[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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