UT theoretical chemistry code forum

Hello everybody,

I am trying to work with the bader-charge code (I AM A BEGINNER), I have modeled the adsorption of NH3 on the surface of the borophene (see attached Figure, FIG1) using Quantum espresso code.

I wanted:
1) first know the atomic charge for the NH3 molecule.
2) calculate the charge transfer
I have attached the three .ACF files
NH3_ACF = NH3
BS_ACF = Borophene
NH3-BS_ACF = NH3-Borophene

I can't figure out how to calculate the atomic charges on the atoms N, H1, H2, and H3 for the isolated molecule (before adsorption) and also after adsorption.

Knowing that, I generated the two .cube files NH3_valence.cube and NH3_allelec.cube, using plot_num = 0 and plot_num = 21 , respectively, with Quantum espresso code.
then, I used the BADER code command:
bader NH3_valence.cube -ref NH3_allelec.cube


Moreover, on the NH3-BS_ACF file, the last four lines 81, 82, 83 and 84 correspond respectively to atoms N, H1, H2, and H3.

I hope my question will be helpful for everyone.

It looks to me like you don't have core charges included. Your N atoms has a charge over 8, which is including the charge on the 3 H atoms. You can still estimate the charge transfer from the Boron surface to the NH3 molecule as 8.1-8=0.1e, but you really need core charges to resolve the charge density on the H atoms.

Thank you very much dear graeme,

In the previous calculation I used: plot_num = 21. knowing that :

21 = all-electron charge density (valence + core).
For PAW calculations only; requires a very dense real-space grid.

So, I recalculated with plot_num = 17, I found the same thing.

17 = all-electron valence charge density
can be performed for PAW calculations only
requires a very dense real-space grid!


Do I have to use other option ??

Input File Description (pp.x)
https://www.quantum-espresso.org/Doc/IN ... html#idm24
=============================================
plot_num INTEGER

Selects what to save in filplot:

0 = electron (pseudo-) charge density

1 = total potential V_bare + V_H + V_xc

2 = local ionic potential V_bare

3 = local density of states at specific energy or grid of energies
(number of states per volume, in bohr ^ 3, per energy unit, in Ry)

4 = local density of electronic entropy

5 = STM images
Tersoff and Hamann, PRB 31, 805 (1985)

6 = spin polarization (rho (up) -rho (down))

7 = contribution of selected wavefunction (s) to the
(pseudo-) charge density. For norm-conserving PPs,
| psi | ^ 2 (psi = selected wavefunction). Noncollinear case:
contribution of the given state to the charge or
to the magnetization along the direction indicated
by spin_component (0 = charge, 1 = x, 2 = y, 3 = z)

8 = electron localization function (ELF)

9 = charge density minus superposition of atomic densities

10 = integrated local density of states (ILDOS)
from emin to emax (emin, emax in eV)
if emax is not specified, emax = E_closed

11 = the V_bare + V_H potential

12 = the sawtooth electric field potential (if present)

13 = the noncollinear magnetization.

17 = all-electron valence charge density
can be performed for PAW calculations only
requires a very dense real-space grid!

18 = The exchange and correlation magnetic field in the noncollinear case

19 = Reduced density gradient
(J. Chem. Theory Comput. 7, 625 (2011), doi: 10.1021 / ct100641a)
Set the isosurface between 0.3 and 0.6 to plot the
non-covalent interactions (see also plot_num = 20)

20 = Product of the electron density (charge) and the second
eigenvalue of the electron-density Hessian matrix;
used to colorize the RDG plot (plot_num = 19)

21 = all-electron charge density (valence + core).
For PAW calculations only; requires a very dense real-space grid.

22 = kinetic energy density (for meta-GGA and XDM only)

I think that you want the all-electron (valence+core) but based upon the total charge in your calculation (248 e) it seems that you only have the valence density in your analysis.

Thank you very much dear graeme, thank you for your time.
I will test again.