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refactor: pair exclude_types as canonical NeighborGraph transform; dpa1 graph path supports exclude_types (decision #18) - #5733

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iProzd merged 66 commits into

deepmodeling:masterfrom

wanghan-iapcm:feat-graph-pair-exclude

Jul 12, 2026

Merged

refactor: pair exclude_types as canonical NeighborGraph transform; dpa1 graph path supports exclude_types (decision #18)#5733
iProzd merged 66 commits into
deepmodeling:masterfrom
wanghan-iapcm:feat-graph-pair-exclude

Commits on Jul 6, 2026
- feat(dpmodel): canonical apply_pair_exclusion graph transform (decision #18)
  Han Wang
  committed
  20fba73
- fix(dpmodel): raise NotImplementedError in apply_pair_exclusion(compact=True) when angle fields are present
  Han Wang
  committed
  cd0cc86
- refactor(dpmodel): atomic-model pair exclusion via apply_pair_exclusion
  Han Wang
  committed
  285f77a
- feat(dpmodel): dpa1 graph path supports exclude_types via apply_pair_exclusion; drop eligibility gate
  Han Wang
  committed
  3386ada
- test(dpmodel/dpa1): parametrize exclude_types graph parity over attn_layer and type_one_side
  Han Wang
  committed
  9e64268
- docs: remove stale exclude_types graph-ineligibility claims
  Han Wang
  committed
  51c5218
- feat(neighbor_graph): dispatcher-level pair_excl post-process (task 3b)
  Han Wang
  committed
  0aae745
- test(pt_expt): pair_exclude_types graph-vs-legacy parity + vacuity check
  Han Wang
  committed
  c2ab950
- docs: add notes on nv_graph_builder pair_excl oracle gap
  Han Wang
  committed
  d0e4ab6
- test(pt_expt): graph-route exclude_types coverage (parity + make_fx)
  Han Wang
  committed
  3394832
- test(pt_expt): descriptor-level exclude_types export + graph-vs-legacy parity
  Han Wang
  committed
  ab1af0d
- fix: add reduced-virial parity assertion in descriptor exclude_types test
  Han Wang
  committed
  b855b19
- fix(neighbor_graph): use logical_and+bool cast in apply_pair_exclusion for array_api_strict compat
  Han Wang
  committed
  df9cfbb
- feat(dpmodel): apply_pair_exclusion_nlist helper + pair_excl on build_neighbor_list/strategies (A4)
  Han Wang
  committed
  facb598
- fix(dpmodel): guard edges+pair_excl, fix base docstring (A4 review)
  Han Wang
  committed
  c960e0e
- feat(pt_expt): serialize pair_exclude_types into .pt2 metadata + C++ cross-refs
  Han Wang
  committed
  398e6b8
- feat(api_cc): C++ pair-exclusion twins at the pt_expt ingestion seam
  Han Wang
  committed
  aab77c7
- test(api_cc): gtest + gen script for C++ pair-exclusion seam (dpa1)
  Han Wang
  committed
  c1e97db
- docs: exclude_types is graph-native; fix stale comments in _call_dense and forward_common_atomic_graph
  Han Wang
  committed
  eced293
- fix(spin): force legacy dense routing in SpinModel.call_common
  Han Wang
  committed
  9f1df4a
- fix(spin): explicit graph-lower opt-out on backbone descriptor
  Han Wang
  committed
  9a06854
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  
  pre-commit-ci[bot]
  authored and
  Han Wang
  committed
  331c9cf
- fix(docs+review): numpydoc See Also->Notes for C++ cross-refs; address CodeQL/CodeRabbit
  Han Wang
  committed
  79d5a89
- feat(dpmodel): compact-mode apply_pair_exclusion supports angle fields
  Han Wang
  committed
  cd46679
- refactor(graph): apply model-level pair_exclude at graph BUILD, not in the atomic model
  Han Wang
  committed
  a051090
- fix(dpmodel): fail fast on inconsistent angle fields in compact apply_pair_exclusion
  Han Wang
  committed
  b543531
- fix(pt_expt): DeepEval graph pair_excl uses a numpy-backed mask (device-safe)
  Han Wang
  committed
  6ff11d2
- DEBUG: instrument applyPairExclusion (REVERT)
  Han Wang
  committed
  4f5fdba
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  
  pre-commit-ci[bot]
  authored and
  Han Wang
  committed
  1dbe313
- Revert "DEBUG: instrument applyPairExclusion (REVERT)"
  Han Wang
  committed
  931f209
- refactor(dense): apply model-level pair_exclude at nlist BUILD, completing A4
  Han Wang
  committed
  e172298
- refactor(jax2tf): reuse dpmodel apply_pair_exclusion_nlist via ndtensorflow
  Han Wang
  committed
  83dd109
- fix(tf2): apply model-level pair_exclude at nlist BUILD; align io test
  Han Wang
  committed
  0125415
- style: isort import order in test_dp_atomic_model (reapply dropped pre-commit.ci autofix)
  Han Wang
  committed
  85e1001
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  
  pre-commit-ci[bot]
  authored and
  Han Wang
  committed
  fd6b475
- fix(jax2tf,tf2): guard model.atomic_model when threading pair_excl
  Han Wang
  committed
  d7c83ed
- docs(se-atten): exclude_types no longer disqualifies from the graph path
  Han Wang
  committed
  8f6b796
- fix(stat): model-level pair_exclude enters input stat at nlist BUILD (Piece A)
  Han Wang
  committed
  f2d750b
- feat(stat): compute dpa1 input stat env matrix via NeighborGraph (Piece B)
  Han Wang
  committed
  dd5de26
- refactor(neighbor_graph): extract graph_from_dense_quartet helper (DRY)
  Han Wang
  committed
  06e6ede
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  pre-commit-ci[bot]
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  c564e2d
Commits on Jul 8, 2026
- fix(pt-expt): apply pair exclusion on the dense multi-rank (with-comm) path
  Han Wang
  committed
  ff28370
- test(lammps): DPA3 dense multi-rank pair-exclusion cell-3 test
  Han Wang
  committed
  0ebe3e2
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  pre-commit-ci[bot]
  committed
  b09fa83
- feat(dpmodel): eager fail-safe guard at the exclusion seam (fail-closed)
  Han Wang
  committed
  5ad1f05
- fix(jax): apply pair exclusion at the jax-md call_lower ingestion seam
  Han Wang
  committed
  5c5889c
- Merge remote-tracking branch 'origin/feat-graph-pair-exclude' into feat-graph-pair-exclude
  Han Wang
  committed
  9a7bc3f
Commits on Jul 9, 2026
- Merge remote-tracking branch 'upstream/master' into feat-graph-pair-exclude
  Han Wang
  committed
  1cdf162
- test(infer): derive deeppot_dpa3_pairexcl_mpi.pt2 by metadata patch, no recompile
  Han Wang
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  a95a958
- test(infer): derive graph pair-exclude fixtures by patch, share helper
  Han Wang
  committed
  6e01b62
- docs: numpydoc-align docstrings added in this PR
  Han Wang
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  9f9da9c
Commits on Jul 10, 2026
- Merge remote-tracking branch 'upstream/master' into feat-graph-pair-exclude
  Han Wang
  committed
  15858b6
- fix(tf2): apply model-level pair_exclude on the live/eager upper path
  Han Wang
  committed
  6535cbd
- test(pt_expt): exercise graph route in dpa1 exportable exclude test
  Han Wang
  committed
  4c15f8c
- feat(jax): apply model-level pair_exclude at the DeepPotJAX nlist seam
  Han Wang
  committed
  33318f4
- refactor(api_cc): extract torch-free nlist pair-exclude filter + unit-test it
  Han Wang
  committed
  4846ec7
- test(consistent): stop skipping tf2 for pair/atom exclusion in test_ener
  Han Wang
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  c5b5345
- test(api_cc): end-to-end DeepPotJAX InputNlist pair-exclusion gtest
  Han Wang
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  4acf4de
Commits on Jul 11, 2026
- fix(tf2): guard atomic_model when threading pair_excl in call_common
  Han Wang
  committed
  79733df
- fix(dpmodel): apply model-level pair_exclude on the returned quartet, not in build()
  Han Wang
  committed
  779b277
- fix(tf2): fold pair_exclude into prepare_lower_inputs for compiled training
  Han Wang
  committed
  9bdda5d
- refactor(dpmodel): builder owns pair_exclude; pass kwarg only when set
  Han Wang
  committed
  8988c05
- style(dpmodel): merge pair_excl build branches via conditional kwargs
  Han Wang
  committed
  a947793
- refactor(tf2): move make_model.py under tf2/model/; builder owns pair_excl
  Han Wang
  committed
  4856eed
- docs(pt_expt): note why deep_eval passes pair_excl directly to its builder
  Han Wang
  committed
  6363eea
- refactor: pass pair_excl to build() directly; pair_excl is part of the contract
  Han Wang
  committed
  a33ff79

Commits

Commits on Jul 6, 2026

Commits on Jul 8, 2026

Commits on Jul 9, 2026

Commits on Jul 10, 2026

Commits on Jul 11, 2026