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

_______________________________________________________________________________
The Quantum ESPRESSO Foundation stands in solidarity with all civilians 
worldwide who are victims of terrorism, military aggression, and indiscriminate 
warfare.
--------------------------------------------------------------------------------
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users mailing list users@lists.quantum-espresso.org
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