Few questions from a beginner

Axel akoh... at gmail.com
Wed Jan 25 04:42:35 CET 2012



On Tuesday, January 24, 2012 10:02:34 PM UTC-5, Chetan Mahajan wrote:
>
> Hello Friends
>
> I am new to cp2k or any quantum calculations, carrying out 
> Born-Oppenheimer molecular dynamics simulations of water solvated acid-base 
> polymer systems. I have some questions on our first output:
>
> 1. Any good reference which would explain all the terms in cp2k output? I 
> have Essentials of Computational Chemistry by Cramer and it is pretty good, 
> but it does not use same or all the terms as cp2k output, so it is 
> confusing for a beginner like me. 
>

the cramer book is very "essential" and does not touch a lot of what is 
relevant for cp2k.
a lot of the "slang" related to cp2k comes from the condensed matter 
physics / electronic
structure area and is best understood, if you also gain some understanding 
of pure
plane wave basis set DFT calculations (e.g. in the form of car-parrinello 
MD).

a good introduction that is palatable for people with a chemistry training 
(there are
other good ones, but they are more accessible to people with a strong 
physics
background), is in my opinion "electronic structure calculations for solid 
and molecules:
theory and computational methods" by jorge kohanoff. 

from there on, you can work your way through some of the cp2k papers
and more specific books. as a rule of the thumb you should keep in mind
that the integral of all evil things remains a constant, i.e. for every 
benefit
there is a disadvantage. which means, that you have to expect to make
some serious mistakes until you get to know those problems. it is 
therefore highly recommended to not start with something too difficult
or too complex. that will just increase the number of possibilities for
errors and decrease the chances to detect them.


> 2. For a classically MD equilibrated input to AIMD, initial energy is 
> -3128.122 H, but for a random, non-equilibrated input (which by the way was 
> my input to classical MD equilibration) to AIMD, initial energy is 
> -3129.058 H. My question is why is energy decreasing for a non-equilibrated 
> system?  I understand we are dealing with ground-states only, but shouldn't 
> quantum mechanical energy be higher if system is not classically 
> equilibrated in general? Is this pointing to any error?
>

this is very difficult to say without knowing the exact difference between
your equilibrated and non-equilibrated system. do they have the same 
volume? are they both neutral?  if the difference is rather small, it can 
just
be that what is equilibrated with a classical model has some too close
contacts for your DFT calculation. also keep in mind that (simple) DFT
(e.g. BLYP) is notoriously bad at representing dispersion interactions.

it could also just mean that you may not have converged one of the 
wavefunctions to the real ground state. there are many things that
can go wrong and it is difficult judge only from the total energy.

axel.


 

> Thanks
> Chetan
>
> -- 
> Chetan V Mahajan
> PhD candidate, Ganesan Group
> Department of Chemical Engineering
> The University of Texas at Austin
>
>  
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