MesoHOPS 1.6.1

[alexiahartzell]

MesoHOPS 1.6.1

This commit upgrades MesoHOPS, adding a new trajectory checkpointing system, options for increased HopsStorage efficiency, overhauled initialization of Noise 2, quality-of-life improvements, and various fixes.

Key improvements and features:

1. Trajectory Checkpointing: Checkpointing allows the user to save and load a trajectory as a .npz file with options to alter the noise going forward, greatly simplifying advanced sampling techniques. In a similar vein, the HopsSystem object may now be saved and loaded to hasten initialization.
2. HopsStorage Step: HopsStorage may now be set to save data from only selected time points, reducing the RAM costs of storing data. This is distinct from the save_slices method of HopsTrajectory, which conveniently saves the data of HopsStorage to disk and has options for slicing and compressing data to reduce hard disk costs.
3. Noise2 Input Management: Noise 2 (typically used for thermal noise and the time-dependent portion of the Hamiltonian) is now initialized with its own parameter dictionary and the user may choose whether to make it purely real. Noise 2 is no longer automatically multiplied by two and converted to its real portion by the equation-of-motion: scripts that used noise 2 in the past must be updated to account for this!
4. Efficient Zero Noise: When noise model “ZERO” is used, HopsNoise RAM usage no longer scales with system size or simulation time.
5. DyadicSpectra Static Filter Input Structure: Updated static filter input structure in DyadicSpectra to properly feed into HopsHierarchy. Checks were added in HopsHierarchy to ensure filters are properly defined for all modes.
6. Pytest.Raises Standardization: Unit tests checking for correct error messages no longer use try/except clauses and are now tested using pytest.raises
7. Spectral Density Streamlining: bcf_convert_sdl_to_exp has been deprecated, and bcf_convert_dl_to_exp_with_Matsubara has been renamed to bcf_convert_dl_to_exp. For treatment of underdamped modes, we recommend using bcf_convert_dl_ud_to_exp.
8. Version Hash Metadata: Current git commit hash can now be accessed and saved from HopsStorage, allowing users to store the commit hash at runtime.
9. HopsDyadic Complex Handling: Fixed an issue where the _M2_dyad_conversion method was restricting the matrix elements to be real in the case where the provided matrix is a dense array.

These enhancements collectively improve the computational efficiency, maintainability, and convenience of MesoHOPS for current and future applications.