[CP2K:1989] Re: Reftraj ensemble

Ondrej Marsalek ondrej.... at gmail.com
Wed Apr 15 11:35:02 UTC 2009

On Wed, Apr 15, 2009 at 13:18, Teodoro Laino <teodor... at gmail.com> wrote:
> Hi Ondrej
> Just a comment about point (1).
> Coordinates are needed to setup the environment. You need them.
> Instead of providing the &COORD section you can provide them using the
> same xyz file.

Sure, I get that. The point was that in principle they could be obtained
from the reftraj without the need for an explicit copy. But that is
actually quite insignificant compared to an additional problem:

When I do remove the i=0 frame as I said and also want cube file from
the run, I get them for different frames than position, and ener file
lines. When I want to start at frame 5000 and go with stride 100, I get
the correct frame numbers in ener and pos, that is 5000, 5100, 5200, ...
The cube file numbers, on the other hand, are: 5000, 5001, 5101, 5201,
... Looking at the coordinates in the cube files, they really seem to be
different from the frames in the pos file.

Overall, the whole reftraj frame numbering business is very confusing.
If anyone is interested, I will create a small testcase that
demonstrates this.


> Cheers
> Teo
> ---------------------------------------------
> Teodoro Laino
> Zurich Switzerland
> Contact info:
> Tel.:     http://www.jajah.com/Teo
> E-mail: teo... at laino.eu
>              teodor... at gmail.com
> ---------------------------------------------
> On 15 Apr 2009, at 12:53, Ondrej Marsalek <ondrej.... at gmail.com>
> wrote:
>> Hi,
>> I am trying to use the reftraj ensemble and there are two things that
>> I find slightly inconvenient.
>> 1) You need to provide coordinates in the input file, although they
>> are not needed, as you get them from the reference trajectory. They
>> are probably (at least I hope) ignored. If they are, it would be nice
>> say that in the input manual at the reftraj entry. It would be even
>> better not to require them at all and use whatever is the first frame
>> requested instead.
>> 2) If you want to get consistent step numbers everywhere, you need to
>> remove the frame with i=0 from CP2K xyz trajectory output that you use
>> as a reference trajectory. Seems to be due to some mixing of
>> zero-based and one-based indexing.
>> As usual with my messages here, nothing critical, but I think it is
>> worth mentioning. Either for people trying to make sense of the
>> numbers (like me a while ago) or for a developer who is really bored
>> ;-)
>> Best,
>> Ondrej
>> >
> >

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