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Analysis functions for diatomic molecules. #329

Merged
merged 32 commits into from
Apr 13, 2024
Merged

Analysis functions for diatomic molecules. #329

merged 32 commits into from
Apr 13, 2024

Commits on Jan 4, 2024

  1. Add Analysis submodule and diatomic molecule analysis functions. 

    - Added new DynamicsOutput: OutputDesorptionTrajectory #317
- Added new DynamicsOutput: OutputDesorptionAngle #317
- Created an `Analysis` submodule for common analysis functions
    @Alexsp32
    Alexsp32 committed Jan 4, 2024
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Commits on Jan 5, 2024

  1. Add Structure submodule from NQCBase

    @Alexsp32
    Alexsp32 committed Jan 5, 2024
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  2. Forgot to export some DynamicsOutputs

    @Alexsp32
    Alexsp32 committed Jan 5, 2024
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  3. Fixed a few self-references

    @Alexsp32
    Alexsp32 committed Jan 5, 2024
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  4. Analysis should load properly now

    @Alexsp32
    Alexsp32 committed Jan 5, 2024
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  5. Cleanup 

    Tried to fix assignment of quantise_diatomic in Analysis

Second attempt

Removed superfluous import of PyCall

Another missing import

Add missing Simulation variants of functions

Maybe it's dot after all?

Stupid Any overload

Second attempt
    @Alexsp32
    Alexsp32 committed Jan 5, 2024
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Commits on Jan 11, 2024

  1. Update docs for Analysis module

    @Alexsp32
    Alexsp32 committed Jan 11, 2024
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  2. Possible fix for OutputDesorptionTrajectory

    @Alexsp32
    Alexsp32 committed Jan 11, 2024
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  3. Update docstrings, fix a type issue

    @Alexsp32
    Alexsp32 committed Jan 11, 2024
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  4. Made another mistake in struct definition

    @Alexsp32
    Alexsp32 committed Jan 11, 2024
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  5. Updated OutputDesorptionAngle, OutputDesorptionTrajectory

    @Alexsp32
    Alexsp32 committed Jan 11, 2024
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  6. Updated Docs for additions

    @Alexsp32
    Alexsp32 committed Jan 11, 2024
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  7. Add rudimentary tests for NQCDynamics.Structure

    @Alexsp32
    Alexsp32 committed Jan 11, 2024
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  8. Fixed issue with new Outputs

    @Alexsp32
    Alexsp32 committed Jan 11, 2024
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  9. Simulation is in under Solution.prob, not under Solution

    @Alexsp32
    Alexsp32 committed Jan 11, 2024
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  10. Another attempt at fixing docs

    @Alexsp32
    Alexsp32 committed Jan 11, 2024
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  11. Logic error in tests

    @Alexsp32
    Alexsp32 committed Jan 11, 2024
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Commits on Jan 12, 2024

  1. Another mistake in tests and hopefully fixed docs refs

    @Alexsp32
    Alexsp32 committed Jan 12, 2024
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  2. I am very confused by Documenter.jl

    @Alexsp32
    Alexsp32 committed Jan 12, 2024
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  3. Another test for cross-references

    @Alexsp32
    Alexsp32 committed Jan 12, 2024
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Commits on Jan 30, 2024

  1. Prevent BoundsError in OutputDesorptionTrajectory

    @Alexsp32
    Alexsp32 committed Jan 30, 2024
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Commits on Apr 8, 2024

  1. Replaced explicit DynamicsVariables array types with AbstractVector

    @Alexsp32
    Alexsp32 committed Apr 8, 2024
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  2. Improved method definitions, possible efficiency gain by using views

    @Alexsp32
    Alexsp32 committed Apr 8, 2024
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  3. This was a major memory hog - using views and pre-allocating v_com ar… 

    …ray helps a lot.
    @Alexsp32
    Alexsp32 committed Apr 8, 2024
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  4. New desorption detection function from DiatomicBasics.jl

    @Alexsp32
    Alexsp32 committed Apr 8, 2024
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  5. Add unit tests for diatomic analysis functions for desorption

    @Alexsp32
    Alexsp32 committed Apr 8, 2024
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  6. And now the unit test works

    @Alexsp32
    Alexsp32 committed Apr 8, 2024
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  7. Add "Analysis" group to unit testing

    @Alexsp32
    Alexsp32 committed Apr 8, 2024
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Commits on Apr 13, 2024

  1. Version bump for merge

    @Alexsp32
    Alexsp32 committed Apr 13, 2024
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  2. Added explanation for Structure module scope

    @Alexsp32
    Alexsp32 committed Apr 13, 2024
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  3. Fixed wrong function name in docstring

    @Alexsp32
    Alexsp32 committed Apr 13, 2024
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  4. Merge branch 'main' into diatomicbasics

    @Alexsp32
    Alexsp32 authored Apr 13, 2024
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