t-0hmura/mlmm_toolkit: v0.2.8

Added

• --refine-path default changed to True: The all command now uses recursive path-search by default.
• --thresh-post: Post-processing convergence threshold for the all command.
• --dft-engine [gpu|cpu]: New option in all command to override DFT engine.
• [freq] output line: Frequency analysis now prints all vibrational frequencies in a summary line.
• track_mode_by_overlap: New rsirfo config option (default False) for TS mode tracking strategy.
• TR projection in TS optimization: Translation/rotation projection applied to Cartesian Hessian before eigendecomposition in RS-I-RFO.
• H_double default changed to True: Hessian computation now uses float64 throughout (analytical and FD), improving numerical precision for PHVA.
• Energy plateau convergence fallback: When the energy range over a window of steps falls below a threshold, the optimization is declared converged. Config options: energy_plateau (default true), energy_plateau_thresh (default 1e-4 au ≈ 0.06 kcal/mol), energy_plateau_window (default 50 steps).

Fixed

• trust_max reduced from 0.20 to 0.10 bohr: Prevents energy oscillations near saddle points in large systems.
• EulerPC corrector infinite loop: Bounded loop with gradient norm check to prevent infinite iteration and NaN propagation.
• PDB MODEL/ENDMDL: Single-frame PDB files no longer include MODEL/ENDMDL records.
• PDB MODEL duplication: Reference PDB template now filtered for MODEL/ENDMDL/END.
• PDB trailing newline: Ensured newline before ENDMDL.
• PDB END filter: Correctly handles END with trailing spaces.
• RS-I-RFO image potential: Uses TR-projected Hessian (cur_H_diag) for eigenvector consistency.
• _active_dof_indices: Fixed attribute name in _tr_project_hessian.
• TS mode tracking log: Fixed .argmax() on scalar; replaced print() with self.log().
• Smoke test flags: --exclude-backbone False → --no-exclude-backbone.