hybrid monte carlo and cp2k
obfis... at gmail.com
Fri Jun 24 08:15:31 CEST 2011
On Jun 23, 7:19 pm, Alin Marin Elena <alinm... at gmail.com> wrote:
> Hi Matt,
> Thank you very much for you fast and detailed answer.
> I read the HMC part from the paper that you suggested, thank you, it made some
> things clearer on what is implemented in cp2k...
> > Good question. HMC is something I've just recently implemented. I've
> > tested it to make sure it samples correctly, but I've noticed too that
> > it's not the easiest to use, unless you happen to be the person who
> > wrote the MC routines (and even then, new issues pop up sometimes).
> they are not so bad... I just want to be sure that I do not miss things that
> can bite me later.
> Is there any pilot study you can point me to for the 0.7 acceptance rate for
> the HMC? I know that the MC schemes efficiency tends to be connected with the
> acceptance rate.
Unfortunately, I can't find any studies that say that. It just seems
to be what is currently used in the literature. You're right,
acceptance ratio really impacts your sampling. The conventional
wisdom in the field is to aim for 50% for moves involving the
Metropolis acceptance ratio, 50% for volume moves (though 30-40 is
good for equilibration), and various guidelines for other move types,
although even these are not set in stone (I've seen arguments for
lower acceptance ratios in translations/rotations, for example, even
as low as 25%). In the end, all you can do is monitor your system and
see when it's equilibrated (according to density, energy, or
whatever). On the plus side, a bad acceptance ratio doesn't lead to
the wrong answer...it just might make you get there slower.
> What I want to sample is indeed a canonical ensemble. The MD part will be DFT,
> so now you may understand my worry on efficiency.
> My system is simple, 23 atoms I do not care about the molecules, so I created
> a topology file that puts all of them in one "macro-molecule". I attached my
> input files, so any feedback is much appreciated...
I took a look at your input file, and I can't see any obvious
problems. I am, however, not the ideal person to comment on the DFT
parameters (I generally rely on other smart people for that :) ). I
have had it recommended to me to use FULL_ALL as the preconditioner
and PS 3 to speed up the MD part, although the first calculation in
any sequence is always going to take more time if the HMC move was
> Now what I try to do... I try to use a metadynamics run with CV and forces
> coming from DFT.
> The acceptance hamiltonian is the one coming from the all system (atoms+CVs)
> but the trajectories for MD are evolved using only the physical forces.
> I was wondering if that is possible to do it in the current state of cp2k or
> should I define my own type of dynamics?
I'm not seeing how that could work at the moment, theoretically or
practically. It would take some time for me to understand
metadynamics (coincidentally, I am just starting a metadynamics
project), so I'm guessing that it's nothing that will happen soon
(bigger priority is to clean up the MC routines). Is there a big
reason why you want to do this over regular MD with meta? I'm not
seeing the advantage, honestly, and I don't see how you would include
metadynamics when your MD run is just a regular NVE (if I'm
understanding you correctly).
> Without Questions there are no Answers!
> Alin Marin ELENA
> Advanced Molecular Simulation Research Laboratory
> School of Physics, University College Dublin
> Ardionsamblú Móilíneach Saotharlann Taighde
> Scoil na Fisice, An Coláiste Ollscoile, Baile Átha Cliath
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