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Implement SpookyNet potential#133

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ArnNag wants to merge 95 commits intochoderalab:mainchoderalab/modelforge:mainfrom ArnNag:spookynetArnNag/modelforge:spookynetCopy head branch name to clipboard

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Commits on May 29, 2024

• Copy SchNet implementation and rename to SpookyNet

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• Merge branch 'main' into spookynet

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Commits on May 31, 2024

• Add spookynet to test environment and list of models. Rename SAKE input dataclass.

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Commits on Jun 3, 2024

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

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Commits on Jun 5, 2024

• Copy SpookyNet interaction module code from reference implementation. Modifications: hardcoded SiLU activation function. Hardcoded approximate attention. Hardcoded initialization of weights of seco…

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Commits on Jun 6, 2024

• Merge branch 'main' into spookynet

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Commits on Jun 11, 2024

• Merge remote-tracking branch 'choderalab/main' into spookynet

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Commits on Jun 14, 2024

• Merge branch 'main' into spookynet

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Commits on Jun 20, 2024

• Hard code one batch (relevant within attention). Rename variables to better match paper.

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Commits on Jun 25, 2024

• More changes. Starting to implement tests

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• Merge remote-tracking branch 'origin/spookynet' into spookynet

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Commits on Jun 26, 2024

• Implement equivalence test for SpookyNet interaction block. First element of tuple return value matches, but second element (after final resblock) does not.

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• Implement SpookyNet radial basis function. Test failing (probably due to unit conversion).

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Commits on Jun 27, 2024

• Begin refactoring radial basis functions

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• Merge branch 'main' into refactor_rbf

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• Update RadialBasisFunction comment

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• Fix references to radial basis centers and scale factors

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• Continue refactoring radial basis functions

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• Merge remote-tracking branch 'origin/refactor_rbf' into refactor_rbf

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Commits on Jun 28, 2024

• Fix SchNet RBF

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• Fix PhysNet and ANI RBF

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• Trying to fix SAKE but failing

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Commits on Jul 2, 2024

• Fix SAKE test

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• Remove unnecessary test

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• Refactor prefactor

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• Update comment for nondimensionalization

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• Fix SAKE and ANI bugs

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• Fix test radial symmetry function

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• Merge branch 'main' into refactor_rbf

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• Merge branch 'refs/heads/refactor_rbf' into spookynet

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Commits on Jul 3, 2024

• Update utils.py

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• typo fix

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Commits on Jul 5, 2024

• Make RadialBasisFunctionCore inherit from nn.Module

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• Remove @staticmethod decorator

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Commits on Jul 6, 2024

• Try to implement Bernstein polynomials

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• Add shape assertion in RadialBasisFunctionCore. Remove unnecessary unsqueeze in PhysNet radial basis function

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• Remove print statement

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• Remove print statements in SAKE

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• Fix SAKE RBF test

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Commits on Jul 9, 2024

• Merge branch 'main' into refactor_rbf

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• Refactor exponential Bernstein polynomials

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• Fix SchNet tests

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• Fix spk tests

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• Clean spk test

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• Merge branch 'refs/heads/refactor_rbf' into spookynet

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• Working on spookynet Bernstein polynomials. Weird shape assertion fail.

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• Broadcast to number of radial basis functions in nondimensionalization of exponential Bernstein polynomials

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Commits on Jul 10, 2024

• update toml

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• transition to new version of postprocessing

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• updated toml

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• update names, intial postprocessing implementation

  

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• working prototype

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Commits on Jul 11, 2024

• update all toml files and all potential output names

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• update input signature and toml files

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• remove legacy code

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• update

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• update loss docstrings

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• fixing tests

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• fixing tests and names

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• fix test

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• Merge branch 'main' into ref-postprocessing-and-loss

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• error calculation tests

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• Merge branch 'ref-postprocessing-and-loss' of https://github.com/choderalab/modelforge into ref-postprocessing-and-loss

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• update

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• add flax

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• update yaml

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• update

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• Add comments for todos

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• Merge remote-tracking branch 'upstream/ref-postprocessing-and-loss' into spookynet

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• Fix schnet test

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• Fix test physnet compare representation

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• Update SpookyNet for postprocessing

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Commits on Jul 12, 2024

• Working through forward test

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• Fix bug that resulted in incorrect dir_ij

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• Replace * with einsum

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• Replace more operations with einsum

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• Replace one more operation with torch.einsum. Fix axis label for n

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• Add explicit broadcast. Reformat code.

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• Fix ini_alpha with units

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Commits on Jul 15, 2024

• Trying to implement embeddings

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Commits on Jul 16, 2024

• More changes

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Commits on Jul 20, 2024

• More changes

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Commits on Jul 23, 2024

• Fix atomic embedding

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Commits on Jul 25, 2024

• Merge branch 'refs/heads/main' into spookynet

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• Fix merge conflict issues

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• Remove unnecessarily hard-coded arrays in the model implementation and cast everything to double in the test

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• Changes to tests and model

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• Copy parameters

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• Add line breaks between different blocks when copying parameters

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Commits on Jul 26, 2024

• Changes to tests and model

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Commits on Jul 30, 2024

• More changes

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Commits on Aug 13, 2024

• Update docstrings

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• Fix naming resblock -> resmlp

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Commits on Aug 21, 2024

• 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

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Commits on Nov 10, 2024

• Merge branch 'main' into spookynet

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