Binding energies¶

You can calculate binding energies with SO3LR as reported in the JACS paper (Fig. 2B).

The method¶

The binding energy is computed as the difference between the energies of the bound dimer and the same dimer with the two monomers translated far apart (beyond the long-range cutoff), with charges assigned to each monomer separately to prevent spurious charge transfer:

E_bind = E_dimer - E_separated

Only the charge equilibration is done per monomer; the charge embedding sees the dimer's total charge in both frames.

Preparing structures¶

For XYZ files with dimer metadata (charge_a, charge_b, selection_a, selection_b, like the NCIAtlas format), generate the original and translated structures:

python -m so3lr.prepare_dimer_xyz --datafile sapt10k.xyz

This writes sapt10k_prepared.xyz with alternating frames: dimer, separated, dimer, separated, … Structures with elements the chosen model does not support are skipped and written to <input>_unsupported.xyz.

Option	Default	Meaning
`--datafile`	required	Input dimers, any file `ase.io` reads
`--output`	`<input>_prepared.xyz`	Output file (extxyz)
`--model`	`so3lr-tauri-m-2606`	Model whose element coverage is checked (`so3lr` for the legacy model)

The selections are 1-based inclusive ranges (selection_a=1-12). Monomer A must be the first atoms and monomer B the rest, and the two selections together must cover every atom. If they do not, the per-monomer charges are silently not applied.

Evaluating¶

so3lr eval --datafile sapt10k_prepared.xyz --targets energy \
    --save-to sapt10k_eval.xyz --lr-cutoff 100

Use --lr-cutoff 100 for these gas-phase dimers, and keep the default --batch-size 1.

Computing the binding energies¶

from ase.io import read

mols = read("sapt10k_eval.xyz", index=":")
energy = [a.info["energy_so3lr"] for a in mols]

# frames alternate dimer / separated
bind_energy = [energy[i] - energy[i + 1] for i in range(0, len(energy), 2)]

The binding energies are in eV, and negative values indicate binding.

Precision of the saved energies

so3lr eval writes energy_so3lr rounded to 6 significant figures, which for a large dimer can reach 0.01 eV (0.23 kcal/mol) per frame. When that matters, evaluate the frames with the ASE calculator and take the difference at full precision.

The energy metrics that so3lr eval prints for these files are not binding-energy errors: both frames carry the reference interaction energy (benchmark_Eint) as their energy label. Compare bind_energy against benchmark_Eint yourself, and check which units it is in.

Data¶

The SAPT10k dataset is bundled under examples/data/sapt10k.zip.