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Graphs_integration #161

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Commits on May 9, 2024

  1. Added placeholders.

    @jintuzhang
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  2. Changed importing styles.

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  3. Added the neighbor list module.

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  4. Added more placeholders.

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  5. Added doc.

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  6. Fixed some styles.

    @jintuzhang
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  7. Added more placeholders.

    @jintuzhang
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  8. Added the graph data module.

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  9. Added doc and more tests.

    @jintuzhang
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  10. Minor fix.

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  11. Switched to new pyg grammar.

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  12. Modified file layouts.

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  13. Added more helper functions.

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  14. Added datamodule.

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  15. Added more functions.

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  16. Fixed some styles.

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  17. Added an alias to the dataset object.

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  18. Resolved the circular dependency problem.

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  19. Added missing type hints.

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  20. Modified file layouts.

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  21. Changed filenames.

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  22. Introduced the dataset class.

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  23. Added the IO function.

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  24. Added selection checks and changed tests.

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  25. Updated __repr__.

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  26. Isolated nodes are not that bad.

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  27. Added radial functions.

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  28. Modified file layouts.

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  29. Added a dataset field to distinguish receivers.

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  30. Added edge encoding function.

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  31. Modified file layouts.

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  32. Fixed typos.

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  33. Fixed typos.

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  34. Added scatter functions.

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  35. Minor fix.

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  36. Updated torch tools.

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  37. Modified shapes of some dataset fields.

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  38. Added models.

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  39. Modified import schemes.

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  40. Renamed a directory.

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  41. Modified import schemes.

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  42. Added a doc string.

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  43. Changed test function outputs.

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  44. Modified shapes of some dataset fields.

    @jintuzhang
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  45. Minor fix.

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  46. Added DeepTDA.

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  47. Fixed lightning training.

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  48. Changed the default batch size.

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  49. Removed nonlinearity in the readout function.

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  50. Updated default parameters.

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  51. Made everything compilable. 

    Deleted `utils.py` to resolve the rebase problem.
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  52. Change units to Angstrom.

    @jintuzhang
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  53. Fixed cell size.

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  54. Added more model attributes.

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  55. Fixed for plumed interface.

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  56. Added tests

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  57. Fixed dtype.

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  58. Modified default parameters.

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  59. Removed unused code.

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  60. Added a dataset option.

    @jintuzhang
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  61. Added a progress bar.

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  62. Be quiet during testing.

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  63. Fixed spaces.

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  64. Added a very basic readme.

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  65. Fixed normal DeepTDA training.

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  66. Added utils.py back.

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Commits on May 13, 2024

  1. Merge branch 'luigibonati:main' into gnn

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Commits on May 17, 2024

  1. Merge branch 'luigibonati:main' into gnn

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Commits on May 23, 2024

  1. Merge branch 'luigibonati:main' into gnn

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Commits on Jun 4, 2024

  1. Updated the dataset code.

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  2. Added comments.

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  3. Added the metaphysics module.

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  4. Allowed to index dataset with a range.

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  5. Added components to the metaphysics module.

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Commits on Jun 5, 2024

  1. Added more tests.

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  2. Changed import order.

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  3. Used batchs in analysis.

    @jintuzhang
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  4. Removed extra keywords.

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Commits on Jun 6, 2024

  1. Sync directory layout from upstream.

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  2. Cleaned code.

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  3. Fixed node indices in output.

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Commits on Jun 10, 2024

  1. Read n_out from model options.

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  2. Added dataset support for DeepTICA.

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Commits on Jun 11, 2024

  1. Make more parameter tests.

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  2. Added GraphDeepTICA.

    @jintuzhang
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  3. Changed data type.

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  4. Made GraphDeepTICA compilable.

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  5. Fixed for PLUMED.

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  6. Merge branch 'luigibonati:main' into gnn

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Commits on Jun 13, 2024

  1. Set default dtype.

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  2. Added tests.

    @jintuzhang
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  3. Merge branch 'luigibonati:main' into gnn

    @jintuzhang
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  4. Added a logo.

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  5. Centered logo.

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  6. Centered logo.

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  7. Centered logo.

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Commits on Jun 14, 2024

  1. Added a normalizing option.

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  2. Merge branch 'luigibonati:main' into gnn

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  3. Changed default parameter.

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Commits on Jun 15, 2024

  1. Merge branch 'luigibonati:main' into gnn

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  2. Changed image width.

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Commits on Jun 16, 2024

  1. Also mask node features.

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Commits on Jul 1, 2024

  1. Added extra loss function options.

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Commits on Jul 5, 2024

  1. Fixed multiple CV sensitivity.

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Commits on Jul 7, 2024

  1. Modified default analysis method.

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Commits on Jul 8, 2024

  1. Fixed import

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Commits on Aug 5, 2024

  1. Added the Gaussian basis function.

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  2. Fixed dim.

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  3. Changed some variable names to be compatible with old models.

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Commits on Aug 7, 2024

  1. Allowed to switch basis function types.

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Commits on Aug 12, 2024

  1. Added SchNet.

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  2. Fixed attributes.

    @jintuzhang
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Commits on Aug 13, 2024

  1. Fixed import.

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  2. Updated one link.

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Commits on Aug 21, 2024

  1. Moved example inputs to the base class.

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    jintuzhang committed Aug 21, 2024
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  2. Removed unused imports.

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    jintuzhang committed Aug 21, 2024
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Commits on Aug 23, 2024

  1. Changed the behavior of building graphs.

    @jintuzhang
    jintuzhang committed Aug 23, 2024
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Commits on Aug 24, 2024

  1. Fixed typo.

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    jintuzhang committed Aug 24, 2024
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  2. Added a method to dump dataset.

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    jintuzhang committed Aug 24, 2024
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Commits on Aug 26, 2024

  1. Made the dataset function more robust.

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    jintuzhang committed Aug 26, 2024
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Commits on Aug 28, 2024

  1. Added buffer region support.

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    jintuzhang committed Aug 28, 2024
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Commits on Sep 2, 2024

  1. Changed the default aggr operation.

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    jintuzhang committed Sep 2, 2024
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Commits on Sep 3, 2024

  1. Only use system node features as CV values.

    @jintuzhang
    jintuzhang committed Sep 3, 2024
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  2. Fixed tests.

    @jintuzhang
    jintuzhang committed Sep 3, 2024
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Commits on Sep 4, 2024

  1. Merge pull request #1 from jintuzhang/neighbor 

    Implemented the truncated graph method.
    @jintuzhang
    jintuzhang authored Sep 4, 2024
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Commits on Sep 12, 2024

  1. Do not compile torch_scatter.

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    jintuzhang committed Sep 12, 2024
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Commits on Sep 16, 2024

  1. Changed the behavior of create_label.

    @jintuzhang
    jintuzhang committed Sep 16, 2024
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  2. Added a mass function.

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    jintuzhang committed Sep 16, 2024
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Commits on Sep 24, 2024

  1. Merge branch 'luigibonati:main' into gnn

    @jintuzhang
    jintuzhang authored Sep 24, 2024
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Commits on Sep 30, 2024

  1. Merge branch 'luigibonati:main' into gnn

    @jintuzhang
    jintuzhang authored Sep 30, 2024
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Commits on Oct 2, 2024

  1. Merge branch 'luigibonati:main' into gnn

    @jintuzhang
    jintuzhang authored Oct 2, 2024
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Commits on Oct 9, 2024

  1. Merge branch 'luigibonati:main' into gnn

    @jintuzhang
    jintuzhang authored Oct 9, 2024
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Commits on Nov 7, 2024

  1. Merge branch 'luigibonati:main' into gnn

    @jintuzhang
    jintuzhang authored Nov 7, 2024
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Commits on Nov 13, 2024

  1. Create graph module in nn

    @EnricoTrizio
    EnricoTrizio committed Nov 13, 2024
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  2. Added tda graph and tda merged as working examples

    @EnricoTrizio
    EnricoTrizio committed Nov 13, 2024
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  3. Moved graph.data into data.graph

    @EnricoTrizio
    EnricoTrizio committed Nov 13, 2024
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  4. modified DictDataset to include metadata and handle graph data

    @EnricoTrizio
    EnricoTrizio committed Nov 13, 2024
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  5. First test to unify data hadling on ff and gnn

    @EnricoTrizio
    EnricoTrizio committed Nov 13, 2024
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  6. Moved graph.utils.io into main.utils.io

    @EnricoTrizio
    EnricoTrizio committed Nov 13, 2024
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  7. Moved progress bar utils to main.utils.plot

    @EnricoTrizio
    EnricoTrizio committed Nov 13, 2024
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  8. added notebook and data for testing

    @EnricoTrizio
    EnricoTrizio committed Nov 13, 2024
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Commits on Nov 14, 2024

  1. Fixed requirements and test env

    @EnricoTrizio
    EnricoTrizio committed Nov 14, 2024
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  2. update example notebook

    @EnricoTrizio
    EnricoTrizio committed Nov 14, 2024
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  3. Moved matscipy to pip

    @EnricoTrizio
    EnricoTrizio committed Nov 14, 2024
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  4. Fixed metadata initialization

    @EnricoTrizio
    EnricoTrizio committed Nov 14, 2024
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