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
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
- 2026.7.13 – Option to set the charges on the structure
New Set as the atomic charges on the structure option (default off). When on, the computed charges are also written to the structure’s standard per-atom charge attribute (in addition to the labeled charges_<label> column), so they travel with the structure – e.g. to write them to an extended-XYZ (extxyz) file for machine-learning training.
- 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.
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