The ABINIT Users Mailing List ( CLOSED )

[Yuanliang Xie <xylnew@gmail.com>]

Dear  Matthieu,
 I want to use abinip other than abinis , any advice or comments please?
thanks
Xie Y.L.

On Mon, Mar 9, 2009 at 11:30 PM, matthieu verstraete <matthieu.jean.verstraete@gmail.com> wrote:

Ok, as a rule there should be no need to increase msym (it corresponds to an upper bound for any "normal" space group). If you are using a supercell, there should be a reason, and you will be introducing some breaking of the full symmetry (liquid state, defect, etc...) usually to much lower symmetry. The only reason I can think of to increase msym forcibly is to test the size-consistency of the code; you should have enough with a defected supercell calculation and a single-unit-cell calculation to get all the quantities you need. This means you don't even have to set chkprim to 0...

As abinit enforces symmetries quite strongly, if you keep them and try to do an MD the positions will stay fully symmetric (or almost) and you will not at all be representing a MC ensemble properly. Very important to break the symmetry of the initial positions. The ideal is to have a thermalized average set of positions, eg from an empirical potential run, but this is not always available.


Matthieu

On Mon, Mar 9, 2009 at 4:19 PM, Yuanliang Xie <xylnew@gmail.com> wrote:

Dear Nuno Galamba,
  Thank you for your advice. It give me new idea about the problem.
Xie Y.L.

 

On Mon, Mar 9, 2009 at 10:29 PM, Nuno Galamba <ngalamba@cii.fc.ul.pt> wrote:

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

--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Matthieu Verstraete

European Theoretical Spectroscopy Facility (ETSF) 
Dpto. Fisica de Materiales, 
U. del Pais Vasco,            
Centro Joxe Mari Korta, Av. de Tolosa, 72,   Phone: +34-943018393
E-20018 Donostia-San Sebastian, Spain        Fax  : +34-943018390

Mail : matthieu.jean.verstraete@gmail.com
http://www-users.york.ac.uk/~mjv500