Fixes bar_with_pessimistic_uncertainty convergence error #1344
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badisa
commented
Jul 16, 2024
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badisa
commented
- A bug introduced in Resolve inconsistency between bar_with_bootstrapped_uncertainty and df_and_err_from_u_kln #1324
unconverged * A bug introduced in #1324
badisa
commented
Jul 16, 2024
| @@ -180,6 +180,11 @@ def test_df_from_u_kln_does_not_raise_on_incomplete_convergence(): | |||
| assert np.isfinite(df) | |||
| assert np.isnan(ddf) # returns NaN for uncertainty on incomplete convergence | |||
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| bootstrap_df, bootstrap_ddf = bar_with_pessimistic_uncertainty(u_kln, maximum_iterations=1) | |||
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This raises an exception without the fix. Didn't launch a CI job as it is an unambigious failure
badisa
commented
Jul 16, 2024
| df, ddf = mbar.getFreeEnergyDifferences() | ||
| full_bar_result = df[0, 1] | ||
| full_bar_err = ddf[0, 1] | ||
| full_bar_result, full_bar_err = df_and_err_from_u_kln(u_kln, maximum_iterations=maximum_iterations) |
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df_and_err_from_u_kln handles the behavior correctly: https://github.com/proteneer/timemachine/blob/master/timemachine/fe/bar.py#L136-L139
badisa
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maxentile
approved these changes
Jul 16, 2024
mcwitt
reviewed
Jul 16, 2024
timemachine/fe/bar.py
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| u_kn, N_k = ukln_to_ukn(u_kln) | ||
| mbar = pymbar.MBAR(u_kn, N_k, maximum_iterations=maximum_iterations) |
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nit: this seems unnecessary vs. setting initial_f_k=None below (or maybe better, initial_f_k=np.array([0.0, full_bar_result]))
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Good call, will replace it with initial_f_k=np.array([0.0, df]) which is the same value without constructing an extra MBAR object
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Set using pre-existing value in a7de23f
mcwitt
approved these changes
Jul 16, 2024
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