The ABINIT Users Mailing List ( CLOSED )

[DORADO Boris Thésard <boris.dorado@cea.fr>]

Dear Xie,

 

This issue occurs when trying to build a supercell with ABINIT. It is because the maximum number of symmetries of the system (defined by msym) is set to 384 in the source code. Therefore, if you wish to build a supercell, you have to change this value in the main abinit.F90 routine and compile your code again. This is what I did for my supercells calculations.

 

If you cannot compile the source code, you can maybe decrease the symmetries in your system “by hand” using the keyword nsym. I’ve never tried it though. But if it works, I believe that the calculations will converge slower/harder due to the lowering of the symmetries.

 

Good luck.

 

Boris D.

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De : Yuanliang Xie [mailto:xylnew@gmail.com]
Envoyé : lundi 9 mars 2009 13:24
À : forum@abinit.org
Objet : Re: [abinit-forum] about supercell and MD

 

Dear Nuno Galamba and others,
 Thank Nuno Galamba for reply.
 Would you please tell me the details how  make a supercell  in ABINIT (  as a 64-atoms NaCl supercell  mentioned  the Nuno Galamba's reply  )?
I made a 64-atoms cubic boron nitride supercell in ABINIT V5.6.4, but it fails.  The inputfile is attached .
The output is

symfind : ERROR -
  The number of symmetries (including non-symmorphic
  translations) is larger than msym= 384
  Action : take a cell that is primitive, or at least
  smaller than the present one.

 leave_new : decision taken to exit ...

Thanks
Xie Y.L.

On Mon, Mar 9, 2009 at 2:19 AM, Nuno Jorge Lopes Galamba <ngalamba@cii.fc.ul.pt> wrote:

Dear Xie Yuanliang,

ABINIT can make molecular dynamics much as any other ab initio molecular dynamics code although there are differences relative to other codes. Of course there are also many differences between different (other than ABINIT) codes.  ABINIT allows carrying out what can be called Hellman-Feynman MD simulations. This means that forces on the nuclei are obtained via the Hellman-Feynman theorem every time-step. This is a striking difference from Car-Parrinello MD (CPMD) with obvious computational costs since in the later the energy functional is not minimized every time-step. Other than that both ABINIT and CPMD both use plane-waves and pseudopotentials. On the other hand since plane-waves are used rather than localized basis functions, allowing to apply the Hellman-Feynman theorem, this is also different from what is frequently called Born-Oppenheimer MD, which uses localized basis functions and therefore the Hellman-Feynman theorem cannot be applied. These different denominations are obviously not the fundamental issue, rather, the approximations involved are. Thus one can find first principles or ab initio MD simulations using very different schemes most of which motivated by the need for less demanding force calculation algorithms under a DFT description. I think ABINIT is not specially devoted to this issue and therefore large systems are in my view prohibitive. I have carried out MD simulations of ABINIT of NaCl and NaI (64 atoms) and they were obviously very demanding, however other systems can be much worst. This shall depend, broadly, on the one hand on the number of valence electrons in your system and on the other on the plane-wave cut-off you need to have reasonably converged forces.

As for the second part of your question this is not difficult. All you need is to have a set of positions and velocities for your atoms and to set the acell variable as to obtain the desired density. Thus you simply treat acell much as if it were the size of the MD box (supercell), rather than the length of the primitive cell. The computations can, for a supercell, be carried out on a single k point (0,0,0) and you are all set. If you can parallelize ABINIT in terms of nbands things can improve, I would guess, although I have never used ABINIP.

Please note I have limited experience with ABINIT, and you may want to check with other ABINIT users.

Take care.


Nuno Galamba
Grupo de Física-Matemática da Universidade de Lisboa.
Portugal



On Sun, 8 Mar 2009 20:51:24 +0800, Yuanliang Xie wrote

> Dear all,
>    I want to know if ABINIT able to do molecular dynamics  calculation  for  a very  big super cell  as other ab initio molecular dynamics codes. Moreover, how can I make a supercell in a single point energy calculation with ABINIT?
>  Thanks.
>
> Xie Yuanliang
> SYIAE, Shenyang, China