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Implement SpookyNet potential #133

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Implement SpookyNet potential #133

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Commits on May 29, 2024

  1. Copy SchNet implementation and rename to SpookyNet

    @ArnNag
    ArnNag committed May 29, 2024
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  2. Merge branch 'main' into spookynet

    @ArnNag
    ArnNag authored May 29, 2024
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Commits on May 31, 2024

  1. Add spookynet to test environment and list of models. Rename SAKE inp… 

    …ut dataclass.
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Commits on Jun 3, 2024

  1. Merge branch 'main' of github.com:choderalab/modelforge into spookynet

    @ArnNag
    ArnNag committed Jun 3, 2024
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Commits on Jun 5, 2024

  1. Copy SpookyNet interaction module code from reference implementation.… 

    … Modifications: hardcoded SiLU activation function. Hardcoded approximate attention. Hardcoded initialization of weights of second linear layer in residual block to 0.
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Commits on Jun 6, 2024

  1. Merge branch 'main' into spookynet

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Commits on Jun 11, 2024

  1. Merge remote-tracking branch 'choderalab/main' into spookynet

    @ArnNag
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Commits on Jun 14, 2024

  1. Merge branch 'main' into spookynet

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    ArnNag authored Jun 14, 2024
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Commits on Jun 20, 2024

  1. Hard code one batch (relevant within attention). Rename variables to … 

    …better match paper.
    @ArnNag
    ArnNag committed Jun 20, 2024
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Commits on Jun 25, 2024

  1. More changes. Starting to implement tests

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  2. Merge remote-tracking branch 'origin/spookynet' into spookynet

    @ArnNag
    ArnNag committed Jun 25, 2024
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Commits on Jun 26, 2024

  1. Implement equivalence test for SpookyNet interaction block. First ele… 

    …ment of tuple return value matches, but second element (after final resblock) does not.
    @ArnNag
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  2. Implement SpookyNet radial basis function. Test failing (probably due… 

    … to unit conversion).
    @ArnNag
    ArnNag committed Jun 26, 2024
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Commits on Jun 27, 2024

  1. Begin refactoring radial basis functions

    @ArnNag
    ArnNag committed Jun 27, 2024
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  2. Merge branch 'main' into refactor_rbf

    @ArnNag
    ArnNag authored Jun 27, 2024
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  3. Update RadialBasisFunction comment

    @ArnNag
    ArnNag authored Jun 27, 2024
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  4. Fix references to radial basis centers and scale factors

    @ArnNag
    ArnNag committed Jun 27, 2024
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  5. Continue refactoring radial basis functions

    @ArnNag
    ArnNag committed Jun 27, 2024
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  6. Merge remote-tracking branch 'origin/refactor_rbf' into refactor_rbf

    @ArnNag
    ArnNag committed Jun 27, 2024
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Commits on Jun 28, 2024

  1. Fix SchNet RBF

    @ArnNag
    ArnNag committed Jun 28, 2024
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  2. Fix PhysNet and ANI RBF

    @ArnNag
    ArnNag committed Jun 28, 2024
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  3. Trying to fix SAKE but failing

    @ArnNag
    ArnNag committed Jun 28, 2024
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Commits on Jul 2, 2024

  1. Fix SAKE test

    @ArnNag
    ArnNag committed Jul 2, 2024
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  2. Remove unnecessary test

    @ArnNag
    ArnNag committed Jul 2, 2024
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  3. Refactor prefactor

    @ArnNag
    ArnNag committed Jul 2, 2024
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  4. Update comment for nondimensionalization

    @ArnNag
    ArnNag committed Jul 2, 2024
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  5. Fix SAKE and ANI bugs

    @ArnNag
    ArnNag committed Jul 2, 2024
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  6. Fix test radial symmetry function

    @ArnNag
    ArnNag committed Jul 2, 2024
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  7. Merge branch 'main' into refactor_rbf

    @ArnNag
    ArnNag authored Jul 2, 2024
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  8. Merge branch 'refs/heads/refactor_rbf' into spookynet 

    # Conflicts:
#	devtools/conda-envs/test_env.yaml
#	modelforge/potential/models.py
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Commits on Jul 3, 2024

  1. Update utils.py 

    Small changes to the dtype that is passed to the RBF. I think it is best to set a default value for the publically exposed class, e.g., `SchNetRadialBasisFunction`) and have optional `dtype` parameters present in the internal classes (which will then fail if it wasn't set in the entry point classes).

Also added parameter docstring to some of the RBF classes.
    @wiederm
    wiederm authored Jul 3, 2024
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  2. typo fix

    @wiederm
    wiederm committed Jul 3, 2024
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Commits on Jul 5, 2024

  1. Make RadialBasisFunctionCore inherit from nn.Module

    @ArnNag
    ArnNag authored Jul 5, 2024
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  2. Remove @staticmethod decorator

    @ArnNag
    ArnNag authored Jul 5, 2024
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Commits on Jul 6, 2024

  1. Try to implement Bernstein polynomials

    @ArnNag
    ArnNag committed Jul 6, 2024
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  2. Add shape assertion in RadialBasisFunctionCore. Remove unnecessary un… 

    …squeeze in PhysNet radial basis function
    @ArnNag
    ArnNag committed Jul 6, 2024
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  3. Remove print statement

    @ArnNag
    ArnNag committed Jul 6, 2024
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  4. Remove print statements in SAKE

    @ArnNag
    ArnNag committed Jul 6, 2024
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  5. Fix SAKE RBF test

    @ArnNag
    ArnNag committed Jul 6, 2024
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Commits on Jul 9, 2024

  1. Merge branch 'main' into refactor_rbf

    @ArnNag
    ArnNag authored Jul 9, 2024
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  2. Refactor exponential Bernstein polynomials

    @ArnNag
    ArnNag committed Jul 9, 2024
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  3. Fix SchNet tests

    @ArnNag
    ArnNag committed Jul 9, 2024
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  4. Fix spk tests

    @ArnNag
    ArnNag committed Jul 9, 2024
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  5. Clean spk test

    @ArnNag
    ArnNag committed Jul 9, 2024
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  6. Merge branch 'refs/heads/refactor_rbf' into spookynet 

    # Conflicts:
#	.gitignore
#	modelforge/potential/sake.py
#	modelforge/potential/utils.py
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  7. Working on spookynet Bernstein polynomials. Weird shape assertion fail.

    @ArnNag
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  8. Broadcast to number of radial basis functions in nondimensionalizatio… 

    …n of exponential Bernstein polynomials
    @ArnNag
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Commits on Jul 10, 2024

  1. update toml

    @wiederm
    wiederm committed Jul 10, 2024
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  2. transition to new version of postprocessing

    @wiederm
    wiederm committed Jul 10, 2024
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  3. updated toml

    @wiederm
    wiederm committed Jul 10, 2024
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  4. update names, intial postprocessing implementation

    wiederm committed Jul 10, 2024
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  5. working prototype

    @wiederm
    wiederm committed Jul 10, 2024
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Commits on Jul 11, 2024

  1. update all toml files and all potential output names

    @wiederm
    wiederm committed Jul 11, 2024
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  2. update input signature and toml files

    @wiederm
    wiederm committed Jul 11, 2024
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  3. remove legacy code

    @wiederm
    wiederm committed Jul 11, 2024
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  4. update

    @wiederm
    wiederm committed Jul 11, 2024
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  5. update loss docstrings

    @wiederm
    wiederm committed Jul 11, 2024
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  6. fixing tests

    @wiederm
    wiederm committed Jul 11, 2024
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  7. fixing tests and names

    @wiederm
    wiederm committed Jul 11, 2024
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  8. fix test

    @wiederm
    wiederm committed Jul 11, 2024
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  9. Merge branch 'main' into ref-postprocessing-and-loss

    @wiederm
    wiederm authored Jul 11, 2024
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  10. error calculation tests

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  11. Merge branch 'ref-postprocessing-and-loss' of https://github.com/chod… 

    …eralab/modelforge into ref-postprocessing-and-loss
    @wiederm
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  12. update

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  13. add flax

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    wiederm committed Jul 11, 2024
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  14. update yaml

    @wiederm
    wiederm committed Jul 11, 2024
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  15. update

    @wiederm
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  16. Add comments for todos

    @ArnNag
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  17. Merge remote-tracking branch 'upstream/ref-postprocessing-and-loss' i… 

    …nto spookynet
    @ArnNag
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  18. Fix schnet test

    @ArnNag
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  19. Fix test physnet compare representation

    @ArnNag
    ArnNag committed Jul 11, 2024
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  20. Update SpookyNet for postprocessing

    @ArnNag
    ArnNag committed Jul 11, 2024
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Commits on Jul 12, 2024

  1. Working through forward test

    @ArnNag
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  2. Fix bug that resulted in incorrect dir_ij

    @ArnNag
    ArnNag committed Jul 12, 2024
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  3. Replace * with einsum

    @ArnNag
    ArnNag committed Jul 12, 2024
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  4. Replace more operations with einsum

    @ArnNag
    ArnNag committed Jul 12, 2024
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  5. Replace one more operation with torch.einsum. Fix axis label for n

    @ArnNag
    ArnNag committed Jul 12, 2024
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  6. Add explicit broadcast. Reformat code.

    @ArnNag
    ArnNag committed Jul 12, 2024
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  7. Fix ini_alpha with units

    @ArnNag
    ArnNag committed Jul 12, 2024
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Commits on Jul 15, 2024

  1. Trying to implement embeddings

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Commits on Jul 16, 2024

  1. More changes

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Commits on Jul 20, 2024

  1. More changes

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Commits on Jul 23, 2024

  1. Fix atomic embedding

    @ArnNag
    ArnNag committed Jul 23, 2024
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Commits on Jul 25, 2024

  1. Merge branch 'refs/heads/main' into spookynet 

    # Conflicts:
#	modelforge/dataset/dataset.py
#	modelforge/potential/ani.py
#	modelforge/potential/models.py
#	modelforge/potential/painn.py
#	modelforge/potential/physnet.py
#	modelforge/potential/processing.py
#	modelforge/potential/sake.py
#	modelforge/potential/schnet.py
#	modelforge/potential/utils.py
#	modelforge/tests/data/training_defaults/default.toml
#	modelforge/tests/test_models.py
#	modelforge/tests/test_painn.py
#	modelforge/tests/test_sake.py
#	modelforge/tests/test_schnet.py
#	modelforge/tests/test_training.py
#	modelforge/train/training.py
    @ArnNag
    ArnNag committed Jul 25, 2024
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  2. Fix merge conflict issues

    @ArnNag
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  3. Remove unnecessarily hard-coded arrays in the model implementation an… 

    …d cast everything to double in the test
    @ArnNag
    ArnNag committed Jul 25, 2024
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  4. Changes to tests and model

    @ArnNag
    ArnNag committed Jul 25, 2024
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  5. Copy parameters

    @ArnNag
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  6. Add line breaks between different blocks when copying parameters

    @ArnNag
    ArnNag committed Jul 25, 2024
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Commits on Jul 26, 2024

  1. Changes to tests and model

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Commits on Jul 30, 2024

  1. More changes

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    ArnNag committed Jul 30, 2024
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Commits on Aug 13, 2024

  1. Update docstrings

    @ArnNag
    ArnNag committed Aug 13, 2024
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  2. Fix naming resblock -> resmlp

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Commits on Aug 21, 2024

  1. Update test so that it compares the results of running the modelforge… 

    … implementation on a batched methane with the reference implementation on a single methane
    @ArnNag
    ArnNag committed Aug 21, 2024
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Commits on Nov 10, 2024

  1. Merge branch 'main' into spookynet

    @wiederm
    wiederm authored Nov 10, 2024
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