[CPMD-list] Quench Bo Electrons

[Samir H. Mushrif]

Hello Axel,
           Thanks for your reply. The suggestions about EKINC and MD 
steps were helpful.       Its not the case that I don't have time to 
implement the solution that you have in mind for my problem. Your 
suggestions have always proven very valuable for me to proceed. I was 
just trying to see if this particular thing can be done without 
parallelization. If it is not possible then I WILL DEFINITELY go for 
parallel option. Since I am a PHD student and there are times when you 
want to get something done due to some deadline constraints and I am 
exactly in that situation.    Adding to the system specifications, I am 
having an AMD 64 opteron machine with dual core. With some of my 
simulations, I used upto 8 GB of memory (as seen in the CPMD output 
file's last few lines) and it worked fine.  Please let me know your 
suggestions and I will work on them.

Thanks again
Best Regards
Samir


Quoting Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu>:

> On Mon, 23 Jul 2007, Samir H. Mushrif wrote:
>
> hello samir,
>
> SM> Hello Axel,
> SM>              Thanks for your reply. Here are some details about the
> SM> discussion (The previous mail communication is at the bottom of this
> SM> e-mail):
> SM>
> SM>           I just performed 50 MD steps and I realized that I need to do
> SM> more MD steps. My sysmtem is huge (210 atoms) and also it is not
> SM> equilibrated classically before start (as it is done for the hydronium
> SM> in bulk water). You also mentioned that the EKINC value is higher. I
> SM> dont have a lot of experience but I thought that it will definitely be
> SM> high since I have 596 electrons in my system. Also looking at the EKS
>
> right. since this number is somewhat arbritrary, it is not
> 'normalized', so with more electrons this should be higher.
> how high is hard to tell. generally, it should be as low as
> possible (without thermostat), and while your system is moving
> towards equilibrium, it is likely that it will increase during
> that process, hence the QUENCH BO before starting the production.
>
> SM> value I noticed that it is continuously decreasing. I guess that I need
> SM> to do a lot more MD steps without thermostat (TEMPCONTROL IONS) to get
>
> a general strategy would be to run with TEMPCONTROL IONS until EKS is
> no longer drifting and then switch to NOSE IONS (try with the MASSIVE
> option for the while to have better ergodicity).
>
> SM> a reasonable value of EKINC. But It is still not clear to me that how
> SM> many times I have to run these steps with the QUENCH BO ELECTRONS ('x'
> SM> number of steps + QUENCH BO ELECTRONS). And as I mentioned that QUENCH
>
> how often you need to quench the system back to the BO surface
> depends on your system. just watch EKINC and whether it is increasing
> or keeping constant. you may also need to 'play' a little with
> the timeptep and fictious mass parameters to get an optimal combination
> for good adiabacity. if your system is behaving well, you may not need
> to quench more than a couple of times.
>
> SM> BO ELECTRONS gives the following error.
> SM>
> SM> ...... (a huge number) WORDS REQUIRED
> SM> PROGRAM STOPS IN SUBROUTINE MEMORY. TOO BIG VALUE.
>
> as already explained. this is a limitation of using regular
> fortran with cray-pointers on a linux machine. the interface
> to malloc only allows to pass memory allocation sizes up to
> 2GB and your job needs more. you _have_ to run in parallel
> or find a way to using 64-bit integers (depends on linux version
> and compiler, whether that can be made to work).
>
> SM> I am running CPMD on a AMD-opteron 64 bit machine in serial, DEBIAN OS
> SM> and it has 32 GB of RAM. I am working on getting CPMD working in
> SM> parallel but it is not done yet. However I would like to know that if I
>
> how many cpus/cores do you have on that machine?
>
> SM> have to still perform the MD, is there a way that I can skip the QUENCH
> SM> BO ELECTRONS. Since I am a PHD student, I want to get this part of my
> SM> project done and hence I don't want to spend a lot of time (since I
> SM> dont have computer science background, it takes me a lot more time than
> SM> others) on getting CPMD run in parallel. It is something that I
>
> well, if you don't have the time, you should not run CPMD, or at
> least not a system of that size on a serial machine. there may be
> some workaround to make it work in serial (i have a couple of ideas),
> however, they are a bit tricky, too, and would require some more testing
> and compiling and/or scripting. but since you don't want to put in 
> the effort...
>
> cheers,
>   axel.
>
> SM> definitely want to do but after getting this particular part of my
> SM> project done.
> SM>
> SM> Thanks and Best Regards
> SM> Samir
> SM>
>
> --
> =======================================================================
> Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>   Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
>
>