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Several improvements to colvar component classes #643

Merged
merged 15 commits into from
Mar 12, 2024
Merged

Several improvements to colvar component classes #643

merged 15 commits into from
Mar 12, 2024

Commits on Mar 12, 2024

  1. Separate creation and initialization of colvar components

    @giacomofiorin
    giacomofiorin committed Mar 12, 2024
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  2. Make simple scalar metrics the default, and only override it when needed 

    Also remove the preprocessor macro defining member functions, in favor of
using C++ inheritance throughout.  Therefore, the decrease in the amount of
duplicated code is much higher than how it appears from the diff.
    @giacomofiorin
    giacomofiorin committed Mar 12, 2024
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  3. Update inheritance metadata

    @giacomofiorin
    giacomofiorin committed Mar 12, 2024
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  4. List forceNoPBC as an option for all components in the doc

    @giacomofiorin
    giacomofiorin committed Mar 12, 2024
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  5. Honor the value of forceNoPBC when comparing values of distanceVec va… 

    …riables
    @giacomofiorin
    giacomofiorin committed Mar 12, 2024
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  6. Remove flag from test input that was absent in reference run 

    In that code version, distanceVec was not yet honoring forceNoPBC
    @giacomofiorin
    giacomofiorin committed Mar 12, 2024
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  7. Condense most implementations of cvc::apply_force() into a single fun… 

    …ction
    @giacomofiorin
    giacomofiorin committed Mar 12, 2024
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  8. Remove some member functions from public scope

    @giacomofiorin
    giacomofiorin committed Mar 12, 2024
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  9. Initialize some plain old data in header

    @giacomofiorin
    giacomofiorin committed Mar 12, 2024
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  10. Use shared pointers to handle the components of one colvar

    @giacomofiorin
    giacomofiorin committed Mar 12, 2024
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  11. Integrate periodicity check in cvc::init()

    @giacomofiorin
    giacomofiorin committed Mar 12, 2024
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  12. Appease compiler warning

    @giacomofiorin
    giacomofiorin committed Mar 12, 2024
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  13. Return early if critical errors are raised in path CV initialization … 

    …code
    @giacomofiorin
    giacomofiorin committed Mar 12, 2024
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  14. Make some CVs (PCVs and NN-based CVs) more robust. 

    Return the error code earlier to prevent crashes in interactive
programs.
    @HanatoK @giacomofiorin
    HanatoK authored and giacomofiorin committed Mar 12, 2024
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  15. Doc formatting minor fixes 

    [update-doc]
    @giacomofiorin
    giacomofiorin committed Mar 12, 2024
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