The ABINIT Users Mailing List ( CLOSED )

[Nuno Galamba <ngalamba@cii.fc.ul.pt>]

Dear Xie Yuanliang,

I also had this problem as explained by Boris D., when I considered the 
solid. 
My MD simulations of NaCl and NaI were for the liquid state. However as I 
recall one could surmount the problem by reducing the symmetry of the system 
through the very coordinates of the system. That is, rather than having:

 0.75 0.25 0.75
 0.25 0.25 0.25
...

you can do something like:

 0.750001 0.250002 0.750003
 0.250004 0.250005 0.250001
...

Something like this. I had my fcc positions being generated for some density 
I 
wanted and therefore this was simple to do.

I made this calculations a long time ago when I was exploring ABINIT and I 
don't recall the details anymore, but I do have the idea of introducing 
some "noise" on the positions to avoid the max. number of symmetry operations 
dimensioned in ABINIT. 

Hopefully I am not  mystaken.

This trick is 0k for a MD simulation starting configuration since we don't 
care about optimized supercells anyway.

Take care.

Nuno Galamba

-- 
Nuno Galamba
Grupo de Fisica-Matematica da Universidade de Lisboa
Av. Prof. Gama Pinto, 2, 1649-003, Lisboa, Portugal
URL: http://gfm.cii.fc.ul.pt/people/ngalamba/
e-mail: ngalamba@cii.fc.ul.pt



 



On Monday 09 March 2009 12:24:24 Yuanliang Xie wrote:
> 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



-- 
Nuno Galamba
Grupo de Fisica-Matematica da Universidade de Lisboa
Av. Prof. Gama Pinto, 2, 1649-003, Lisboa, Portugal
URL: http://gfm.cii.fc.ul.pt/people/ngalamba/
e-mail: ngalamba@cii.fc.ul.pt