CHAPTER 11 · BASICS · CALCULATION TYPES

Densities and potentials

pp.x and plot_num, extracting charge densities and potentials, cube files, and visualization tools.

On this page

pp.x extracts densities and potentials from a finished SCF onto real-space grids and writes them in visualizable formats. Its input has two namelists: what to extract (&INPUTPP) and how to write it (&PLOT).

Input skeleton

&INPUTPP
  prefix   = 'si'
  outdir   = './tmp/'
  filplot  = 'si.rho.dat'
  plot_num = 0              ! 0 = valence charge density
/
&PLOT
  nfile         = 1
  filepp(1)     = 'si.rho.dat'
  weight(1)     = 1.0
  iflag         = 3         ! 3 = 3D
  output_format = 6         ! 6 = Gaussian cube
  fileout       = 'si.rho.cube'
/

iflag: 0 = 1D line, 1 = spherical average, 2 = 2D plane, 3 = 3D. output_format: 0 = gnuplot, 5 = XSF (XCrySDen), 6 = Gaussian cube, among others.

Frequently used plot_num values

Value Quantity Use
0 Valence charge density Bonding character
1 Total potential (V_bare + V_H + V_xc)
2 Local ionic potential
5 STM image Surfaces
6 Spin density ρ↑ − ρ↓ Visualizing magnetism
8 ELF (electron localization function) Bonds and lone pairs
11 Bare + Hartree potential Work-function calculations

The remaining values, and the PAW all-electron density options, vary by version; always check the Doc/INPUT_PP.txt of your install.

The skeleton of a work-function calculation

For a slab, extract the potential with plot_num=11, take the planar average parallel to the surface (with average.x or your own parser), and then:

$$\Phi = V_{\mathrm{vacuum}} - E_F$$

The vacuum level is the flat plateau of the planar-averaged potential in the middle of the vacuum. The full procedure, including the dipole correction, is in Chapter 15 and Example E13.

Bader charges are not built into QE

Bader analysis means exporting the density as a cube with pp.x and feeding it to the Henkelman group's bader code. With PAW you must export the all-electron density (check the corresponding plot_num in your version's Doc/INPUT_PP.txt); running Bader on the valence-only density distorts the result because the core charge is missing.

Visualization tools

  • VESTA: structures plus cube isosurfaces; the easiest starting point.
  • XCrySDen: the classic companion to QE (XSF format).
  • Python (ASE, pymatgen): get in the habit of parsing outputs yourself; it pays off the moment you need automation. Every figure in this guide is drawn with Python.
Common mistakes

Extracting the spin density (plot_num=6) and getting nearly zero: check spin_component, and first check whether the SCF actually converged to a magnetic solution at all (total/absolute magnetization). Also, cube files reach hundreds of MB quickly; manage the grid with nx, ny, nz and your disk.