| """Core helpers for the TRIP50 dataset: alias resolution and reaction quantities. |
| |
| Used by the release producer (`build_hf_release.py`), the round-trip verifier |
| (`examples/verify_release.py`), and the example MLIP evaluator |
| (`examples/evaluate_mlip.py`). Kept dependency-light so it ships with the |
| release without pulling in optional libraries. |
| """ |
|
|
| from __future__ import annotations |
|
|
| HARTREE_TO_KCAL = 627.5094740631 |
| ROLES = ("R1", "R2", "TS", "P1", "P2") |
|
|
|
|
| def lookup(species_name, source, alias_map): |
| """Energy for `species_name` in `source` (a Mapping or pandas Series indexed |
| by species id), with alias resolution. Returns None if not present.""" |
| name = alias_map.get(species_name, species_name) |
| return source.get(name, None) |
|
|
|
|
| def required_roles(rxn_id, dlpno_source, alias_map): |
| """Roles that the rxn definition requires (i.e., DLPNO has a non-null value |
| for that species). Unimolecular legs (R2 and/or P2 absent) drop out.""" |
| return {role for role in ROLES |
| if lookup(f"{rxn_id}-{role}", dlpno_source, alias_map) is not None} |
|
|
|
|
| def reaction_quantities(source, dlpno_source, alias_map): |
| """Compute ΔE_rxn, ΔE_fwd, ΔE_rev (kcal/mol) for every TRIP50 reaction |
| defined in `dlpno_source`. A reaction's quantity is included only when |
| every role required by the DLPNO definition is also resolvable in `source`. |
| Unimolecular legs (roles absent from DLPNO) contribute 0 H on both sides. |
| |
| Returns three dicts {rxn_id: kcal_value}. |
| """ |
| rxn, fwd, rev = {}, {}, {} |
| for r in range(1, 51): |
| req = required_roles(r, dlpno_source, alias_map) |
| e = {role: (lookup(f"{r}-{role}", source, alias_map) or 0.0) for role in ROLES} |
| ok = lambda needed: all((lookup(f"{r}-{role}", source, alias_map) is not None) |
| for role in (needed & req)) |
| if {"R1", "P1"} <= req and ok({"R1", "R2", "P1", "P2"}): |
| rxn[r] = ((e["P1"] + e["P2"]) - (e["R1"] + e["R2"])) * HARTREE_TO_KCAL |
| if {"R1", "TS"} <= req and ok({"R1", "R2", "TS"}): |
| fwd[r] = (e["TS"] - (e["R1"] + e["R2"])) * HARTREE_TO_KCAL |
| if {"P1", "TS"} <= req and ok({"P1", "P2", "TS"}): |
| rev[r] = (e["TS"] - (e["P1"] + e["P2"])) * HARTREE_TO_KCAL |
| return rxn, fwd, rev |
|
|
|
|
| def slugify_method(name): |
| """Reversible slug for a method/theory name. Mapping is recorded in |
| methods.json at release time so consumers can recover the display name.""" |
| s = name |
| s = s.replace("ω", "omega").replace("Ω", "omega") |
| s = s.replace("κ", "kappa").replace("Κ", "kappa") |
| s = s.lower() |
| out = [] |
| for ch in s: |
| if ch.isalnum(): |
| out.append(ch) |
| elif ch in "-/() ": |
| out.append("_") |
| |
| slug = "".join(out) |
| while "__" in slug: |
| slug = slug.replace("__", "_") |
| return slug.strip("_") |
|
|
