atomic-charges-step 2026.6.29

A SEAMM plug-in for computing atomic (partial) charges from a converged

SEAMM Atomic Charges Plug-in

A SEAMM plug-in for computing atomic (partial) charges from a converged electron density.

• Free software: BSD-3-Clause

• Documentation: https://molssi-seamm.github.io/atomic_charges_step/index.html

• Code: https://github.com/molssi-seamm/atomic_charges_step

Features

This plug-in is a post-processing step: it runs after a quantum-chemistry step (VASP, Gaussian, Psi4, ORCA, …) that has produced an electron density, reads that density, and uses a real-space density-partitioning program to assign a partial charge to each atom. The charges are written back into the configuration as a labeled charge set (e.g. charges_DDEC6) so several schemes can coexist on the same structure.

Supported methods

• DDEC6 (via the Chargemol program) – ESP-faithful, chemically transferable charges that work for molecular and periodic systems, including metals. The recommended general-purpose / force-field charge.

• Bader / QTAIM (via the Henkelman bader code) – a rigorous topological partition of the density, the charge solid-state users expect.

Both consume a real-space density grid (or cube), so they apply equally to periodic and molecular calculations. They need the all-electron density from the upstream step (for VASP, CHGCAR plus AECCAR0/AECCAR2 via LAECHG=.TRUE.).

• Free software: BSD-3-Clause license

• Documentation: https://molssi-seamm.github.io/atomic_charges_step/index.html

Acknowledgements

Developed by the Molecular Sciences Software Institute (MolSSI), which receives funding from the National Science Foundation under award CHE-2136142.

History

2026.6.29 – Run Chargemol from a dedicated conda environment

• The installer now creates a ‘seamm-chargemol’ conda environment containing Chargemol (for DDEC6), and the step runs Chargemol in that environment – no hand-built installation or PATH setup is needed. Run ‘atomic-charges-step-installer install’ to set it up.

• The reference atomic densities are found automatically inside the seamm-chargemol environment; the ‘DDEC reference densities’ setting is now needed only to point at a different copy.

2026.6.28 – Citations, charge normalization, and GUI fixes

• The DDEC6 (Manz & Limas) and Bader (Henkelman) methodology papers are now cited for the charge method that is run.

• The charges are normalized to the known net charge of the system with a small, reported uniform shift; this can be turned off.

• Accepts an analytic wavefunction (.wfx) from a preceding ORCA step, in addition to Gaussian, for molecular DDEC6.

• Fixed: the Results tab in the GUI was empty and selected results were not saved. The atomic charges, net charge, residual, and method are now listed and stored.

• The charge method now offers Bader only when a density grid is available (a periodic/VASP density or explicit files); molecular densities offer DDEC6. Bader reports a clear message that it awaits periodic support.

2026.6.27 – Initial release of the Atomic Charges step

• Computes DDEC6 atomic charges (via Chargemol) from a molecular Gaussian wavefunction (.wfx), storing them as a labeled charge set on the structure.