[CPMD-list] Quench Bo Electrons

[Axel Kohlmeyer]

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
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If you make something idiot-proof, the universe creates a better idiot.