[CPMD-list] Quench Bo Electrons

[Samir H. Mushrif]

Hello Axel,
             Thanks for your reply. Here are some details about the 
discussion (The previous mail communication is at the bottom of this 
e-mail):

          I just performed 50 MD steps and I realized that I need to do 
more MD steps. My sysmtem is huge (210 atoms) and also it is not 
equilibrated classically before start (as it is done for the hydronium 
in bulk water). You also mentioned that the EKINC value is higher. I 
dont have a lot of experience but I thought that it will definitely be 
high since I have 596 electrons in my system. Also looking at the EKS 
value I noticed that it is continuously decreasing. I guess that I need 
to do a lot more MD steps without thermostat (TEMPCONTROL IONS) to get 
a reasonable value of EKINC. But It is still not clear to me that how 
many times I have to run these steps with the QUENCH BO ELECTRONS ('x' 
number of steps + QUENCH BO ELECTRONS). And as I mentioned that QUENCH 
BO ELECTRONS gives the following error.

...... (a huge number) WORDS REQUIRED
PROGRAM STOPS IN SUBROUTINE MEMORY. TOO BIG VALUE.

I am running CPMD on a AMD-opteron 64 bit machine in serial, DEBIAN OS 
and it has 32 GB of RAM. I am working on getting CPMD working in 
parallel but it is not done yet. However I would like to know that if I 
have to still perform the MD, is there a way that I can skip the QUENCH 
BO ELECTRONS. Since I am a PHD student, I want to get this part of my 
project done and hence I don't want to spend a lot of time (since I 
dont have computer science background, it takes me a lot more time than 
others) on getting CPMD run in parallel. It is something that I 
definitely want to do but after getting this particular part of my 
project done.

Thanks and Best Regards
Samir

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

> On Fri, 20 Jul 2007, Samir H. Mushrif wrote:
>
> SM> Hello CPMD users,
>
> hello samir!
>
> SM>                   Thank you Axel for your suggestions on my previous
> SM> mail regarding the monoclinic cell symmetry problem and the unit cell
> SM> size problem (CPMD list digest - July 10). As per your suggestions, I
> SM> did several single point calculations and then used the Murnaghan
> SM> equation of state to find the optimum lattice constant. It is working
> SM> well and is solving my purpose.
>
> ok. great.
>
> SM>      The question I have this time is regarding the MD. As per the
> SM> instructions given on your website (for hydronium ion in bulk water)
> SM>
> SM> 
> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-intro.html#relax
>
> please note, that the number of timesteps for the 'initial'
> NVE calculation of this example is the absolute minimum for
> a configuration that has been well pre-equilibrated. most
> systems need more (a couple of thousand MD steps or more)
> until the system is reasonably equilibrated.
>
> SM> I did the initial MD (after optimizing the wavefunction) without using
> SM> thermostat (using TEMPCONTROL IONS) to find out the EKINC value (which
> SM> comes to ~0.17 for my system) and then I tried to do QUENCH BO
> SM> ELECTRONS. But my output gives error as
>
> hmmm, 0.17 looks a little high for typical systems. for how long
> did you run with NVE and how did EKS behave during that time?
> did it fluctuate around a simple average value or did you still
> see a drift.
>
> SM> PROGRAM STOPS IN SUBROUTINE MEMORY. TOO BIG VALUE.
>
> what platform are you running on?
> 32-bit/64-bit, OS, compiler, parallel/serial, etc...
>
> can you provide the few lines of output before and after
> this message (so we can see where it comes from)?
>
> quench bo needs a little more (temporary) memory than
> the regular code, and if your malloc uses a 32-bit integer
> for the size, if may not be able to handle this allocation.
> note, this error does not come from the fact, that you don't
> have any free memory, but that you are requesting, too large
> a block at a time (which is strange, too, but can happen).
>
> SM> For my system, the MD run (as well as thew initial wavefunction
> SM> optimization step) takes approximately 6.5 GB of memory and the total
> SM> memory of my machine is 24 GB. So why should this problem come when I
> SM> am trying to do the QUENCH BO option? Does it need more memory than a
> SM> typical wavefunction optimization? If yes, what is the other way to
> SM> proceed without using the QUENCH BO option?
>
> the easiest way to reduce the size of memory allocations in cpmd would
> be to run across more nodes in parallel. if you have enough memory in
> the machine, you may want to try using twice as many cpus than you have
> physically. there will be some overhead, but this should work around
> the large allocation issue.
>
> cheers,
>   axel.
>
> SM>
> SM> Thanks for all your help and suggestions.
> SM>
> SM> Best Regards
> SM> Samir
> SM>   _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
> SM>
> SM> Samir H. Mushrif
> SM> Department of Chemical Engineering
> SM> McGill University
> SM> 3610 University Street
> SM> Montreal, Quebec H3A2B2
> SM> Canada
> SM> Ph: (Lab)514-398-5170
> SM>     (Off)514-398-4169
> SM>
> SM> _______________________________________________
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> 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.
>
>