> > 4) a new -suffix command line option. If you put -suffix
020906.1.4proc
> > in the command line, then all the output files will have this appended
to
> > the default name unless you explicitly specified a name for them on
the
> > command line. So this applies to mdout, mdinfo, mden, mdcrd, mdvel,
> > restrt, and logfile (pmemd now permits logfile naming also with a -l
flag).
> > This is a really simple, easy-to-use command line interface
enhancement you
> > all may want to pick up for sander. The code is in get_cmdline.fpp
for
> > pmemd.
>
> It sounds like a nice idea to me--it would get us a long way towards
having
> a more standardized file nomenclature. I'm just posting this to the
> developers' list to see if people have either objections or better ideas
along
> this line.
I like this idea in some respect, but most likely would not use it in
general. As I run now, I do:
set pre = 1;
set cur = 2;
sander -O -c restrt.$pre -o mdout.$cur -i mdin -p prmtop -r restrt.$cur
-x traj.$cur
and then update the script to increment $pre and $cur.
The -suffix option doesn't help me in this case since (1) both the prmtop
and mdin files do not need a suffix as the same files are typically used
throughout a long series of runs (i.e. I don't want to have to move the
mdin and prmtop files to prmtop.suffix/mdin.suffix every run as I update
suffix), and (2) I would have to move the previous restrt to the new
inpcrd.suffix; so, I do not see a significant benefit for my usage
pattern.
I would happily use -prefix though! This would be advantageous for
multisander since I could for each instance use the default names and give
each a different sub-directory for the files via -prefix ...
--tom
(p.s. DAC, ptraj in the tree was -DBINTRAJ wrapped and I'll get on final
NetCDF mods, cluster + docs next week)
Received on Wed Apr 05 2006 - 23:49:42 PDT
