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Simplify Chemical System #616

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Simplify Chemical System #616

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Commits on Nov 19, 2024

  1. Add trajectory methods for reading atom properties

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 19, 2024
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Commits on Nov 20, 2024

  1. Add method for adding a single atom to trajectory database

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 20, 2024
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  2. Merge branch 'protos' of https://github.com/ISISNeutronMuon/MDANSE in… 

    …to maciej/atom-database-in-trajectory
    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 20, 2024
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  3. Merge branch 'protos' of https://github.com/ISISNeutronMuon/MDANSE in… 

    …to maciej/atom-database-in-trajectory
    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 20, 2024
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Commits on Nov 21, 2024

  1. Make converters add standars atom database to trajectory

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 21, 2024
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  2. Read atom properties from trajectory

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 21, 2024
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  3. Make weights configurator depend on trajectory

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 21, 2024
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  4. Add types to the database

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 21, 2024
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  5. Replace recursive graph walking with networkx

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 21, 2024
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  6. Merge branch 'protos' of https://github.com/ISISNeutronMuon/MDANSE in… 

    …to maciej/atom-database-in-trajectory
    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 21, 2024
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  7. Merge branch 'maciej/improve-trajectory-editor' into maciej/atom-data… 

    …base-in-trajectory
    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 21, 2024
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  8. Make molecule detection fault-tolerant

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 21, 2024
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Commits on Nov 22, 2024

  1. Remove most ChemicalEntity subclasses

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 22, 2024
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  2. Remove most of ChemicalEntity.py

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 22, 2024
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Commits on Nov 25, 2024

  1. Remove references to other chemical entities

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 25, 2024
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  2. Remove references to other chemical entities

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 25, 2024
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Commits on Nov 26, 2024

  1. Simplify configuration writing

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 26, 2024
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  2. Update Configuration code

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 26, 2024
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  3. Remove Graph.py

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 26, 2024
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  4. Update TrajectoryUtils

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 26, 2024
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  5. Correct some tests

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 26, 2024
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Commits on Nov 27, 2024

  1. Make converter tests pass

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 27, 2024
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  2. Enable loading old trajectories

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 27, 2024
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  3. Make GUI jobs executable

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 27, 2024
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  4. Remove unused Cython code

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 27, 2024
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  5. Replace contiguous_coordinates.pyx with Python code

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 27, 2024
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Commits on Nov 28, 2024

  1. Make configuration unit tests pass

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 28, 2024
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  2. Simplify continuous coordinate calculation

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 28, 2024
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  3. Replace com_trajectory extension with Python code

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 28, 2024
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  4. Make tests runnable

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 28, 2024
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  5. Make unittest tests pass

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 28, 2024
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  6. Fix problems with TrajectoryEditor

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 28, 2024
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Commits on Nov 29, 2024

  1. Remove mic_fast_calc from Extensions

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 29, 2024
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  2. Make all tests pass

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 29, 2024
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  3. Rewrite SolventAccesibleSurface

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 29, 2024
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  4. Correct the SolventAccessibleSurface implementation

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 29, 2024
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  5. Clean up unneccessary files

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 29, 2024
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  6. Remove unused cluster class

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 29, 2024
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  7. Remove unused extension imports

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Nov 29, 2024
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Commits on Dec 1, 2024

  1. Correct Voronoi coordinate padding

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Dec 1, 2024
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Commits on Dec 2, 2024

  1. Correct the Solvent Accessible Surface calculation

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Dec 2, 2024
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  2. Add periodic boundary condition handling to solvent accessible surface

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Dec 2, 2024
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  3. Reduce the number of structure analysis tests

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Dec 2, 2024
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  4. Enable CentreOfMass trajectories with fake atoms

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Dec 2, 2024
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Commits on Dec 3, 2024

  1. Remove the last Cython extension

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Dec 3, 2024
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  2. Reduce the number of open and close operations when reading trajectories

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Dec 3, 2024
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  3. Merge GUI changes

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Dec 3, 2024
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  4. Improve the separation into inter and intra in PDF

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Dec 3, 2024
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  5. Explicitly close trajectory in test_converter.py

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Dec 3, 2024
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  6. Add tests for centre-of-mass trajectory with artificial atoms

    @MBartkowiakSTFC
    MBartkowiakSTFC committed Dec 3, 2024
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