[CP2K:979] Re: time for every MD step

LIANG Yunfeng liangy... at gmail.com
Fri Apr 25 03:40:48 CEST 2008


To run cp2k starting a configuration (not from previous ab initio), do we
need relax the configuration firstly and then introduce a small amount
random distortions to the position as cpmd does.

Even though to obtain a fully equilibrated velocity for system takes
time(0.5ps?). Actually we should not be very worried about the energy
conservation, you see the last 1000 steps of my *.ener file, which seems ok.
A drift 0.008 Ry/192 is still physical, isn't it?

Can you draw some lines related to the optimizing procedure to the
equilibrium state for cp2k MD user?

Sincerely, Yunfeng

On Thu, Apr 24, 2008 at 6:56 PM, Axel <akoh... at gmail.com> wrote:

>
> dear yunfeng,
>
> have you run that input without a thermostat?
> does it conserve energy, i think not. you need
> to fix that first. remember the GI-GO principle.
>
> your timestep of 1fs is very "ambitious" for
> water without any constraints or fudging
> with masses.
>
> cheers,
>     axel
>
>
>
>
> On Apr 24, 7:20 pm, "LIANG Yunfeng" <liangy... at gmail.com> wrote:
> > Wow, I'm the first guy!
> >
> > Attached are the *.ener file. I thought the input file (attached in the
> > previous email) has already contained full information. If necessary,
> I'll
> > send you the coordinates(thanks for your correction) as well. Thanks!
> >
> > Sincerely, Yunfeng
> >
> > On Thu, Apr 24, 2008 at 4:38 PM, Teo <teodor... at gmail.com> wrote:
> >
> > > Dear Yunfeng,
> >
> > > since you deleted the "coordinations"  (?!?) we can practically do
> > > NOTHING.
> > > Anyway I suspect that your system is blowing up.. I mean.. your scf is
> > > becoming more and
> > > more difficult to converge.. probably the problems are really the
> > > coordinates (is this what you call coordinations ??)..
> >
> > > Since you are the first in so many years to observe something like
> > > that.. please consider the idea that it could be
> > > due to your errors.
> > > Or possibly due to kind of miscompilation of the buggy winner prize
> > > PGI compiler.
> >
> > > Can you post coordinates as well? or at least the .ener file?
> > > Thanks,
> > > Teo
> >
> > > On Apr 25, 12:20 am, "LIANG Yunfeng" <liangy... at gmail.com> wrote:
> > > > See attachment. I just deleted the coordinations.
> >
> > > > Sincerely, Yunfeng
> >
> > > > On Thu, Apr 24, 2008 at 4:13 PM, Matt W <MattWa... at gmail.com>
> wrote:
> >
> > > > > How much input/output information are you using?
> >
> > > > > Matt
> >
> > > > > On Apr 24, 11:06 pm, "LIANG Yunfeng" <liangy... at gmail.com>
> wrote:
> > > > > > Dear Axel,
> >
> > > > > > it is only a water system. For a small system(with 16 molecules),
> you
> > > > > will
> > > > > > only see it (the consuming time increase) after 5000 step(5ps),
> and
> > > > > becoming
> > > > > > apparent after 10,000 steps. For a large system(with 192
> molecules),
> > > you
> > > > > can
> > > > > > see it around 500 steps. Well, nothing serious...The architecture
> is
> > > amd
> > > > > > machine with infiniband and pgi compiler.
> >
> > > > > > Sincerely, Yunfeng
> >
> > > > > > On Wed, Apr 23, 2008 at 11:20 AM, Axel <akoh... at gmail.com>
> wrote:
> >
> > > > > > > On Apr 23, 12:00 pm, "LIANG Yunfeng" <liangy... at gmail.com>
> > > wrote:
> > > > > > > > Dear All,
> >
> > > > > > > > Have you everyone notice the consuming time for Quickstep is
> > > > > increasing
> > > > > > > as
> > > > > > > > the MD is propagating with the time?
> >
> > > > > > > no. i don't see this. can you provide an
> > > > > > > input example...
> >
> > > > > > > cheers,
> > > > > > >   axel.
> >
> > > > > > > > I guess there will be a way to solve...
> >
> > > > > > > > Sincerely, Yunfeng
> >
> > > >  192H2O-md.inp
> > > > 2KDownload
> >
> >
> >
> >  192H2O-md-1.ener
> > 328KDownload
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20080424/4794293e/attachment.html>


More information about the CP2K-user mailing list