One unintended side effect of this change is that now during trajectory
post-processing the output trajectory potentially gets written twice, once
during the minimization in runmin.f and once after minimization in trajene.f
(this is what's happening now that's causing the trajene and trajene_netcdf
trajectory write tests to fail). The way I see there are two ways to
proceed. One is to disable trajectory writing in runmin.f if imin==5, the
other is to disable trajectory writing in trajene.f altogether. The former
preserves the original behavior, but only allows writing of
post-minimization coordinates. The latter allows writing of as many
coordinates during the minimization step as you would like, but requires
more care in choosing ntwx. Either way would be fairly easy to implement.
Does anyone have an opinion either way?
-Dan
On Mon, Aug 24, 2009 at 9:30 AM, Ben Roberts <roberts.qtp.ufl.edu> wrote:
> Hi Ross,
>
> Ross Walker wrote:
>
>> Hi Ben,
>>
>> I think this would be useful and should probably be done in the same way a
>> negative ntwr works write now. E.g sequentially numbered restart files
>> every
>> abs(ntwr) steps. It should be fairly simple to do I think. Just find where
>> the minimization writes a restart file at the end and have it call an
>> equivalent routine after the coordinates have been updated in runmin based
>> on the value of ntwr with the filename based on whether ntwr is positive
>> or
>> negative.
>>
>>
> OK, I've done that, more or less, and have just uploaded the changes to the
> CVS tree.
>
> In brief:
>
> I've shifted the "write restart file" command from sander.f to runmin.f.
> This allows better logging of the file writing, so it will now say "writing
> restart file at X number of steps" for the last restart file as well as for
> the intermediate ones, if any.
>
> Along with that, I moved the "write restart file" command in sander.f
> inside the XMIN and LMOD switches. Those calls are still in sander.f,
> though, not inside the XMIN and LMOD subroutines. For the sake of
> consistency, I suppose it would be good to move them into those routines,
> but not understanding so much about what XMIN and LMOD did, I didn't really
> want to mess with them right now.
>
> Runmin.f and its counterpart, minrit.f, allow writing of restart files so
> that ntwr > 0 will overwrite "restrt" every ntwr steps, and ntwr < 0 will
> create a unique "restrt" every ntwr steps. Similarly, ntwx > 0 will now
> write a coordinate trajectory with frames saved every ntwx steps. It seemed
> best to make the behaviour of "ntwr" and "ntwx" under minimisation match the
> same under dynamics as closely as possible.
>
> Cheers,
> Ben
>
>
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>
--
Daniel R. Roe, Ph.D.
Research Chemist
National Institute of Standards and Technology
100 Bureau Drive, Stop 8443
Gaithersburg, MD 20899-8443
(301) 975-8741
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Received on Mon Sep 14 2009 - 13:40:29 PDT
