am1-rs-python 0.1.3__tar.gz

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  1. am1_rs_python-0.1.3/CHANGELOG.md +49 -0
  2. am1_rs_python-0.1.3/Cargo.lock +1176 -0
  3. am1_rs_python-0.1.3/Cargo.toml +38 -0
  4. am1_rs_python-0.1.3/LICENSE +674 -0
  5. am1_rs_python-0.1.3/PKG-INFO +238 -0
  6. am1_rs_python-0.1.3/README.md +224 -0
  7. am1_rs_python-0.1.3/THIRD_PARTY_NOTICES.md +80 -0
  8. am1_rs_python-0.1.3/docs/python-api.md +182 -0
  9. am1_rs_python-0.1.3/docs/rust-api.md +221 -0
  10. am1_rs_python-0.1.3/docs/scope.md +26 -0
  11. am1_rs_python-0.1.3/docs/theory.md +105 -0
  12. am1_rs_python-0.1.3/examples/bench102.xyz +104 -0
  13. am1_rs_python-0.1.3/examples/ethanol.xyz +11 -0
  14. am1_rs_python-0.1.3/examples/methane.xyz +7 -0
  15. am1_rs_python-0.1.3/examples/water.xyz +5 -0
  16. am1_rs_python-0.1.3/pyproject.toml +21 -0
  17. am1_rs_python-0.1.3/python/am1_rs/__init__.py +27 -0
  18. am1_rs_python-0.1.3/python/am1_rs/ase.py +134 -0
  19. am1_rs_python-0.1.3/python/am1_rs/native.py +144 -0
  20. am1_rs_python-0.1.3/src/basis.rs +61 -0
  21. am1_rs_python-0.1.3/src/bcc.rs +304 -0
  22. am1_rs_python-0.1.3/src/bin/am1_rs.rs +283 -0
  23. am1_rs_python-0.1.3/src/constants.rs +47 -0
  24. am1_rs_python-0.1.3/src/data/am1_parameters.csv +115 -0
  25. am1_rs_python-0.1.3/src/data/bccparm.dat +405 -0
  26. am1_rs_python-0.1.3/src/data_tables.rs +123 -0
  27. am1_rs_python-0.1.3/src/dual.rs +268 -0
  28. am1_rs_python-0.1.3/src/dual2.rs +288 -0
  29. am1_rs_python-0.1.3/src/error.rs +49 -0
  30. am1_rs_python-0.1.3/src/fock.rs +161 -0
  31. am1_rs_python-0.1.3/src/gradient.rs +531 -0
  32. am1_rs_python-0.1.3/src/hamiltonian.rs +125 -0
  33. am1_rs_python-0.1.3/src/hessian.rs +1074 -0
  34. am1_rs_python-0.1.3/src/integrals.rs +473 -0
  35. am1_rs_python-0.1.3/src/lib.rs +54 -0
  36. am1_rs_python-0.1.3/src/linalg.rs +238 -0
  37. am1_rs_python-0.1.3/src/math.rs +136 -0
  38. am1_rs_python-0.1.3/src/optimizer.rs +253 -0
  39. am1_rs_python-0.1.3/src/overlap.rs +443 -0
  40. am1_rs_python-0.1.3/src/overlap_numeric.rs +206 -0
  41. am1_rs_python-0.1.3/src/params.rs +284 -0
  42. am1_rs_python-0.1.3/src/python.rs +282 -0
  43. am1_rs_python-0.1.3/src/repulsion.rs +297 -0
  44. am1_rs_python-0.1.3/src/scf.rs +887 -0
  45. am1_rs_python-0.1.3/src/system.rs +149 -0
  46. am1_rs_python-0.1.3/src/topology.rs +274 -0
  47. am1_rs_python-0.1.3/tests/molecules.rs +67 -0
  48. am1_rs_python-0.1.3/tests/test_python_api.py +207 -0
  49. am1_rs_python-0.1.3/third_party/antechamber/ATOMTYPE_BCC.DEF +154 -0
  50. am1_rs_python-0.1.3/third_party/pyseqm/LICENSE +37 -0
am1_rs_python-0.1.3/CHANGELOG.md ADDED
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+ # Changelog
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+
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+ ## 0.1.3
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+
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+ ### Added
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+ - **Explicit RHF/UHF reference selection**, independent of the spin multiplicity — a closed-shell
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+ singlet can now be run either restricted or unrestricted (e.g. as a broken-symmetry starting
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+ point):
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+ - Rust: new `ScfReference` enum (`Auto` / `Restricted` / `Unrestricted`) and an
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+ `Am1Options.reference` field (default `Auto`, preserving previous behavior). `run_am1` honors
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+ it; `Restricted` on an open shell is rejected (no ROHF).
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+ - Python native: every function (`single_point`, `gradient`, `optimize`, `frequencies`,
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+ `hessian`) takes a `reference="auto"|"rhf"|"uhf"` keyword.
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+ - ASE: `AM1(..., reference="auto")`, or per structure via `atoms.info["reference"]`; a change
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+ invalidates cached results.
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+ - CLI: `--reference auto|rhf|uhf`, with `--rhf` / `--uhf` shortcuts.
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+
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+ ### Notes
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+ - `Auto` reproduces the historical selection (RHF for a closed-shell singlet, UHF for an open
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+ shell), so existing callers are unaffected. Forcing UHF on a symmetric singlet converges to the
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+ RHF energy (zero spin density).
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+
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+ ## 0.1.2
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+
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+ ### Added
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+ - **Hessian API for Python.** Both layers now expose the analytic (CPHF) Cartesian Hessian,
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+ which previously was only reachable indirectly through `frequencies`:
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+ - `am1_rs.hessian(numbers, positions, charge=0.0, multiplicity=1)` returns the full `3N × 3N`
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+ matrix in **atomic units** (`hessian_hartree_per_bohr2`) and, for convenience, in eV/Ų
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+ (`hessian_ev_per_angstrom2`), plus `ndof`. Row/column `3*i + k` is atom `i`, axis `k`.
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+ - `am1_rs.ase.AM1.get_hessian(atoms=None)` returns the Hessian as a NumPy array in **eV/Ų**
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+ (ASE convention). Closed-shell RHF and open-shell UHF are both supported.
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+ - **Per-structure charge / multiplicity for the ASE calculator.** In addition to the constructor
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+ arguments `AM1(charge=…, multiplicity=…)`, charge and spin multiplicity may now be supplied at
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+ calculation time via `atoms.info["charge"]` / `atoms.info["multiplicity"]`. An `atoms.info`
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+ entry overrides the constructor value for that structure, and a change in either invalidates
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+ cached results (`check_state`).
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+
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+ ### Verified
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+ - Confirmed (with tests) that charge and spin multiplicity are received and actually used in
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+ both the Python-native functions (per call) and the ASE calculator (at construction *and* at
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+ calculation time): charge and multiplicity change the SCF energy, and an electron-count /
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+ multiplicity parity mismatch raises. See `tests/test_python_api.py`.
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+
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+ ### Notes
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+ - Units are unchanged and follow each layer's convention: the native surface reports atomic
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+ units (Hartree/Bohr²) with eV/Ų provided alongside; the ASE layer reports eV/Ų.
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+ - No changes to the Rust crate's public API (the analytic Hessian was already available there as
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+ `am1_rs::analytic_hessian`, eV/Bohr²).