[QE-users] pp.x does not appear to recognize all atoms in the cell

[Vahid Askarpour]

Dear QE Community,

I ran a self consistent calculation with QE-7.3.1 using the following input:

&CONTROL
  calculation = 'scf'
  outdir = './'
  prefix = 'Br2K'
  pseudo_dir = './' 
  tprnfor = .true.
  tstress = .true.
  verbosity = ‘high'
/
&SYSTEM
  ecutwfc=   180
  ecutrho =  750
  ibrav = 0
  celldm(1)= 20.45
  nat = 6
  ntyp = 2
  occupations = 'smearing'
  smearing = 'gauss'
  degauss=0.02
  lspinorb=.true.
  noncolin=.true.
  vdw_corr = 'dft-d3',
  dftd3_version=4,
  dftd3_threebody=.false.
/
&ELECTRONS
  conv_thr =   1.0d-10
  electron_maxstep = 500
  mixing_mode='local-TF'
/
ATOMIC_SPECIES
K    39.098    K.rel-pbe-spn-kjpaw_psl.1.0.0.UPF
Br   79.904 Br.rel-pbe-dn-kjpaw_psl.1.0.0.UPF

CELL_PARAMETERS (alat= 20.45000000)
   0.336619648   0.223517680   0.000000000
   0.113216294   0.560074311   0.000000000
   0.000000000   0.000000000   2.313660000

ATOMIC_POSITIONS (crystal)
K                0.5002685977        0.4998912364        0.6250553296
Br               0.5000964551       -0.0000308156        0.5506101065
Br               0.4999035449        1.0000308156        0.4493898935
K                0.4997314023        0.5001087636        0.3749446704
Br               0.4997086268        1.0001150915        0.3327077817
Br               0.5002913732       -0.0001150915        0.6672922182

K_POINTS (automatic)
20 20  1 0 0 0

Then, I ran pp.x on the following input:

&inputpp
 prefix='Br2K',
 outdir=‘./',
 plot_num=0,
/
&plot
 iflag=3,
 output_format=6,
 fileout='rho.cube',
/

The cube file has the following first few lines:

 Cubefile created from PWScf calculation
Contains the selected quantity on a FFT grid
    6    0.000000    0.000000    0.000000
   75    0.091785    0.060946    0.000000
  108    0.021438    0.106051    0.000000
  432    0.000000    0.000000    0.109524
   19   19.000000    4.601170    8.012210   29.574085
    0    0.000000    5.757802   13.739076   26.051758
    0    0.000000    3.441343    2.285380   21.262589
   19   19.000000    4.597975    8.012246   17.740262
    0    0.000000    3.440197    2.285455   15.741851
    0    0.000000    5.758948   13.739002   31.572496

The charge zed=19 for K and 35 for Br but here, Br atoms are not read and their charge is zero.

Is this a bug or an error on my part?

Thanks,
Vahid

Vahid Askarpour
Department of Physics and Atmospheric Science
Dalhousie University
Halifax, NS, CANADA