover Thermostat

[William French]

Hello HOOMD users and developers,

I am a LAMMPS user in the process of familiarizing myself with HOOMD.  The question I have regards the implementation of the Nose-Hoover thermostat in HOOMD.  How does it compare to the LAMMPS implementation?  I have been running some tests on identical systems in LAMMPS and HOOMD, and I am finding that for a 1000-particle LJ system, the temperature evolution in LAMMPS and HOOMD differs.  The equilibrium value is correct in both cases, but HOOMD takes a bit longer to equilibrate around the target temperature and the fluctuations in temperature during that period are much larger than those in LAMMPS.  Is this expected behavior?  I have used the same temperature damping parameter values, called "Tdamp" in LAMMPS and "tau" in HOOMD. I assume these parameters are defined in the same way, and as far as I can tell they are. 

I have attached the LAMMPS and HOOMD input scripts as well as the data files for the example I have described.  I initialize all the particles with a velocity of zero and then set a target temperature of T* = 1.2.  I have also attached a .png image showing the discrepancy in the temperature evolution for the first 10,000 time steps.

Any thoughts/comments are welcome.

Best,

William French      

[Joshua A. Anderson]

tau and Tdamp have the same definition in hoomd and lammps, respectively. The difference is that LAMMPS implements thermostat chains, while hoomd does not. From the lammps documentation, "The keyword defaults are tchain = 3 ...", so chains are enabled by default. I would guess that if you disabled chains, your comparison plot would line up better, but I haven't tried this.
--------
Joshua A. Anderson, Ph.D.
Chemical Engineering Department, University of Michigan

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[Li Wan]

Jushua,

Thank you.  That also solved my problem. But since I want to move all simulations previously done by LAMMPS to hoomd, how could I change tchain value in hoomd?  

Li

--
Li Wan
Chemical Engineering Graduate Student
Vanderbilt University
e-mail: constel...@gmail.com

[Joshua A. Anderson]

You can't change an option that doesn't exist.

--------
Joshua A. Anderson, Ph.D.
Chemical Engineering Department, University of Michigan

[william....@gmail.com]

Thanks, Josh. That did the trick. I knew LAMMPS incorporated
thermostat chains, but I was unaware that tchain was 3 by default.

> > For more options, visit this group athttp://groups.google.com/group/hoomd-users?hl=en.

[Joshua A. Anderson]

I will accept a patch that implement chains in hoomd, of course :)

--------
Joshua A. Anderson, Ph.D.
Chemical Engineering Department, University of Michigan