pdb2reaction

[0.3.8] — 2026-05-01

Added

• pdb2reaction dft --lowmem/--no-lowmem (default True): closed-shell GPU SCF now uses gpu4pyscf.dft.rks_lowmem.RKS (direct-JK, no density fitting). Open-shell / CPU / older gpu4pyscf paths fall back to standard RKS/UKS. YAML key dft.lowmem.

Changed

• Closed-shell GPU DFT defaults switch from DF + standard RKS to direct-JK rks_lowmem.RKS. Absolute energies shift by sub-mHa; pass --no-lowmem to reproduce v0.3.6/v0.3.7 numbers.
• Documentation pruned (EN+JA): per-command pages drop redundant Summary↔At a glance↔intro repetitions, version-stamp annotations are moved to the CHANGELOG, and decorative --- separators between H2 headings are removed.

Fixed

• OrbASECalculator default precision changed from 'float32' (silent slow path, blocks autograd Hessian) to 'float32-high', matching OrbCalculator.
• dft.py exception handler: out_dir_path is now pre-bound before YAML override resolution, so apply_yaml_overrides failures no longer mask the original exception with NameError.
• freq.py analytical-Hessian path now clones the result before mass-weighted projection, preventing in-place mutation of the cached Geometry Hessian.
• freq.py prepared_input cleanup span widened so the temp file is removed even when an exception fires before the main try block.
• solvent.py: when the wrapped backend returns a torch GPU tensor for the Hessian, it is detached to CPU/numpy before adding the xTB delta correction.
• path_opt.py finally block: shared_calc = gs = geoms = None indent corrected so it runs once outside the cleanup loop.
• summary_log.py: nu_imag resolution no longer treats 0.0 as missing; seg_NN tag fallback width unified to :03d.
• Documentation realigned with source: uma-pysis.md return_partial_hessian default is False; scan2d output filenames are distance-tag (point_iDDD_jDDD); all.md output tree expands models/, freq/{R,TS,P}/, tsopt_single/; path-opt.md lists final_geometries.pdb (no _trj); path-search.md adds missing per-segment mep_seg_NN / hei_seg_NN files; JA getting-started.md adds the missing Agent Skills section.
• Internal cleanup: removed unused CliArgBuilder class and dead YAML-merge trampolines in all.py; removed legacy argparse main() in add_elem_info.py; dropped sister-project reference from defaults.py module docstring.
• Tests: test_summary_log.py no longer skips silently when fairchem is absent; unused imports cleaned up in 4 test files.