SEAMM MBE Plug-in

A SEAMM plug-in for many-body expansion (MBE) corrections of periodic cells and clusters

• Free software: BSD-3-Clause

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

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

History

2026.10.4.1 – Pairwise counterpoise corrects the high level only by default

• ‘pairwise’ counterpoise now corrects each pair at the high level only. The new choice ‘pairwise, both levels’ also corrects the molecular low level, as ‘pairwise’ did before. In tests on Li⁺/BF₄⁻/water/EC clusters the r2SCAN-D4 correction was tiny where it could be computed, and its ghost calculations sometimes ended at spurious energies, while the revDSD correction was 3–4 kJ/mol per molecule.

• The user guide notes that ORCA’s ghost-atom gradients are unreliable for double hybrids such as revDSD, so counterpoise-corrected forces from them need caution.

2026.10.4 – Requires seamm-exec 2026.10.3.2 for running on a cluster

• Requires seamm-exec 2026.10.3.2: each bundle of calculations sent to a cluster’s queue now runs on one node, a calculation runs inside the job itself only when it fits there, and bundles get a time limit from their calculations’ estimated cost. Before, a VASP or ORCA calculation could be spread over several nodes and fail, or be cut off by the queue’s default time limit.

• Checked end to end on TinkerCliffs: the 64-water pilot frame reproduces the prototype’s labels (energy to 0.001 meV, forces to 0.2 meV/Å RMS, pressures to about 1 atm).

2026.10.3 – Initial release: many-body expansion (MBE) corrections

• A step that estimates high-level energies, forces and, for periodic cells, the stress of a cell or a large cluster: a low-level calculation of the whole system plus [high - low] corrections computed on monomers, pairs and triples of molecules, using the seamm_mbe library.

• The levels are model chemistries: the high level, a molecular low level, and optionally a periodic low level (e.g. VASP) for the fragments of periodic cells, run as batches of calculations through seamm_exec.

• Pair and triple cutoffs, a rule for which triples to include, and a check that the cell is large enough for the chosen cutoffs.

• For a periodic low level, the fragments are placed on the cell’s FFT grid so that the grid errors cancel between the cell and its fragments.

• Optional pairwise counterpoise correction of the basis-set superposition error.

• Optional energy offsets per molecule type, and the results stored as properties and written to an extended XYZ file for training machine-learned force fields.