Hello everybody,
I am trying to work with the badercharge 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
NH3BS_ACF = NH3Borophene
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 NH3BS_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.
Atomic Bader charge and charge transfer using Quantum Espresso
Moderator: moderators

 Posts: 3
 Joined: Fri Dec 04, 2020 2:26 am
Atomic Bader charge and charge transfer using Quantum Espresso
 Attachments

 After Adsorption
 FIG1.png (107.14 KiB) Viewed 3280 times

 NH3BS_ACF.txt
 ACF file of NH3BS
 (6.92 KiB) Downloaded 187 times

 NH3_ACF.txt
 ACF file of NH3
 (684 Bytes) Downloaded 179 times

 BS_ACF.txt
 ACF file of BS (Borophene)
 (6.61 KiB) Downloaded 179 times
Re: Atomic Bader charge and charge transfer using Quantum Espresso
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 8.18=0.1e, but you really need core charges to resolve the charge density on the H atoms.

 Posts: 3
 Joined: Fri Dec 04, 2020 2:26 am
Re: Atomic Bader charge and charge transfer using Quantum Espresso
Thank you very much dear graeme,
In the previous calculation I used: plot_num = 21. knowing that :
21 = allelectron charge density (valence + core).
For PAW calculations only; requires a very dense realspace grid.
So, I recalculated with plot_num = 17, I found the same thing.
17 = allelectron valence charge density
can be performed for PAW calculations only
requires a very dense realspace grid!
Do I have to use other option ??
Input File Description (pp.x)
https://www.quantumespresso.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 normconserving 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 = allelectron valence charge density
can be performed for PAW calculations only
requires a very dense realspace 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
noncovalent interactions (see also plot_num = 20)
20 = Product of the electron density (charge) and the second
eigenvalue of the electrondensity Hessian matrix;
used to colorize the RDG plot (plot_num = 19)
21 = allelectron charge density (valence + core).
For PAW calculations only; requires a very dense realspace grid.
22 = kinetic energy density (for metaGGA and XDM only)
In the previous calculation I used: plot_num = 21. knowing that :
21 = allelectron charge density (valence + core).
For PAW calculations only; requires a very dense realspace grid.
So, I recalculated with plot_num = 17, I found the same thing.
17 = allelectron valence charge density
can be performed for PAW calculations only
requires a very dense realspace grid!
Do I have to use other option ??
Input File Description (pp.x)
https://www.quantumespresso.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 normconserving 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 = allelectron valence charge density
can be performed for PAW calculations only
requires a very dense realspace 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
noncovalent interactions (see also plot_num = 20)
20 = Product of the electron density (charge) and the second
eigenvalue of the electrondensity Hessian matrix;
used to colorize the RDG plot (plot_num = 19)
21 = allelectron charge density (valence + core).
For PAW calculations only; requires a very dense realspace grid.
22 = kinetic energy density (for metaGGA and XDM only)
Re: Atomic Bader charge and charge transfer using Quantum Espresso
I think that you want the allelectron (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.

 Posts: 3
 Joined: Fri Dec 04, 2020 2:26 am
Re: Atomic Bader charge and charge transfer using Quantum Espresso
Thank you very much dear graeme, thank you for your time.
I will test again.
I will test again.