[CP2K:1990] Re: Reftraj ensemble

[Teodoro Laino]

Or even better.. instead of waiting.. if you already have an idea how to 
patch the indexing behavior just send us the
patch.. I will be more than happy to apply it to the CVS.

Regards,
Teo

Ondrej Marsalek wrote:
> 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.
>
> Ondrej
>
>
>   
>> 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
>>>
>>>       
>
> >
>