feat(dpmodel): NeighborGraph 3-body angle machinery (PR-E)#5717
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wanghan-iapcm wants to merge 12 commits into
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feat(dpmodel): NeighborGraph 3-body angle machinery (PR-E)#5717wanghan-iapcm wants to merge 12 commits into
wanghan-iapcm wants to merge 12 commits into
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No actionable comments were generated in the recent review. 🎉 ℹ️ Recent review info⚙️ Run configurationConfiguration used: Repository UI Review profile: CHILL Plan: Pro Run ID: 📒 Files selected for processing (2)
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📝 WalkthroughWalkthroughThis PR adds angle-graph support to ChangesAngle graph construction and aggregation
Estimated code review effort: 3 (Moderate) | ~30 minutes Possibly related PRs
Suggested labels: Suggested reviewers: 🚥 Pre-merge checks | ✅ 5✅ Passed checks (5 passed)
✨ Finishing Touches🧪 Generate unit tests (beta)
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Actionable comments posted: 1
🧹 Nitpick comments (1)
source/tests/common/dpmodel/test_angle_builder.py (1)
326-364: 📐 Maintainability & Code Quality | 🔵 Trivial | ⚡ Quick winAdd a padded-
angle_indexcase to the aggregation tests.Both aggregation tests here only use angle data where every slot is real (no padding). Given the padding-mask precondition gap noted in
angles.py(angle_to_edge_sum/angle_to_node_sum), a test with a paddedangle_indexand non-zero paddingdatavalues would catch regressions if that precondition is ever violated.🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@source/tests/common/dpmodel/test_angle_builder.py` around lines 326 - 364, The aggregation tests in test_angle_builder only cover fully real angle slots, so add a new padded-angle case for angle_to_edge_sum and angle_to_node_sum using a padded angle_index with non-zero data in the padded positions. Reuse the existing test_angle_aggregation and test_angle_aggregation_torch_namespace patterns, but assert that padding is ignored in both the numpy and torch-namespace paths so regressions around the padding-mask precondition are caught.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@deepmd/dpmodel/utils/neighbor_graph/segment.py`:
- Around line 59-89: The masked softmax in segment_softmax can overflow because
shifted is computed from raw data instead of data_for_max, allowing masked
entries to produce inf and then nan when multiplied by the zero mask. Update
segment_softmax to base the subtraction on data_for_max so masked elements
remain -inf before exp, keeping segment_sum and the denom_e guard from being
poisoned; use the existing segment_max, segment_sum, and mask handling paths to
locate the fix.
---
Nitpick comments:
In `@source/tests/common/dpmodel/test_angle_builder.py`:
- Around line 326-364: The aggregation tests in test_angle_builder only cover
fully real angle slots, so add a new padded-angle case for angle_to_edge_sum and
angle_to_node_sum using a padded angle_index with non-zero data in the padded
positions. Reuse the existing test_angle_aggregation and
test_angle_aggregation_torch_namespace patterns, but assert that padding is
ignored in both the numpy and torch-namespace paths so regressions around the
padding-mask precondition are caught.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
⚙️ Run configuration
Configuration used: Repository UI
Review profile: CHILL
Plan: Pro
Run ID: b038075f-6809-4579-8ce1-5cf5d1d41c90
📒 Files selected for processing (17)
deepmd/dpmodel/descriptor/dpa1.pydeepmd/dpmodel/utils/neighbor_graph/__init__.pydeepmd/dpmodel/utils/neighbor_graph/angles.pydeepmd/dpmodel/utils/neighbor_graph/env.pydeepmd/dpmodel/utils/neighbor_graph/graph.pydeepmd/dpmodel/utils/neighbor_graph/pairs.pydeepmd/dpmodel/utils/neighbor_graph/segment.pysource/tests/common/dpmodel/test_angle_builder.pysource/tests/common/dpmodel/test_center_edge_pairs.pysource/tests/common/dpmodel/test_dpa1_call_graph_block.pysource/tests/common/dpmodel/test_dpa1_graph_attention_parity.pysource/tests/common/dpmodel/test_graph_angle_cos_parity.pysource/tests/common/dpmodel/test_segment_softmax.pysource/tests/pt_expt/descriptor/test_dpa1.pysource/tests/pt_expt/model/test_dpa1_graph_lower.pysource/tests/pt_expt/model/test_linear_model.pysource/tests/pt_expt/utils/test_neighbor_list.py
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Files 988 990 +2
Lines 110876 111079 +203
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- Misses 19247 19375 +128
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- Remove unused locals flagged by CodeQL (ai_def/ai_full in the ordered-superset test, ev in the angle-cos parity test); strengthen the ordered+include_self test to assert the default pairs are an actual subset of the full pair set (using the previously-dead ai_def/ai_full). - Add masked-padding aggregation tests (CodeRabbit nitpick): pin the precondition that angle_to_edge_sum/angle_to_node_sum ignore guard angles only once data is zeroed via angle_mask, in numpy and torch.
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Summary
NeighborGraph PR-E: the optional 3-body angle extension of the edge-graph neighbor-list contract (design discussion wanghan-iapcm#4). An angle is a pair of edges sharing a center (
dst(edge_a) == dst(edge_b)), stored asangle_index (2, A)into[0, E)+angle_mask (A,)—edge_vecstays the ONLY geometry leaf, so force/virial assembly is untouched (proven by an invariance test).What's added (all in
deepmd/dpmodel/utils/neighbor_graph/)pad_and_guard_angles(graph.py) — angle-axis padder mirroringpad_and_guard_edges(dynamic guard append / staticangle_capacitywith overflow ValueError).angles.py(new):build_angle_index(edge_index, edge_vec, edge_mask, n_total, a_rcut, *, ordered=False, include_self=False, layout=None)— unordered, no-self pairs of edges sharing a center where BOTH edges are withina_rcut; built on PR-D'scenter_edge_pairs;pair_maskfolded intoangle_mask(never discarded).attach_angles(graph, a_rcut, ...)— post-hoc: edge graph in, graph with angle fields out (dataclasses.replace); default builders keep anglesNone.angle_to_edge_sum/angle_to_node_sum— segment-sum aggregation to the query edge / shared center.graph_angle_cos(angle_index, edge_vec, eps=1e-6)— per-angle cos θ mirroring dpa3 repflowscosine_ijeps placement exactly (+epsin norm denominators,*(1-eps)on the product).angle_padding_fraction(graph)— mask-derived padding-waste report for static capacities.Semantics / decisions
a_sel x a_selsquare including thej==kdiagonal; the graph set keeps one entry per unordered{j,k}pair and moves the degenerate diagonal to the (a_rcut-filtered) edge channel. Dense parity is therefore asserted against the OFF-DIAGONALcosine_ij[j,k](j != k) at rtol/atol 1e-12 (same-math fp64), at non-bindinga_sel. The ordered+self full square stays available via flags.a_sel= normalization-only (carry-all withina_rcut), consistent with the edge-seldecision.sw == 1regime (rtol 1e-12).Tests
source/tests/common/dpmodel/test_angle_builder.py(21) +test_graph_angle_cos_parity.py(6): brute-force triplet oracle (all flag combinations, multi-center, static layout,node_capacitybranch), dpa3 dense-parity + no-self-angle assertion, se_t coordinate oracle, force/virial bit-exact invariance with/without angles, padding-fraction (incl.total==0), torch-namespace smoke tests for every new function. Full neighbor-graph suite: 54 passed.Known limitations
mixed_types=False), used as oracle only.nonzeroincenter_edge_pairs) even when a staticlayoutis passed —angle_capacityfixes the output shape only; shape-static enumeration for export is deferred to PR-G.angle_maskbefore summing (padding angles point at edge 0).A ~ sum(deg^2)capacity overhead mitigated bya_rcut < rcutand reported byangle_padding_fraction.Summary by CodeRabbit
New Features
Tests