The ABINIT Users Mailing List ( CLOSED )

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

To learn how to do MD with ABINIT you should read in the input variables 
description the variable IONMOV

http://www.abinit.org/Infos_v5.5/input_variables/varrlx.html#ionmov

Starting from here you can readily understand what are the fundamental 
variables you must set up to carry out a simulation as they are all linked to 
IONMOV

As for the efficiency there's not much I can help you on.

Nuno Galamba

On Monday 09 March 2009 16:50:28 Yuanliang Xie wrote:
> Dear Nuno Galamba,
>    Thank you. I  UNDERSTOOD your trick.  it is  one of  MD basic skills as
> discussed by many
>    text books or other mail lists.
>    After  skip the ABINIT documents, I cannot get  a detailed  introduction
> on controlling  MD calculation in
> ABINIT (e.g.  how to set the ensemble  ).
>   I have just tested a system ( 64B + 64N ,gamma point). It seems not very
> efficient as I want.
> Xie Y.L.
>
> On Tue, Mar 10, 2009 at 12:18 AM, Nuno Galamba <ngalamba@cii.fc.ul.pt>wrote:
> > As I referred to that trick of changing a little bit the coordinates to
> > break
> > symmetry I assumed that was the case. That is, that Xie Y.L. does not
> > have an
> > equilibrated configuration for his system and he is simply looking for a
> > fast
> > way of looking at the computational cost of the simulation.
> >
> >
> >
> > Nuno Galamba
> >
> > On Monday 09 March 2009 15:30:42 matthieu verstraete 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 <http://gfm.cii.fc.ul.pt/people/ngalamba/%0Ae-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 <http://gfm.cii.fc.ul.pt/people/ngalamba/%0Ae-mail>:
> > > >> ngalamba@cii.fc.ul.pt
> >
> > --
> > 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 <http://gfm.cii.fc.ul.pt/people/ngalamba/%0Ae-mail>:
> > ngalamba@cii.fc.ul.pt



-- 
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