[Pw_forum] "Wrong atomic coordinates" message

[Eyvaz Isaev]

Dear Sergei,
  
--- Sergey Levchenko <levuser at gmail.com> wrote:

> Dear friends,
> 
> I am terribly sorry, I made a mistake in my input
> file. With the coordinates> specified in that file
>(Li 0.5 0.5 0.5, H 0.6 0.00.0) I also don't >get the 
error message. The problem seems to occur >only for
atomic coordinates (Li
> 0.5 0.5 0.5, H 0.5 0.0 0.0).
 
Exactly, because these two positions are equivalent
in combination with basis vectors you used. Just draw
an FCC lattice (cubic cell) on a piece of a paper and
you immediately can see that they are equivalent if
you shift atom (0,0,1/2) along [110] direction. 

If you use basis vectors for simple cubic lattice, no
error message appeares.

So, check your atomic positions again or basis
vectors.

Bests,
Eyvaz.

> 
> Thank you for your patience.
> 
> Sincerely,
> 
> Sergey Levchenko,
> University of Penn.
> 
> 
> On 9/12/07, Xunlei Ding <ding at sissa.it> wrote:
> >
> > Dear Eyvaz,
> >
> > Yes, I did the same test as you, and no error like
> "Wrong atomic
> > coordinates" was found.
> > But when I used xcrysten to see the input file,
> > it was found that the distance between H and Li is
> about 0.4A.
> > I am not sure whether some versions of espresso
> will think this too
> > close distance as "Wrong atomic coordinates".
> >
> > My suggestion to Sergey is:
> > at first, check what Eyvaz has said , ie "Check
> your own file in your
> > computer whether it contains any extra symbol at
> the end of a line
> > (usually ^M due to DOS, Windows).".
> > If no problem, then add "crystal" to the line
> "ATOMIC_POSITIONS" to see
> > what will happen.
> >
> > Best regards,
> > Ding
> >
> > Eyvaz Isaev wrote:
> >
> > >Hi Sergei,
> > >
> > >--- Sergey Levchenko <levuser at gmail.com> wrote:
> > >
> > >
> > >>I think I know what my mistake was. I specified
> > >>atomic_positions card with default option which
> is >
> > >>
> > >>
> > >alat, but that is still in cartesian coordinates,
> > >
> > >
> > >>right? I wanted to specify in the basis of the
> > >>lattice vectors. Do I have to  use option
> crystal?
> > >>
> > >>
> > >
> > >No, the error is not related to specifing atomic
> > >coordinates either in cartesian or wrt lattice
> > >vectors. Of course, you will find incorrect
> symmetry
> > >if you setup atomic positions improperly. This
> will
> > >result in incorrect total energy.
> > >
> > >Actually I used your input file, except
> > >Pseudopotentials name, but did not observe any
> message
> > >like you mentioned (more strictly, no message).
> So,
> > >your input file looks correct. Check your own
> file in
> > >your computer whether it contains any extra
> symbol at
> > >the end of a line (usually ^M due to DOS,
> Windows).
> > >Use "vi" editor for this purpose.
> > >It might also be you need an extra blank at the
> > >beginning of these lines.
> > >
> > >Bests,
> > >Eyvaz.
> > >
> > >
> > >>Here is my input:
> > >>
> > >>LiH
> > >>&CONTROL
> > >>  calculation = 'scf'
> > >>  restart_mode    =  'from_scratch'
> > >>  prefix      = 'lih'
> > >>  pseudo_dir  = '/workspace/lev/PWSCF/LiH'
> > >>  outdir      = '/workspace/lev/PWSCF/LiH'
> > >>  iprint      = 2
> > >>  verbosity   = 'high'
> > >>  tprnfor         =  .true.
> > >>/
> > >>&SYSTEM
> > >>  ibrav       = 0,
> > >>  celldm(1)   = 7.5557540587,
> > >>  nat         = 2,
> > >>  ntyp        = 2,
> > >>  ecutwfc     = 70.0,
> > >>  occupations = 'fixed',
> > >>  nosym = .true.
> > >>/
> > >>&ELECTRONS
> > >>  conv_thr    = 1.D-6,
> > >>  mixing_beta = 0.3D0,
> > >>/
> > >>ATOMIC_SPECIES
> > >>Li 1.0 li-3.ncpp
> > >>H 1.0 h.ncpp
> > >>ATOMIC_POSITIONS
> > >>Li 0.5 0.5 0.5
> > >>H 0.6 0.0 0.0
> > >>K_POINTS {automatic}
> > >>4 4 4 0 0 0
> > >>CELL_PARAMETERS
> > >>0.0 0.5 0.5
> > >>0.5 0.0 0.5
> > >>0.5 0.5 0.0
> > >>
> > >>Thanks!
> > >>
> > >>Sergey.
> > >>
> > >>On 9/11/07, Eyvaz Isaev <eyvaz_isaev at yahoo.com>
> > >>wrote:
> > >>
> > >>
> > >>>Hi Sergey,
> > >>>
> > >>>It seems something wrong in your input file.
> Could
> > >>>
> > >>>
> > >>you
> > >>
> > >>
> > >>>please post your input file?
> > >>>I can suggest that you specify only ireeducible
> > >>>
> > >>>
> > >>atomic
> > >>
> > >>
> > >>>positions while all atomic positions have to be
> > >>>listed.
> > >>>
> > >>>Bests,
> > >>>Eyvaz.
> > >>>
> > >>>--- Sergey Levchenko <levuser at gmail.com> wrote:
> > >>>
> > >>>
> > >>>
> > >>>>Hi!
> > >>>>
> > >>>>I've encountered a peculiar problem. I want to
> > >>>>
> > >>>>
> > >>run
> > >>
> > >>
> > >>>>PWSCF 3.2 for the
> > >>>>following atomic system:
> > >>>>
> > >>>>Li 0.5 0.5 0.5
> > >>>>H 0.5 0.0 0.0
> > >>>>
> > >>>>lattice vectors (fcc):
> > >>>>
> > >>>>0.0 0.5 0.5
> > >>>>0.5 0.0 0.5
> > >>>>0.5 0.5 0.0
> > >>>>
> > >>>>alat=7.555754 bohr
> > >>>>
> > >>>>I specify ibrav = 0, and nosym true. But the
> > >>>>
> > >>>>
> > >>program
> > >>
> > >>
> > >>>>crashes right at the
> > >>>>beginning with the message:
> > >>>>
> > >>>>from setup : error #              1
> > >>>>Wrong atomic coordinates
> > >>>>
> > >>>>I get the same message with ibrav=2.
> 
=== message truncated ===>
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-------------------------------------------------------------------
Prof. Eyvaz Isaev, 
Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and 
Condensed Matter Theory Group, Uppsala University, Sweden Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com


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