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Implementations of 2 new cvs: native contact fraction Q and angles between two vectors #327

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Implementations of 2 new cvs: native contact fraction Q and angles between two vectors #327

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Commits on Jun 26, 2024

  1. implement angles between two vectors as new cv

    @yihengwuKP
    yihengwuKP committed Jun 26, 2024
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Commits on Jul 7, 2024

  1. Initial implementation of Q (still has nan deriv)

    @yihengwuKP
    yihengwuKP committed Jul 7, 2024
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  2. remove unused component cv and rename plot_q.py

    @yihengwuKP
    yihengwuKP committed Jul 7, 2024
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Commits on Jul 9, 2024

  1. add contacts to the documentation

    @yihengwuKP
    yihengwuKP committed Jul 9, 2024
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  2. implement checks for forces of Q

    @yihengwuKP
    yihengwuKP committed Jul 9, 2024
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  3. get rid of unused import in check_force.py

    @yihengwuKP
    yihengwuKP committed Jul 9, 2024
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  4. bug fix: fix diverging derivs by mask trick

    @yihengwuKP
    yihengwuKP committed Jul 9, 2024
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  5. Implement automatic testing of cv q and its deriv

    @yihengwuKP
    yihengwuKP committed Jul 9, 2024
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  6. correct the path name cv_Q

    @yihengwuKP
    yihengwuKP committed Jul 9, 2024
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Commits on Jul 10, 2024

  1. bug fix: name issue in ci, check_q.py->check_Q.py

    @yihengwuKP
    yihengwuKP committed Jul 10, 2024
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Commits on Jul 16, 2024

  1. def contacts by filtering 1-4 bonding pairs 

    update the examples, this is simply a better choice of
the contacts. Otherwise it contains bonded pairs which
will always be there.
    @yihengwuKP
    yihengwuKP committed Jul 16, 2024
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Commits on Jul 17, 2024

  1. get rid of the dependency of networkx in the eg

    @yihengwuKP
    yihengwuKP committed Jul 17, 2024
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Commits on Aug 9, 2024

  1. remove the unnecessary @Multicomponent

    @yihengwuKP
    yihengwuKP committed Aug 9, 2024
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  2. get rid of unused import multicomponent

    @yihengwuKP
    yihengwuKP committed Aug 9, 2024
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  3. reduce code duplication by using lambda function

    @yihengwuKP
    yihengwuKP committed Aug 9, 2024
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  4. bug fix: change the name from vector_angle to angle

    @yihengwuKP
    yihengwuKP committed Aug 9, 2024
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Commits on Aug 10, 2024

  1. reimplement remap_indices by argsort

    @yihengwuKP
    yihengwuKP committed Aug 10, 2024
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  2. bug fix: index_mapping creation in remap_indices

    @yihengwuKP
    yihengwuKP committed Aug 10, 2024
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Commits on Sep 5, 2024

  1. add options for clip large exponentials

    @yihengwuKP
    yihengwuKP committed Sep 5, 2024
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  2. bug fix: fix math formats

    @yihengwuKP
    yihengwuKP committed Sep 5, 2024
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  3. bug fix: documentation wording & math issues

    @yihengwuKP
    yihengwuKP committed Sep 5, 2024
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Commits on Sep 10, 2024

  1. bug fix: proper clipping in the Q

    @yihengwuKP
    yihengwuKP committed Sep 10, 2024
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  2. Merge branch 'main' into Q-vector-angle

    @yihengwuKP
    yihengwuKP committed Sep 10, 2024
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  3. refactorizing Q calculation for easy understanding

    @yihengwuKP
    yihengwuKP committed Sep 10, 2024
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