[CP2K:162] Re: about output handling in cp2k
teodor... at gmail.com
Wed Jul 11 16:13:49 CEST 2007
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..
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
>> 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
>>> and restarted counters. is there an alternative way to get the
>> 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 @@
> + RESTART_FILE_NAME H2O-md-1.restart
> + RESTART_COUNTERS T
> + RESTART_POS T
> + RESTART_VEL T
> METHOD Quickstep
> @@ -48,7 +53,7 @@
> 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
> 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 ...
>>> 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
>>> 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 :-)
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