[Pw_forum] "Wrong atomic coordinates" message

degironc degironc at sissa.it
Wed Sep 12 15:45:05 CEST 2007


Dear Sergey,
   0.5 0.5 0.5 and 0.5 0.0 0.0 are connected by a Bravais lattice vector.
   You are  putting two atoms in the same position.
   stefano

Sergey Levchenko 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 0.0 0.0) 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).
>  
> Thank you for your patience.
>  
> Sincerely,
>  
> Sergey Levchenko,
> University of Penn.
>
>  
> On 9/12/07, *Xunlei Ding* <ding at sissa.it <mailto: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
>     <mailto: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
>     <mailto: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
>     <mailto: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.
>     >>>>
>     >>>>What could be the problem?
>     >>>>
>     >>>>Thank you.
>     >>>>
>     >>>>Sincerely,
>     >>>>
>     >>>>Sergey Levchenko,
>     >>>>University of Pennsylvania.
>     >>>>
>     >>>>
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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 <mailto:Eyvaz.Isaev at fysik.uu.se>,
>     eyvaz_isaev at yahoo.com <mailto:eyvaz_isaev at yahoo.com>
>     >>>
>     >>>
>     >>>
>     >>>
>     >>>
>     >>>
>     >>>
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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 <mailto:Eyvaz.Isaev at fysik.uu.se>,
>     eyvaz_isaev at yahoo.com <mailto:eyvaz_isaev at yahoo.com>
>     >
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