Feature minimise #163
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Feature minimise #163
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…ixed a bug in the new functionality where a default lever for a force was not being picked up (i.e. `ghost/ghost::*` was not taking precedence over, e.g. `*::charge`) I've updated the unit tests to catch these edge cases
…times to find a stable starting dynamics structure. This solves the weird aladip structure problem, but runs minimisation too long for tyk2 (getting confused when constraints are re-applied)
…ore robust with the way constraints are handled.
This includes vectorising for Apple Silicon and adding more tests for convergence so that we can have more confidence that the structures output are sensible. Also made sure that optimised compilation (-O3) is used for all of the plugins (SireOpenMM, SireGemmi and SireRDKit). They were previously compiled with wrapper options (e.g. -Os). Minimisation now gives better progress updates, using a progress bar to show progress towards the maximum number of iterations. This has been reduced to 1500 by default. Also, if the minimisation fails to create a structure that obeys constraints on the first pass, then the minimisation is repeated, with the maximum number of iterations reset. If it fails again, then this structure, with constraints re-applied, is returned.
Ran the wrapper generation again, which added docs to PerturbableOpenMMMolecule Moved the optimised cxxflags to a higher-level CMakeLists.txt and added this properly, rather than duplicating flags. Will see if this fixes the Linux compile error. (will check locally, hence skipping CI) [ci skip]
…ebugging info to minimisation output for problematic cases
minimisation to the user via arguments with sensible defaults to the minimisation functions. The documentation of the functions explains how the ratchetting algorithm works. Also updated the progress bar so that you can see the number of repeats and number of ratchets (e.g. 1.5 would be the sixth ratchet of the first run) Also fixed the double-header output for the create_wrapper script and regenerated the SireOpenMM wrappers. This also now automatically finds the python header files.
[ci skip]
…things. You can print the log using the `.get_log()` function of `Minimisation`, e.g. ``` m = mols.minimisation().run() print(m.get_log()) ```
This now will do a hard reset and repeat once only, if a NaN or other extremely broken state is detected. It will also reset the minimizer parameters if they get into a weird state. This still doesn't successfully minimise everything - but it isn't bad :-)
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This PR brings back the improved minimiser code (originally in #162). This makes the minimiser even more robust, and includes better detection of NaNs, and tuning from the return value of the underlying algorithm.
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]Suggested reviewers:
@lohedges
Any additional context of information?
It's worth testing again as I have updated the default parameters. They are now all exposed via the
Minimisation.run()function.