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Implement SpookyNet potential #133

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Implement SpookyNet potential #133

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@ArnNag ArnNag commented May 29, 2024 •
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Todos

  • Module dropout
  • Batching (relevant in attention for the charge embedding and nonlocal interactions)
    • Figured it out for charge embedding, more involved for nonlocal interactions

Questions

  • Do I need to add trainable element and charge biases? Are we doing this in other models?
  • Where is charge balancing being taken care off?

Status

  • Ready to go

@wiederm wiederm added the enhancement New feature or request label Jun 2, 2024
ArnNag and others added 25 commits June 3, 2024 10:29
@ArnNag
Merge branch 'main' of github.com:choderalab/modelforge into spookynet
359f632
@ArnNag
Copy SpookyNet interaction module code from reference implementation.…
a6e8ce5 
… Modifications: hardcoded SiLU activation function. Hardcoded approximate attention. Hardcoded initialization of weights of second linear layer in residual block to 0.
@ArnNag
Merge branch 'main' into spookynet
06d85ca
@ArnNag
Merge remote-tracking branch 'choderalab/main' into spookynet
f3448c6
@ArnNag
Merge branch 'main' into spookynet
7d858b4
@ArnNag
Hard code one batch (relevant within attention). Rename variables to …
fe5cd04 
…better match paper.
@ArnNag
More changes. Starting to implement tests
2747fba
@ArnNag
Merge remote-tracking branch 'origin/spookynet' into spookynet
b4f1b72
@ArnNag
Implement equivalence test for SpookyNet interaction block. First ele…
4a5e072 
…ment of tuple return value matches, but second element (after final resblock) does not.
@ArnNag
Implement SpookyNet radial basis function. Test failing (probably due…
16538b6 
… to unit conversion).
@ArnNag
Begin refactoring radial basis functions
9a210b8
@ArnNag
Merge branch 'main' into refactor_rbf
2930e44
@ArnNag
Update RadialBasisFunction comment
6e7b10e
@ArnNag
Fix references to radial basis centers and scale factors
b6f1149
@ArnNag
Continue refactoring radial basis functions
7757010
@ArnNag
Merge remote-tracking branch 'origin/refactor_rbf' into refactor_rbf
b4ea01f
@ArnNag
Fix SchNet RBF
e4af371
@ArnNag
Fix PhysNet and ANI RBF
6398cf8
@ArnNag
Trying to fix SAKE but failing
7e375e8
@ArnNag
Fix SAKE test
e48a395
@ArnNag
Remove unnecessary test
fdfa4d5
@ArnNag
Refactor prefactor
c4b24b4
@ArnNag
Update comment for nondimensionalization
25a5ac9
@ArnNag
Fix SAKE and ANI bugs
c0280fb
@ArnNag
Fix test radial symmetry function
a3bfc0e
wiederm and others added 30 commits July 11, 2024 23:34
@wiederm
update yaml
909238a
@wiederm
update
629df00
@ArnNag
Add comments for todos
5cf4314
@ArnNag
Merge remote-tracking branch 'upstream/ref-postprocessing-and-loss' i…
bc78257 
…nto spookynet
@ArnNag
Fix schnet test
f522208
@ArnNag
Fix test physnet compare representation
eda75b9
@ArnNag
Update SpookyNet for postprocessing
3e0e4d7
@ArnNag
Working through forward test
c4d61fe
@ArnNag
Fix bug that resulted in incorrect dir_ij
f7b132d
@ArnNag
Replace * with einsum
9a52c01
@ArnNag
Replace more operations with einsum
2ec3f3f
@ArnNag
Replace one more operation with torch.einsum. Fix axis label for n
5a32fe4
@ArnNag
Add explicit broadcast. Reformat code.
6ce39e4
@ArnNag
Fix ini_alpha with units
b7a2b28
@ArnNag
Trying to implement embeddings
731bd7b
@ArnNag
More changes
71c3fea
@ArnNag
More changes
e548bf1
@ArnNag
Fix atomic embedding
5ea8988
@ArnNag
Merge branch 'refs/heads/main' into spookynet
b61649e 
# 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
Fix merge conflict issues
5a60c2c
@ArnNag
Remove unnecessarily hard-coded arrays in the model implementation an…
e4dd91c 
…d cast everything to double in the test
@ArnNag
Changes to tests and model
5e00a6d
@ArnNag
Copy parameters
6ad3712
@ArnNag
Add line breaks between different blocks when copying parameters
0539ed3
@ArnNag
Changes to tests and model
b613586
@ArnNag
More changes
10c9914
@ArnNag
Update docstrings
d170b79
@ArnNag
Fix naming resblock -> resmlp
5f9666d
@ArnNag
Update test so that it compares the results of running the modelforge…
57e7b49 
… implementation on a batched methane with the reference implementation on a single methane
@wiederm
Merge branch 'main' into spookynet
b28d660
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@ArnNag @wiederm