Re: how to get cell vectors in tcl forces script

From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Wed Mar 12 2014 - 09:26:46 CDT

Hi Norman & Salvatore,

I also thought about reading in the .xsc file but that would slow down the
simulation. Fortunately, the cell vectors do not change drastically - and
precision is
 unnecessary in my case- therefore lowering too much restartfreq is not
needed.

Norman can you give an example of using the output command within a
jobscript file? I don't understand how you can write restart files more
frequently than restartfreq does.

thanks,
Thomas

On 12 March 2014 16:01, Cosseddu, Salvatore <S.M.Cosseddu_at_warwick.ac.uk>wrote:

> Hi Norman,
>
>
> This is what I usually do, I set restartfreq
> conveniently. To be honest I don't know either about "output" command
> within tclforces.
>
>
> Best wishes
>
> Salvatore M Cosseddu
> ------------------------------
> *From:* Norman Geist <norman.geist_at_uni-greifswald.de>
> *Sent:* 12 March 2014 12:54
> *To:* Cosseddu, Salvatore
>
> *Cc:* Namd Mailing List
> *Subject:* AW: namd-l: how to get cell vectors in tcl forces script
>
>
> Yes, I mean I don't know if the "output" command works from TclForces. He
> need to try, otherwise he would have to set the restartfreq suitable for
> his needs.
>
>
>
> Norman Geist.
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Cosseddu, Salvatore
>
> *Gesendet:* Mittwoch, 12. Mrz 2014 13:06
> *An:* Namd Mailing List
> *Betreff:* RE: namd-l: how to get cell vectors in tcl forces script
>
>
>
> Dear Norman and Thomas,
>
>
>
> It works also within tclforces. You must be ready to a slight loss
> of performance for the additional I/O work. Anyway the following procedure
> has been tested and have worked fine for me since version 2.8. Hope it will
> help
>
>
>
> ------------------------------------
>
> proc readcell {xscfile}
> {
>
>
>
> if {[catch {open "${xscfile}" r} xsc]}
> {
>
> puts stderr "ERROR opening
> ${xscfile}
>
> CHECK!!!"
>
> exit
> 1
>
>
> }
>
>
>
> set in [read
> $xsc]
>
> set bcell [list [lindex $in 28] [lindex $in 32] [lindex $in
> 36]]
>
> print "readcell: read cell, at step [lindex $in 27] was
> $bcell"
>
> close
> $xsc
>
> return
> $bcell
>
> }
>
> -------------------------------------
>
>
>
> simply usage:
>
>
>
> set boxcell [readcell <xsc filename>]
>
>
>
> Best regards
>
> Salvatore M Cosseddu
>
>
> ------------------------------
>
> *From:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
> Norman Geist <norman.geist_at_uni-greifswald.de>
> *Sent:* 12 March 2014 07:29
> *To:* 'Thomas Evangelidis'
> *Cc:* Namd Mailing List
> *Subject:* AW: namd-l: how to get cell vectors in tcl forces script
>
>
>
> Hi,
>
>
>
> I was also searching for such a command, but the only way you are
> currently able to do it, seems to be using the "output" command to write a
> set of restarts and read the box info out of the xsc file. No idea if this
> is also possible within TclForces, but its working from jobscript context--089e01419f346634bf04f469a078--

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