[Question] P atoms receive zero Bader basin from out_chg cube with NC pseudopotential and NLCC #8220

Details

Details

I am performing Bader analysis on ABACUS charge-density cube files for a Li-rich layered oxide/Li3PO4 heterojunction. After merging the spin-up and spin-down charge densities, Henkelman Bader 1.05 assigns all P atoms in the Li3PO4 part to 0 electrons and 0 volume.

I would like to confirm whether this is expected for the charge density exported by out_chg, and what workflow ABACUS recommends for obtaining a core-corrected or all-electron density for per-atom Bader analysis.

Current setup

• ABACUS: v3.10.1 (LTS)
• Basis: lcao
• Exchange-correlation functional: PBE
• Spin: nspin = 2
• Charge-density output: out_chg = 1
• P pseudopotential: P.PD04.PBE.UPF
• P pseudopotential header:

pseudo_type="NC"
is_paw="F"
core_correction="T"
z_valence="5.00"

The UPF contains PP_NLCC and PP_RHOATOM sections.

The charge-density grid is 480 × 125 × 216, and the cube density is in e/Bohr^3.

Reproduction steps

1. Run ABACUS SCF with nspin = 2 and out_chg = 1.
2. Obtain SPIN1_CHG.cube and SPIN2_CHG.cube.
3. Merge the two spin channels pointwise.
4. Run Henkelman Bader 1.05 on the merged cube.
5. Read the atomic populations from ACF.dat.

The procedure follows the Bader workflow in ABACUS-agent-tools bader.py.

Observed result

For the complete heterojunction:

Integrated density:    1131.0051225 e
Assigned Bader charge: 1131.0051140 e

The total electron conservation is therefore valid. The empty P basins are reproduced by both neargrid and ongrid modes. The same behavior in the frozen Li3PO4 fragment shows that it is not caused only by the interface.

Interpretation concern

The CUBE atom records contain a reference value of 5 for P. The post-processing convention in bader.py computes:

net_bader_charge = cube_atom_reference_charge - ACF_bader_electrons

For an empty P basin this gives 5 - 0 = +5 e. I do not interpret this as a physical P chemical charge. It appears to result from using a pseudopotential valence density whose topology has no Bader basin at the P sites.

Questions

1. Is SPIN*_CHG.cube from out_chg expected to contain only the self-consistent pseudopotential valence density, rather than an all-electron or core-reconstructed density?
2. Does ABACUS provide a documented parameter or post-processing tool to export the core-correction density or a reconstructed all-electron density on the same real-space grid for Bader analysis?
3. If PP_NLCC and PP_RHOATOM are used internally, is there a supported method to reconstruct their contribution into a compatible CUBE file?
4. Is an empty Bader basin for P expected or known for this norm-conserving P pseudopotential?
5. What workflow does the ABACUS team recommend for quantitative per-atom Bader charges in P-containing systems?

Attached evidence

I attached a compact evidence bundle containing the per-atom CSV files, JSON summaries, the P pseudopotential header, and the independent Bader validation summary. The large CUBE and complete ACF.dat files can be provided if needed.

ABACUS Bader issue evidence.zip

Have you read FAQ on the online manual http://abacus.deepmodeling.com/en/latest/community/faq.html

• Yes, I have read the FAQ part on online manual.

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