[CP2K:162] Re: about output handling in cp2k

Teodoro Laino teodor... at gmail.com
Wed Jul 11 16:13:49 CEST 2007


Ciao Axel,
The bug with the DCD should be fixed now.. check when you've occasion  
to do that and let me know in case of other problems..

Cheers
Teo

On 9 Jul 2007, at 19:56, Axel wrote:

>
>
> On Jul 9, 1:06 pm, Teodoro Laino <teodor... at gmail.com> wrote:
>
>> Regarding this one:
>>
>> At the moment we had no time to convert the RESTART of QS to a
>> print_key..
>> When  it will be a print_key you will be able to do it.. i.e. print
>> every n-th step of MD..
>> It's in our todo list.. but as you can imagine with a low priority...
>
> ok. great.
>
>>> finally, i noticed that .dcd files are missing the header part
>>> when i am using &EXT_RESTART to continue a calculation but
>>> rename the files for each run. the only workaround i found so far
>>> is to set RESTART_COUNTERS to .false., but since my jobs can
>>> have different length (due to dynamic backfill queueing they can
>>> be allowed to run for anything between 2 and 12 hours) it would be
>>> extremely nice to have my cake and eat it, i.e. .dcd files with
>>> headers
>>> and restarted counters. is there an alternative way to get the  
>>> header
>>> written?
>>
>> This was a bug but as far as I know Will fixed it.. are you using a
>> recent version?
>
> just updated the cvs and rechecked. yes, it still creates .dcd without
> a header. to reproduce it try the following:
> take the test/QS/H2O-md.inp file and change it:
> [akohlmey at vitriol ak]$ diff -u ../H2O-md.inp H2O-md.inp
> --- ../H2O-md.inp       2006-08-14 11:39:59.000000000 -0400
> +++ H2O-md.inp  2007-07-09 13:44:26.000000000 -0400
> @@ -65,4 +65,9 @@
>        MTS 2
>      &END NOSE
>    &END MD
> +  &PRINT
> +    &TRAJECTORY
> +      FORMAT DCD
> +    &END
> +  &END
>  &END MOTION
>
> run it and then i restart with a further modified file:
> diff -u H2O-md.inp restart.inp
> --- H2O-md.inp  2007-07-09 13:44:26.000000000 -0400
> +++ restart.inp 2007-07-09 13:46:54.000000000 -0400
> @@ -1,4 +1,9 @@
> -
> +&EXT_RESTART
> +   RESTART_FILE_NAME H2O-md-1.restart
> +   RESTART_COUNTERS  T
> +   RESTART_POS  T
> +   RESTART_VEL  T
> +&END
>  &FORCE_EVAL
>    METHOD Quickstep
>    &DFT
> @@ -48,7 +53,7 @@
>  &GLOBAL
>    FFTLIB FFTSG
>
> -  PROJECT H2O-md
> +  PROJECT H2O-md-a
>    RUN_TYPE MD
>    PRINT_LEVEL LOW
>  &END GLOBAL
>
> and bingo:
> [akohlmey at vitriol ak]$ strings H2O-md-pos-1.dcd | head -2
> CORD
> REMARK FILETYPE CORD DCD GENERATED BY
> CP2K                                      REMARK Support new DCD
> format with cell information
> [akohlmey at vitriol ak]$ strings H2O-md-a-pos-1.dcd | head -2
> [akohlmey at vitriol ak]$
>
> ...even if i am doing something wrong here, i think
> the second .dcd file should have a header.
>
>>> since cp2k already seems to append some sort of serial number to
>>> outputs, the most desirable (to me) way of writing output would
>
> btw. i forgot to ask: where do i set this number?
> i would have expected that this is a flag somewhere
> in &GLOBAL ...
>
>>> actually
>>> be to have a parameter that specifies how many steps would go into
>>> a single file (e.g. 2000, derived from the time step number) and  
>>> then
>>> start a new file when that is reached and step up the serial number.
>>> could that be implemented with reasonable effort?
>>
>> don't think so.. again Fawzi can comment on the print_keys better
>> than I can do..
>> (i.e. I like this way of numbering ;-) )
>
> well, feel free to add it to the ever growing TODO list :-)
>
> cheers,
>    axel.
>
>>
>> Teo
>>
>>> thanks,
>>>    axel.
>
>
> >




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