Hi Ben,
Ben Roberts wrote:
> Hi all,
>
> I'm wondering if someone could give me a few pointers here.
>
> I'm trying to include writing restart and trajectory files in the XMIN algorithm, initially for my use in QM/MM calculations, so I can save files at each step instead of having to go back to the start if the calculation fails (since each step may take an hour or more).
>
> My initial solution, which works passably well, was to call minrit and corpac (based on ntwr and ntwx) at the end of the main do loop in run_xmin. (At the moment, this is only done if run_xmin is called directly, not from run_lmod.) This is based on n_force_calls. The problem is that some steps do more than one force call, so that a trajectory written on every force call contains more steps than the corresponding mdout file. Ideally, the steps counted to determine ixdump and itdump would be those that are counted for mdout-writing purposes.
Each xmin step does a line search which requires several gradient
evaluations (force calls). You don't want to write coordinates during
the line search but only for each new xmin step.
> Inside the do loop, I can see a rather complicated case switch, and it's not obvious to me which branches start a new "step", and which ones do another force evaluation within the same "step". Could anyone clarify which is which? I would guess that "case (CALCENRG_NEWNBL, CALCGRAD_NEWNBL, CALCBOTH_NEWNBL)" does not do a new step and that "case (CALCENRG_OLDNBL, CALCGRAD_OLDNBL, CALCBOTH_OLDNBL)" does, but I'm not certain...
As far as I can see, a new xmin step is done for
case ( CALCENRG_NEWNBL, CALCGRAD_NEWNBL, CALCBOTH_NEWNBL )
which is also when the minimization progress is printed. This is where
you want to write the coordinates.
All the best,
Andy
> Thanks!
>
> Ben
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
--
Dr. Andreas W. Goetz
San Diego Supercomputer Center
Tel : +1-858-822-4771
Email: agoetz.sdsc.edu
Web : www.awgoetz.de
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Fri May 07 2010 - 18:30:08 PDT
