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feat(dpa4): DPA4/SeZM on the NeighborGraph lower — graph-native port, multi-rank, native spin, charge-spin/bridging - #5884

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wanghan-iapcm merged 221 commits into

deepmodeling:masterfrom

wanghan-iapcm:feat-graph-dpa4

Jul 26, 2026

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feat(dpa4): DPA4/SeZM on the NeighborGraph lower — graph-native port, multi-rank, native spin, charge-spin/bridging#5884
wanghan-iapcm merged 221 commits into
deepmodeling:masterfrom
wanghan-iapcm:feat-graph-dpa4

Commits on Jul 12, 2026
- feat(dpmodel): segment_max/segment_softmax over trailing feature dims
  Han Wang
  committed
  8bea38f
- feat(dpmodel): repformer graph twins for cal_hg/cal_grrg/symmetrization_op
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  ba95854
- feat(dpmodel): repformer layer graph twins for g1_conv / g2_g1g1
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  79dc371
- refactor(dpmodel): graph-twin naming convention <func_name>_graph
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  b513622
- feat(dpmodel): graph twins for repformer attention ops
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  2c32acc
- feat(dpmodel): RepformerLayer.call_graph
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  83babe4
- test(dpmodel): cover update_chnnl_2=False and cal_gg1=None in RepformerLayer.call_graph parity
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  b75374f
- feat(dpmodel): DescrptBlockRepformers.call_graph + exchange seam
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  a1e00c3
- feat(dpmodel): graph-native DPA2 (uses_graph_lower, call_graph, dense adapter)
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  3b89378
- test(dpmodel): pin dpa2 adapter davg-nonzero divergence; exercise real _block_graph
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  21a4ee1
- docs(dpmodel): correct davg-residual root-cause framing in dpa2 call_graph Notes
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  9fbe20d
- feat(pt_expt): dpa2 graph lower routing tests + border_op graph exchange
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  69f4c4b
- test(pt_expt): pin repformer parallel test to the dense route
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  6c7c7f4
- feat(dpmodel,pt_expt): owned-node (n_local) energy mask in graph output reduction
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  b08304d
- feat(pt_expt): with-comm graph .pt2 artifact for message-passing models
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  650b715
- test(cc): dpa2 graph .pt2 fixtures + universal gtest row
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  99d714e
- feat(cc): multi-rank message-passing graph route (run_model_graph_with_comm)
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  c9e91ae
- fix(cc): fail loudly on empty rank in MP graph route; fix stale comment
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  fef2d53
- test(lmp): dpa2 graph LAMMPS single- and multi-rank tests
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  83179f1
- fix(cc): put nlocal/nghost comm tensors on model device for graph with-comm route
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  b0fe611
- docs: DPA-2 graph-native inference route (pt_expt)
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  6d7e151
Commits on Jul 13, 2026
- test(lmp): scale dpa2 MP virial tolerance; bound empty-rank deadlock with timeout
  Han Wang
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  1e9c15b
- fix(pt_expt): derive graph-trace device from model params, not global DEVICE
  Han Wang
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  966d378
- test(pt_expt): dpa2 joins KNOWN_GRAPH_DENSE_DIVERGENT in default-fallback test
  Han Wang
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  9a365e3
- test(pt_expt): per-model divergence envelopes in default-fallback test
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  854d654
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  
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  2e49936
- style: fix ruff C408/B905 in repformer graph-ops test
  Han Wang
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  1e5cd13
- fix(dpmodel): dpa2 dense call must not route through divergent graph adapter
  Han Wang
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  bc0d70a
- test(dpa2): exclude AOTInductor graph .pt2 from LeakSanitizer build
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  778a4bc
- [pre-commit.ci] auto fixes from pre-commit.com hooks
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- test(dpa2): make LSAN graph-section skip deterministic via explicit env flag
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  10a359d
- docs(dpa2): note graph-route attention cutoff smoothness
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  c633186
- feat(dpmodel): fixed-phantom-count smooth attention on the dpa2 graph route
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Commits on Jul 14, 2026
- docs(dpmodel): numpydoc sections for the phantom-compensated attention kernels
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- docs(dpmodel,pt_expt): numpydoc sections for all remaining PR-added methods
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  58c23e4
- fix(pt_expt): collective empty-rank preflight + extended-axis aparam on graph MP route
  Han Wang
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  34370df
- test(dpa2): address review nits (pairs=None coverage, dup fixture, NoPBC check, unused import)
  Han Wang
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  314a371
- [pre-commit.ci] auto fixes from pre-commit.com hooks
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- test(dpa2): tighten graph-vs-dense envelope post-compensation + prove graph route taken
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  569dfd7
- test(lammps): DPA2 graph empty-subdomain (nlocal=0, nghost>0) MP==SP regression
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  1265c66
- docs(dpa2): document pt_expt eager/training default-flip + legacy escape hatch
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  a266a3b
- feat(pt_expt): graph-native Hessian + fix fparam graph export/train (OutisLi P1s)
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  ffbc655
- [pre-commit.ci] auto fixes from pre-commit.com hooks
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- fix(pt_expt): derive graph trace edge_capacity from real edge count, not sel
  Han Wang
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  2acc142
- fix(pt_expt,dpmodel): graph-lower aparam is flat (N, nda) on the node axis
  Han Wang
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  37ce12d
- fix(pt_expt): gate the graph default-flip to energy-output models
  Han Wang
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  cc29057
- fix(cc): graph aparam width + ghost-only-rank synthesis; bound all MPI test runs
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  e95f2ba
- [pre-commit.ci] auto fixes from pre-commit.com hooks
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- perf(cc,pt_expt): cache empty-rank preflight on ago==0; split n_local from host comm scalars
  Han Wang
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  acc973d
- [pre-commit.ci] auto fixes from pre-commit.com hooks
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- fix(pt_expt): persist disable_graph_lower across checkpoint restart
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- [pre-commit.ci] auto fixes from pre-commit.com hooks
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- fix(dpmodel): signed phantom count -- smooth graph attention for arbitrary degree
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Commits on Jul 15, 2026
- fix(pt_expt): keep the graph-lower routing bool out of traced forwards; CI fixes
  Han Wang
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  95b3dee
- Merge master into feat-graph-dpa2 (integrate #5758 dpa1 graph CUDA rework)
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- [pre-commit.ci] auto fixes from pre-commit.com hooks
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- fix(dpmodel,pt_expt): gate nonzero-mean dpa2 off the graph default; dpa2-aware torch<2.6 guard
  Han Wang
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  41bbd49
- style(pt_expt): explicit device on the graph_lower_disabled buffer init
  Han Wang
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  bc90a20
- docs: use the LAMMPS-native 'ghost' terminology for the extended region
  Han Wang
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  d33ad3b
- fix(dpmodel,cc): strictly positive phantom floor; device-edge flat aparam; effective-layer pair capability
  Han Wang
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  8248d4d
- hardening(cc): assert the flat graph-route aparam contract at the runner boundary
  Han Wang
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  643bb15
- hardening: assert three latent invariants surfaced by the merge audit
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  486b146
- fix(pt_expt): fold extended_virial in the compiled translate; document per-task hatch granularity
  Han Wang
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  3006793
- fix(dpmodel): gate the phantom denominator floor to the negative-count regime
  Han Wang
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- [pre-commit.ci] auto fixes from pre-commit.com hooks
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Commits on Jul 16, 2026
- fix(pt_expt): scope the Triton exclude_types veto to the graph dispatch
  Han Wang
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  017f861
- fix(dpmodel): soft slot-occupancy phantom denominator (positive AND cutoff-continuous)
  Han Wang
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  8011829
- Merge branch 'feat-graph-dpa2' of github.com:wanghan-iapcm/deepmd-kit into feat-graph-dpa2
  Han Wang
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  7e11d63
- fix(dpmodel): make _slot_occupancy export-safe on the unbacked pair axis
  Han Wang
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  206810e
- chore(tests): resolve CodeQL findings (import style, keepalive del)
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  04ad574
- fix(dpmodel): keep gradients off the water-filling cumsum (inductor unbacked_bindings)
  Han Wang
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  8a1ac1f
- test(pt_expt): move graph with-comm export tests next to the dense twin
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  9ed7caf
- fix(dpmodel): C1 slot-occupancy denominator (no force kink at the below-phantom surface)
  Han Wang
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  dfd49ef
- fix(dpmodel): log-space chi -- no division by a subnormal ph_e in the tail
  Han Wang
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  002713d
- Merge upstream/master into feat-graph-dpa2
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- fix(dpmodel): float64 cut selection in the water-filling; correct the positivity proof
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Commits on Jul 18, 2026
- Merge branch 'master' into feat-graph-dpa2
  OutisLi
  authored
  652ace4
- fix: address CodeRabbit round-3 findings (MPI fence placement, LSAN stale fixtures, accessor guard, ABI docs)
  Han Wang
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  48ae340
- Merge branch 'feat-graph-dpa2' of github.com:wanghan-iapcm/deepmd-kit into feat-graph-dpa2
  Han Wang
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  13b098b
- refactor(dpmodel): extract DPA4 flat edge-native core from call_with_edges
  Han Wang
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  3ae87a8
- refactor(dpmodel): descriptor-owned graph type-embedding table at the atomic-model seam
  Han Wang
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  95f2375
- feat(dpmodel): DPA4 graph-native forward (call_graph) and graph-lower capability flags
  Han Wang
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  288cddf
- test(dpmodel): use message-sensitive DPA4 fixture in call_graph parity tests
  Han Wang
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  adf4027
- test(dpmodel): pin dpa4_ener fitting on the flat-N graph seam
  Han Wang
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  d0d8883
- feat(pt_expt): route DPA4 through the NeighborGraph lower with a persisted disable knob
  Han Wang
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  502b794
- fix(dpmodel): DPA4 declares no cross-rank exchange; multi-rank now fails fast instead of dead-comm
  Han Wang
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  12fe36c
- test(dpmodel): golden pin of DPA4 dense call outputs (Task 7 Step 1.5)
  Han Wang
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  2ac2ba5
- refactor(dpmodel): DPA4 dense call is a NeighborGraph adapter; one graph-native math owner
  Han Wang
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  63f6f2f
- refactor(dpmodel): delete the retired DPA4 padded dense builder; repoint padded parity tests at the surviving seam
  Han Wang
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  de0b2e9
- feat(pt_expt): DPA4 graph .pt2 export (auto lower kind resolves to graph)
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  34fe1cc
- test(pt_expt): de-vacuate DPA4 AOTI freeze parity via jittered weights
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  8174ee6
- test(infer,cc,lmp): DPA4 graph .pt2 inference fixtures, C++ row, LAMMPS single-rank
  Han Wang
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  5c85599
- refactor(dpmodel): remove the DPA4 loose-edge-list API in favor of NeighborGraph
  Han Wang
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  bc9e215
- chore(pt_expt,cc): deprecate the legacy edge_vec .pt2 lower schema loaders
  Han Wang
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  9086af9
- docs(dpa4): document graph-native inference route and correct multi-rank status
  Han Wang
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  fd76e45
- docs(dpa4): final-review fix batch — stale docstrings, dead param, error-site wording
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Commits on Jul 19, 2026
- test(pt_expt): move DPA4 export-test artifact inputs to the compile device
  Han Wang
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  b6c3c37
- test(pt_expt): keep the DPA4 dense-branch eager reference on CPU
  Han Wang
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  33cf0a4
- test(dpa4): promote jitter_zero_arrays to a shared fixture module
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  0c956cf
- test(pt_expt): pin do_atomic_virial=False filtering on the DPA4 graph lower
  Han Wang
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  7a270d1
- refactor(pt_expt): route the canonical-graph tebd table via the descriptor hook
  Han Wang
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  c15a255
- refactor(dpmodel): DPA4 graph trunk threads comm_dict; dense adapter owns the rejection
  Han Wang
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  a9bad15
- fix(dpmodel): dense comm rejection fires before the graph build
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  cb77639
- feat(pt_expt): border_op ghost exchange for the DPA4 graph route
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  489bdb0
- test(pt_expt): pin the DPA4 exchange spin-comm rejection
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  e1ba8bf
- feat(pt_expt): DPA4 declares graph-route cross-rank exchange; with-comm artifact gate is lower-kind-aware
  Han Wang
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  e99709a
- test(pt_expt): DPA4 graph .pt2 embeds the with-comm sidecar; nlist stays single-artifact
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  bd17eba
- docs(test): correct test_dpa4_freeze_to_pt2 docstring to the kind-conditional artifact layout
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  c3ed314
- test(lmp): DPA4 graph multi-rank MPI tests (MP==SP gate + empty-rank bound)
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  566050d
- docs(dpa4): multi-rank supported on the graph .pt2 via the with-comm artifact
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  21bffe9
- docs(plan): DPA4 native spin on the NeighborGraph route
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Commits on Jul 20, 2026
- feat(dpmodel): thread native spin through the DPA4 graph lower chain
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  d94a1cf
- refactor(dpmodel): explicit supports_native_spin capability method
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  dc312c9
- feat(dpmodel): DPA4NativeSpinModel on the NeighborGraph route
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  cc07c4a
- fix(dpmodel): DPA4NativeSpinModel translated_output_def + builder-guard tests
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  f9bc474
- feat(pt_expt): force_mag autograd on the DPA4 graph lower
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  143a725
- docs(pt_expt): correct pt joint-grad citation line number
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  cb5eeb6
- feat(pt_expt): DPA4NativeSpinModel wrapper with graph-route force_mag
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  d13a85c
- fix(pt_expt): restore Spin DPA4 rejection message + cover native-spin builder guards
  Han Wang
  committed
  0316072
- feat(pt_expt): graph-spin .pt2 exportable ABI (spin at index 10)
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  afa68a1
- fix(pt_expt): keep the energy graph exportable spin-free (conditional spin arity)
  Han Wang
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  5f23c00
- feat(pt_expt): graph-kind .pt2 freeze for native-spin DPA4 (no with-comm)
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  78a5a01
- feat(pt_expt): DeepEval graph fast path for native-spin .pt2
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  8a30fb1
- test(infer): native-spin DPA4 graph .pt2 fixture generator
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  7ab9d09
- test(infer): build native-spin fixture from inline config+seed, drop committed weights yaml
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  88a81e3
- feat(cc): DeepSpinPTExpt NeighborGraph route for native-spin graph .pt2
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  9fb7485
- test(lmp): single-rank LAMMPS deepspin on the DPA4 graph .pt2
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  f731a19
- feat(pt_expt): native-spin DPA4 training smoke + docs + fixture-regen comment
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  3047dc9
- test(dpmodel): pin the ener_spin flat-label reshape numerically
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  2a3c0f9
- chore: stop tracking docs/superpowers working plans
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  cf103d6
- docs: correct DeepSpinPTExpt guard location in comments (compute, not compute_inner)
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  6f039ab
- Merge upstream/master (dpa2 graph #5779) into feat-graph-dpa4
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  dcc1a5b
- feat(dpa4): wire charge-spin FiLM + SFPG bridging onto the graph route
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  3d0e7ba
- test(pt_expt): device-conditional tolerance for the spin-less determinism check (CUDA index_add atomics)
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  8db86c1
- test(lmp): source native-spin LAMMPS references from the regenerated .expected sidecar (was stale hardcoded)
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  5994a5c
- test(lmp): load build-test custom op lib in the native-spin reference subprocess
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Commits on Jul 21, 2026
- refactor(dpa4): merge _call_graph_common into _run_graph; clarify exclusion ownership
  Han Wang
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  0ee0a4f
- fix(tf2): unpack the 7-tuple _input_type_cast (spin slot) at all tf2 call sites
  Han Wang
  committed
  f0a3d2b
- test(dpa4): make the charge_spin routing spy version-stable
  Han Wang
  committed
  8ae3e5d
- test(dpa4): fix CodeQL py/modification-of-default-value in jitter_zero_arrays
  Han Wang
  committed
  4dea3f2
- test(dpa4): make jitter_zero_arrays pure to clear CodeQL py/modification-of-default-value
  Han Wang
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  144f245
- chore(dpa4): clear CodeQL notes/warning (cyclic-import, unnecessary-delete, import-and-import-from)
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  26593a1
- test(tf2): update FakeDPModel._input_type_cast mock to the 7-tuple signature
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Commits on Jul 22, 2026
- docs(dpa4): close an unbalanced inline literal in translated_output_def docstring
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Commits on Jul 23, 2026
- refactor(dpmodel): declare supports_native_spin/supports_charge_spin on BaseDescriptor
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  2027976
- docs(dpmodel): keep BaseDescriptor spin-capability docstrings descriptor-agnostic
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  91c7684
- refactor(dpmodel,pt_expt): declare the graph-lower capability cluster on BaseDescriptor
  Han Wang
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  e8d1b8a
- refactor(dpmodel,pt_expt,jax): declare has_spin on the base model; drop dead-defensive capability probes
  Han Wang
  committed
  4d1138d
- fix(dpa4): restore pt training-time random_gamma semantics on the shared trunk
  Han Wang
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  3c108c4
- fix(dpmodel,pt_expt): normalize use_spin forms and forward allow_missing_label in the native-spin builders
  Han Wang
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  73a851f
- refactor(pd): drop the has_spin getattr dances for direct base-model calls
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  efb6fb9
- refactor(dpmodel): make_native_spin_model class factory + registered NativeSpinEnergyModel
  Han Wang
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  24abf3c
- refactor(pt_expt): NativeSpinEnergyModel via make_native_spin_model; registry dispatch replaces native-spin seams
  Han Wang
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  71239f9
- test(pt_expt): pin the public-BaseModel native-spin round trip
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- [pre-commit.ci] auto fixes from pre-commit.com hooks
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- feat(dpmodel): native spin combined with charge-spin FiLM (review 3638047227, task 1)
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  c4ddea3
- feat(pt_expt): combined native spin + charge-spin FiLM eager path (review 3638047227, task 2)
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  57a008e
- feat(pt_expt): charge_spin slot in the graph-spin .pt2 ABI (review 3638047227, task 3)
  Han Wang
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  9cf9f36
- feat(infer,cc): feed the graph-spin charge_spin slot in DeepEval and C++ (review 3638047227, task 4)
  Han Wang
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  d1dac26
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Commits on Jul 24, 2026
- feat(dpmodel): backend-agnostic InterPotential (analytical ZBL bridging term)
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  0c388be
- feat(dpmodel): inject the ZBL bridging term at the atomic layer (review 3638077323, task 2)
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  3251411
- feat(pt_expt): ZBL bridging eager path + ownership on DPAtomicModel (review 3638077323, task 3)
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  412cc21
- feat(pt_expt): ZBL bridging export/training e2e + argcheck (review 3638077323, task 4)
  Han Wang
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  69a2697
- [pre-commit.ci] auto fixes from pre-commit.com hooks
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  f51ca5e
- refactor(dpmodel,pt_expt): ZBL bridging as atomic-model COMPOSITION (review 3638077323, redesign)
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  6a2e9de
- refactor(dpmodel,pt_expt): address review batch on the bridging composition
  Han Wang
  committed
  eccc7c3
- refactor(dpmodel,pt_expt): DPA4EnergyModel owns the dpa4-family wire types and pt-checkpoint interop (review items 9+10)
  Han Wang
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  e8ecfd4
- test(pt_expt): repoint the pt-checkpoint interop tests at DPA4EnergyModel
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  1fcdeeb
- test(pt_expt): training fakes implement the pinned has_spin interface (review 3644445970)
  Han Wang
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  e23f5f7
- fix(pt_expt): resolve native-spin freeze to the graph lower at the public freeze layer (review 3638183251)
  Han Wang
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  35dd228
- fix(pt_expt): synthesize the real mask_mag in graph-native-spin DeepEval (review 3644497941)
  Han Wang
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  2ff9f25
- test(pt_expt): exercise the native-spin capability gate with a standard config (review 3644811385)
  Han Wang
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  62a2bff
- fix(dpmodel,pt_expt): narrow the native-spin TypeError translation (review 3644847676)
  Han Wang
  committed
  27678e6
- Merge branch 'master' of https://github.com/deepmodeling/deepmd-kit into feat-graph-dpa4
  Han Wang
  committed
  0b31256
- [pre-commit.ci] auto fixes from pre-commit.com hooks
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- test(pt_expt): make the tf32 warn-once test immune to global logging state
  Han Wang
  committed
  bfa0c4c
- refactor(pt_expt): the native-spin model owns mask_mag; DeepEval reads it
  Han Wang
  committed
  0965e29
- refactor(native-spin): dedup pt_expt forward against dpmodel's call
  Han Wang
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  06ba579
- refactor(native-spin): one translation owner for eager and graph paths
  Han Wang
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  3a13be0
- fix(dpmodel): linear model is graph-capable iff ALL children are
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Commits on Jul 25, 2026
- fix(ci): keep the linear wire type shared, count tf32 warns at the source
  Han Wang
  committed
  acd68f8
- fix(api_cc): apply model-level pair exclusion when building the spin graph
  Han Wang
  committed
  ecfb7a8
- [pre-commit.ci] auto fixes from pre-commit.com hooks
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- fix: refresh the ZBL lookup on change_type_map; allow native spin + bridging
  Han Wang
  committed
  e48b6e2
- refactor: the atomic model answers supports_native_spin, not a descriptor hunt
  Han Wang
  committed
  2f4e63d
- refactor(dpmodel): query supports_native_spin through the interface
  Han Wang
  committed
  cadd737
- feat(pt_expt): native spin supports multi-rank on the graph lower
  Han Wang
  committed
  804cc57
- fix: composition forwards charge_spin capabilities; real multi-rank spin test
  Han Wang
  committed
  5f837d5
- test(zbl): first C++ coverage for DPA4 + analytical ZBL bridging
  Han Wang
  committed
  648b3db
- fix(test): include DeepPotPTExpt.h so the ZBL C++ suite actually runs
  Han Wang
  committed
  459e0ff
- test(zbl): magnitude-scaled fp32 bound for the ZBL C++ comparison
  Han Wang
  committed
  2824e14
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  pre-commit-ci[bot]
  committed
  f7d3067
- fix(api_cc): extended-region output remap for multi-rank graph spin
  Han Wang
  committed
  0123bcb
- fix(api_cc): keep graph edges extended for multi-rank native-spin
  Han Wang
  committed
  1d560a1
- refactor(pt_expt): drop the duplicated graph-eligibility guard
  Han Wang
  committed
  18b7459
- fix(dpmodel): draw the DPA4 random-gamma roll with the backend's RNG
  Han Wang
  committed
  1e80e0b
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  pre-commit-ci[bot]
  committed
  0a77df3
- fix(dpa4): pair exclusion must reach the ZBL composition
  Han Wang
  committed
  749fd49
- fix(pt_expt): freeze a graph-capable model through the graph lower
  Han Wang
  committed
  881e208
- feat(api): runtime charge_spin for the DeepSpin inference path
  Han Wang
  committed
  ee1026e
- feat(api): charge_spin through DeepSpinModelDevi
  Han Wang
  committed
  c3f61a7
- test(spin): functional coverage for runtime charge_spin
  Han Wang
  committed
  fb1f8d6
- fix(api_cc): give DeepSpinPTExpt the safety machinery DeepPot has
  Han Wang
  committed
  5f67515
- test(dpa4): cover native-spin+ZBL below Python, and ZBL under LAMMPS
  Han Wang
  committed
  7537e6a
Commits on Jul 26, 2026
- fix(dpa4): atom exclusion and stat capabilities must reach the composition
  Han Wang
  committed
  d7287ef
- style: trim the exclusion and capability comments
  Han Wang
  committed
  963b284
- fix(dpmodel): reject an intensive/extensive composition at construction
  Han Wang
  committed
  206102d
- test: complete the linear-model test double
  Han Wang
  committed
  0053e27
- fix(dpmodel): a composition default requires agreement among active children
  Han Wang
  committed
  f937b89
- fix(pt_expt): warn when a requested lower_kind is overridden
  Han Wang
  committed
  c40f018
- [pre-commit.ci] auto fixes from pre-commit.com hooks
  pre-commit-ci[bot]
  committed
  126eec8
- docs(cli): --lower-kind no longer advertises a dense default
  Han Wang
  committed
  436c46e
- test: drop the dual-import pattern CodeQL flagged
  Han Wang
  committed
  c20b4ca
- fix(dpmodel): composition consumers must agree on fparam/aparam dimension
  Han Wang
  committed
  89a3f65
- refactor(dpmodel): restore the PT-aligned method order in dpa4
  Han Wang
  committed
  37f1ce0
- docs(dpa4): correct the freeze and multi-rank capability matrix
  Han Wang
  committed
  aa10829
- test(zbl): restore through the pt_expt class so the roundtrip runs on CUDA
  Han Wang
  committed
  b4afa3c
- test(spin): the native-spin graph .pt2 must carry the with-comm artifact
  Han Wang
  committed
  5385950

Commits

Commits on Jul 12, 2026

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Commits on Jul 20, 2026