[Pw_forum] Dynamic Temperature Control and Select Stationary Ions.

[Tim Teatro]

Thank you so very much. I appreciate your help. I can't wait to try
this autopilot.

One thing though, I don't need to stop atoms dynamically. They can be
static from the start of the simulation. What input do I specify to do
this?

Thanks again.


On 6/12/06, Yonas Abraham <yonasb at yahoo.com> wrote:
> Dear Tim,
>
> In CP (QE >= 3), there is a way to change temperature
> on the fly  during the MD simulation. look at
> Doc/AUTOPILOT file on how to  use it. In fact, it will
> let you change up to 10 CP (like dt, isave, iprint
> etc)  variables on the fly. in addition, you can even
> PAUSE the simulation while you are deciding what value
> to use!
>
> but the current AUTOPILOT implementation doesn't allow
> you to fix certain atoms on the fly. But if you are
> serious, you can extend AUTOPILOT to do so.
>
>
> But I don't know if there is such thing on pw.x.
>
> /yonas
>
> --- Tim Teatro <timtro at gmail.com> wrote:
>
> > Dear Nicola,
> >
> > Thank you for your reply. I am working on large
> > clusters, so
> > calculation time is not a problem. Unfortunately I
> > will not have
> > access to cp.x for a few days because the computer
> > cluster on which I
> > was able to compile it is down. Therefore, I will
> > need to use pw.x for
> > now.
> >
> > Could you give me a list of input parameters I would
> > need for changing
> > the temperature during a MD simulation, and for
> > holding a few specific
> > ions still while others are able to move? It seems I
> > can only find
> > references to temperature rescaling and the Nose
> > thermostat, which
> > require the temperature to be specified ahead of
> > time. And of course I
> > can turn the ion dynamics off easily enough, but not
> > for certain
> > atoms.
> >
> > If you have any examples, this would be great too.
> >
> > Thanks again.
> >
> > Cheers.
> >
> > On 6/10/06, Nicola Marzari <marzari at mit.edu> wrote:
> > >
> > >
> > > Dear Tim,
> > >
> > >
> > > you can do this both with CP or PWSCF. CP would be
> > the ideal code,
> > > provided the system remains insulating.
> > > On a single state-of-thje-art Pentium I think you
> > can get nowadays
> > > 1ps/day, for a system with ~250 electrons.
> > >
> > > Otherwise, you should use Born-Oppenheimer
> > dynamics (that is the
> > > standard mode for PWSCF, and is
> > > available as an option in CP).
> > >
> > > Melting and quenching has been used often - you
> > could look e.g. at the
> > > works by Alfredo Pasquarello at EPFL (especially
> > > from the ~1998 Nature on SiO2 onwards).
> > >
> > > Car-Parrinello MD, and to a certain extent
> > Born-Oppenheimer MD, require
> > > a good understanding of several concepts -
> > > we'll run a school on "Ab-initio molecular
> > dynamics" in
> > > Urbana-Champaign, at the beginning of
> > > August, and attending that would probably be very
> > useful:
> > > http://www.mcc.uiuc.edu/summerschool/2006/
> > >
> > > At a minimum, have a close look at the review
> > papers on the web -
> > > especially the one
> > > by Marx and Hutter
> > >
> >
> (http://www.theochem.ruhr-uni-bochum.de/research/marx/cprev.en.html)
> > or the
> > > shorter one by Galli and Pasquarello. The
> > RevModPhys review of Payne
> > > from 1992 is another very
> > > good reference. As a word of care, look also at
> > the 2002 and 2004 JCP
> > > from Tangney/Scandolo and
> > > from the Galli group.
> > >
> > >
> > >              nicola
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > Tim Teatro wrote:
> > > > Hello.
> > > >
> > > > I believe I posted a similar question a year or
> > two ago, but A) I
> > > > don't think the question was resolved and B) the
> > code has changed, so
> > > > perhaps what was once a problem is not now.
> > > >
> > > > My group has a situation where we need to melt a
> > crystal system, and
> > > > then cool it back down to make an amorphous
> > structure. Is this
> > > > possible using any of the codes in the ESPRESSO
> > package?
> > > >
> > > > If so, how? Do you happen to have an input
> > example?
> > > >
> > > > Also, we have another system in which it would
> > be useful to hold
> > > > certain ions stationary while others are free to
> > move under the Verlet
> > > > algorithm. Of course we could cheat and set the
> > mass of these atoms to
> > > > be extremely high, but I think it would be
> > better to simply stop them
> > > > completely.
> > > >
> > > > Thank you for your time.
> > > >
> > > > --
> > > > Timothy A.V. Teatro
> > > > University of Ontario Institute of Technology
> > > > e.  timtro at gmail.com <mailto:timtro at gmail.com>
> > > > p.  905.579.9248
> > > > c.  905.442.9248
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> >
> >
> >
> > --
> > Timothy A.V. Teatro
> > University of Ontario Institute of Technology
> > e.  timtro at gmail.com
> > p.  905.579.9248
> > c.  905.442.9248
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


-- 
Timothy A.V. Teatro
University of Ontario Institute of Technology
e.  timtro at gmail.com
p.  905.579.9248
c.  905.442.9248