Refactor entropy calculations: switch to per-timestep computation with molecule-type grouping#126

Merged

harryswift01 merged 26 commits intomainfrom

30-averaging-over-molecules-of-the-same-type

Aug 4, 2025

Commits on Jul 3, 2025

Switching loops to loop over timesteps first and then molecules when calculating the covariance matrices and separating the entropy calculation from the loop that makes the matrices. Part 1.
skfegan
committed

Commits on Jul 10, 2025

applying pre-commit hooks and linting for code quality
harryswift01
committed

Commits on Jul 11, 2025

Commits on Jul 21, 2025

Refactor get_beads to remove padding and simplify force/torque matrix storage
harryswift01
committed

Commits on Jul 22, 2025

add in averaging over the `number_frames` for each of the forces and torques matrices
harryswift01
committed

Commits on Jul 24, 2025

Commits on Jul 28, 2025

Commits on Jul 29, 2025

Commits on Jul 30, 2025

Commits on Jul 31, 2025