[QE-users] Wrong interpretation of atomic number and missing atoms in .cube file generated by pp.x utility

[Paolo Giannozzi]

Does this happen with QE v.7.3? Then this might be the problem:
   https://gitlab.com/QEF/q-e/-/issues/645
and this the solution:
   https://gitlab.com/QEF/q-e/-/merge_requests/2247/diffs
Was fixed in v.7.3.1

Paolo
On 06/01/2025 11:01, Ankush Bharti via users wrote:
> Dear All
> 
> Performed scf calculation followed by pp.x with input :
> 
> &inputpp
>      prefix = 'MoSSe',
>      outdir = './',
>      filplot = 'charge_density',
>      plot_num = 0
> /
> &plot
>      nfile = 1,
>      filepp(1) = 'charge_density',
>      weight(1) = 1.0,
>      iflag = 3,
>      output_format = 6
>      fileout= 'charge_density.cube'
> /
> 
> But the generated output charge_density wrongly interprets atoms:
> 
>        27      27     180      27      27     180       3       3
>       0        5.98268394      0.00000000      0.00000000      
> 0.00000000      0.00000000      0.00000000
>     1.0000000000000000        0.0000000000000000        0.0000000000000000
>    0.49996841340535103       0.86597069419766792        0.0000000000000000
>     0.0000000000000000        0.0000000000000000        6.3158343598976590
>        181.3269592522        4.0000000000       50.0000000000     0
>     1   Mo   14.00
>     2         6.00
>     3   S    16.00
>     1       1.258220000    1.095970000    2.425560000    1
>     2       2.516310000    2.193870000    1.936220000    2
>     3       2.516310000    2.193870000    2.975630000    3
> And also wrong and missing atoms in .cube file with the header:
> 
>   Cubefile created from PWScf calculation
> Contains the selected quantity on a FFT grid
>      3    0.000000    0.000000    0.000000
>     27    0.221581    0.000000    0.000000
>     27    0.110783    0.191883    0.000000
>    180    0.000000    0.000000    0.209920
>     42   42.000000    4.536380    1.376013   14.511359
>      0    0.000000    3.089297    2.763573   11.583792
>     16   16.000000    3.089297    2.763573   17.802254
>    Is there something wrong with my input files ?????
> 
> *Ankush Bharti*
> Theoretical and Computational
> Condensed Matter Physics
> Department of Physics
> Himachal Pradesh University
> Shimla-171005
> Contact: +91-9459681650
> 
> 
> 
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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216