[CP2K:768] Re: nose thermostat

[Diederica Claeys]

hi

thanks a lot for all the explanations! The MD is running well now

greetz,
Diederica

On Mon, Mar 10, 2008 at 10:37 PM, Teodoro Laino <teodor... at gmail.com>
wrote:

> Ciao Nick,
>  On 10 Mar 2008, at 22:28, Nichols A. Romero wrote:
>
> To elaborate on what Teo said, (he can correct me if I am wrong)
>
> In NVT, the total energy of the *real sytem + thermostat* should be
> conserved.
> (I don't remember if CP2K outputs this quantity, but most codes should).
>
> Exactly.. and this quantity is what we call CONSERVED QNTY or you can find
> the same number in the 6th column of the .ener file.
>
> The total energy of just the real system (atoms,molecules,etc.) should
> have a mean value (after equilibration) with fluctuations proportional to
> 1/sqrt(N) (or something like that).
>
> If the total energy of the real system increases or decreases without
> bounds, then there is something wrong.
> Or maybe you are near some phase transition.
>
> Absolutely correct. In this case I think that the forces computed have
> something wrong..
> Let me explain better once for all. The SCF module is still not fully
> completed. The most important part missing is
> the ewald for the coulomb part (we have a project going on for that, so it
> should be hopefully fixed one day ;-) ).
> This means that at the moment the coulomb is evaluated through a neighbor
> lists.
> This creates ENORMOUS problem if you condensed phases (same problem of
> using a cutoff to truncate the electrostatic interactions
> in force field based calculations) but also if you do big molecules (and
> this is her case) and don't set properly
> the parameter I wan mentioning in my last e-mail.
> What happens here is that during the MD you've interactions turned on and
> off at the boundary and the contribution is such that
> you observe a drift.
>
> Of course I could be wrong.. but since the nose-hoover thermostat has been
> so extensively tested i would rarely look for a bug in it ;-)
>
> Teo
>
>
>
> On Mon, Mar 10, 2008 at 4:37 PM, Teodoro Laino <teodor... at gmail.com>
> wrote:
>
> >
> > Ciao Diederica,
> >
> > >
> > > These are added, as an attachment this time
> >
> > Thanks.. will look into this problem ASAP.
> >
> > > I'm modelling an isolated molecule, it should fit in the box. Using
> > > NVE without temperature rescaling, with an analogue structure, an
> > > energy drift was observed, that got worse after about 20 ps, though
> > > no non-convergence was observed. The input file and an energy-plot
> > > are added.
> > If you have a drift with NVE this means that energy and forces are
> > not consistent.. or (what I assume) that the cutoff for the coulomb
> > interactions is not large enough..
> >
> > Please put all of the  RC_COULOMB and RC_INTERACTION and RC_RANGE to
> > 50.0.
> > You've the problem that in your cell the standard range (24 bohr)
> > does not fully cover the extension of your molecule (more than 26 bohr).
> > Use a larger box (30.0 Angstrom) and set the above keywords to 50.0
> > bohr.
> > You should not see any jump in the energy (or drift)..
> >
> > > The potential and kinetic energy are conserved indeed, but the
> > > conserved quantity is not
> > Sorry to disprove you, but it is not possible that in an NVT you have
> > kinetic and potential conserved, since the thermostat
> > is continuously exchanging energy with the system.  I't s a matter of
> > concept.. we may discuss about the magnitude of the
> > thermostat energy.. but that's another story..
> >
> > Cheers
> > teo
> >
> >
> >
> > >
> > >
> > >
> > > For the next time, can you please put tables and input files as
> > > attachment (maybe .tgz) so that the formatting of mail readers are
> > > not changed and the input files not digested ? Thanks..
> > >
> > > Ciao,
> > > teo
> > >
> > > Thanks for helping!
> > >
> > > Greetz,
> > > Diederica
> > >
> > >
> > >
> > >
> > > >
> > > <mailcp2k.tgz>
> >
> >
> >
> >
>
>
> --
> Nichols A. Romero, Ph.D.
> DoD User Productivity Enhancement and Technology Transfer (PET) Group
> High Performance Technologies, Inc.
> Reston, VA
> 443-567-8328 (C)
> 410-278-2692 (O)
>
>
>
>
> >
>
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