Version 0.9.0

Here we list important changes made since the later version of 0.8.0. The full changelog can be found here. In the next release, we plan to significantly improve the code coverage and documentation.

• Deployed the package to PyPI: https://pypi.org/project/ensemble-md/0.9.0/
• We decided to rename the method as REXEE, which is short for Replica EXchange of Expanded Ensemble that combines the working principles of replica exchange (REX) and expanded ensemble (EE). Accordingly, we have modified all relevant files to swap out EEXE with REXEE, including in the filenames, file contents, and documentation. (For more details, please see PR #27.)
• We corrected the code for calculating the acceptance ratio. This would influence the result of weight-updating REXEE simulations but not fixed-weight ones. (For more details, please see PR #28.)
• We simplified the options available in REXEE simulations, especially for those related to weight combinations. This includes the following. (For more details, please see PR #31.)
  • Removing the functionality relevant to rmse_cutoff
  • Removing the option final from the YAML parameter w_combine
    • Turning the YAML parameter w_combine into a boolean
    • Removing the function prepare_weights
  • Deprecating the schemes of multiple swaps.
  • Provide a YAML parameter w_mean_type to specify using simple means or weighted means in weight combination
  • Compartmentalize the histogram correction method
  • Update the documentation
  • Update the unit tests
• The following YAML parameter acceptance was removed, and the documentation has been updated accordingly.
• The function get_delta_w_updates was added.
• The following functions were tweaked. Some details can be found in the PR #36.
  • get_g_evolution
  • _calculate_weighted_df, which was later renamed as _combine_df_adjacent
  • convert_npy2xvg
  • stitch_time_series
  • cluster_traj
  • The CLI analyze_REXEE
• Minor bugfixes.
• Updated README and the documentation