MDAnalysis2.9.0: native serial/multiprocessing density; native HES numerical functions and CES; separately named own diffusion embedding.
Native DiffusionMap2.9.0 vectors failed the frozen1e-10 eigen residual gate; original failure is reproduced and retained. Native embedding is unqualified and is not used as a scientific result. Installed source is never patched.
HES convenience wrapper float32 means retained; native numerical covariance/HES functions explicitly use double coordinates.
Coordinates are real earlier owned water/protein trajectories. No newMD, freeenergy, kinetic states, thermodynamic convergence or long-time sampling is claimed.
bash run.sh
bash verify.sh
bash plot.sh
Density uses2 CPU workers; run within your allocation.
