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Checklist
This PR aims to not only address issue #29 but also include some additional tasks. Here is the checklist:
rmse_cutofffinalfrom the YAML parameterw_combinew_combineinto a booleanprepare_weightsw_mean_typeto specify using simple means or weighted means in weight combinationSome justifications
Generally, the idea is to simplify the options available in REXEE simulations, especially for those related to weight combinations. Since the weight combination does not seem to bring advantages, we plan to keep the most basic functionalities for demonstration purposes in the paper.
1. Removing the functionality relevant to
rmse_cutoffPreliminary data have shown that weight combination does not accelerate weight convergence in weight-updating simulations in most cases. Using
rmse_cutoffwas shown to alleviate the issue, but that is merely reflecting the fact that the combination is performed less frequently. Therefore, we decided to remove the YAML parameterrmse_cutoffand the relevant functionalities.2. Removing the option
finalfrom the YAML parameterw_combineThe final weights are known to be noisy compared to the time-averaged weights and should never be used for weight combinations. Therefore, we decide to remove the option
finalfrom the choices of the YAML parameterw_combine. This would lead to only two options forw_combine, includingNoneandavg. Therefore, we turned the parameterw_combineinto a boolean - whenever weight combination is activated, we always use time-averaged weights. Additionally, we will need to remove the functionprepare_weights.3. Deprecating multiple exchange proposal scheme
As discussed in the paper, the multiple exchange proposal scheme does not have symmetric proposal probabilities, while the derivation of the acceptance ratio assumes symmetric proposal probabilities, which are much more common in replica exchange methods. That is, using the multiple exchange proposal scheme with the acceptance ratio derived in the paper would lead to a violation of the detailed balance. As such, we decided to deprecate the codes implementing the multiple exchange proposal scheme by commenting out the code. Note that we do not remove the codes completely as the detailed balance might still be obeyed if the acceptance ratio is carefully designed to accommodate the asymmetry of the proposal probabilities of the multiple exchange proposal scheme. Still, this is outside the scope of our paper, so the option will be made unavailable in the package. To do this, the following is required:
n_ex.multiplefrom the YAML parameterproposal.4. Provide a YAML parameter to specify using simple means or weighted means in weight combination.
Currently, the implementation only uses inverse-variance weight means in weight combinations, but both options should be available as the inverse-variance weighted means do not always perform better than simple means.
5. Compartmentalize the histogram correction method
Currently, the histogram correction method is implemented in
combine_weightsand is always applied after weight combination. We decided to compartmentalize the histogram correction method and let users decide whether to perform histogram correction by specifying the new YAML parameter that we are also adding here,hist_corr.