[Pw_forum] error two atoms overlap

[Axel Kohlmeyer]

On Mon, Mar 26, 2012 at 6:33 PM, mohamed makhyoun <makhyoun2 at yahoo.com>wrote:

> Dear All:
>
> By running the given input file for pw.x I get the error:
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from check_atoms : error #         1
>      atoms #   1 and #   2 overlap!
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Although I checked the input by XCRYSDEN visualization program and nothing
> is wrong.
>  I appreciate any help.
>

there is a lot wrong.

on a crystal lattice positions

0.0 0.0 0.0

and

-1.0 0.0 0.0

are indeed the same,
just shifted by an entire cell.
your structure should have
only one Nb atom.

axel.



>
> Best Regard
>
> Mohamed
> ###################################################################
>
> &CONTROL
>                  calculation = 'scf' ,
>                  prefix='cu3nbs4'
>                 restart_mode = 'from_scratch' ,
>                   outdir = '$TMP_DIR/' ,
>                   pseudo_dir = '/home/mohamed/espresso/exec/pseudo' ,
>                   verbosity = 'default' ,
>
>  /
>  &SYSTEM
>                            ibrav=1
>                            celldm(1)= 10.397 ,
>                            nat = 20,
>                         ntyp = 3,
>                      ecutwfc = 60. ,
>                      nbnd=90,
>  /
>  &ELECTRONS
>               conv_thr=1.0D-8 ,
>  /
> ATOMIC_SPECIES
>    Nb  92.9064   Nb.pbe-sR-sc-us.UPF
>    Cu  63.546    Cu.pbe-sR-us.UPF
>     S   32.06     S.pbe-van-bm.UPF
>  ATOMIC_POSITIONS crystal
> Nb       0.000000000      0.000000000      0.000000000
> Nb      -1.000000000      0.000000000      0.000000000
> Nb       0.000000000      0.000000000     -1.000000000
> Nb       1.000000000      0.000000000      0.000000000
> Cu       0.500000000      0.000000000      0.000000000
> Cu       0.000000000      0.000000000     -0.500000000
> Cu      -0.500000000      0.000000000      0.000000000
> Cu       0.000000000     -0.500000000      0.000000000
> Cu       0.000000000      0.500000000      0.000000000
> Cu       0.000000000      0.000000000      0.500000000
> S        0.242599953      0.242599953      0.242599953
> S        0.242599953     -0.242599953     -0.242599953
> S       -0.242599953      0.242599953     -0.242599953
> S       -0.242599953     -0.242599953      0.242599953
> S       -0.757400047      0.242599953      0.242599953
> S        0.242599953      0.242599953     -0.757400047
> S       -0.757400047     -0.242599953     -0.242599953
> S        0.757400047      0.242599953     -0.242599953
> S       -0.242599953     -0.242599953     -0.757400047
> S        0.757400047     -0.242599953      0.242599953
> K_POINTS gamma
>
>
>
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>
>


-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com  http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.
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