feat(dpmodel): NeighborGraph foundation — contract, segment toolkit, numpy builder, edge force/virial - #5581

Merged

wanghan-iapcm merged 24 commits into

deepmodeling:masterfrom

wanghan-iapcm:feat-dpmodel-neighbor-graph

Jun 25, 2026

Commits on Jun 24, 2026

feat(dpmodel): add NeighborGraph/GraphLayout contract dataclasses
Han Wang
committed
44f44ac
feat(dpmodel): derive node validity mask from n_node (compact-prefix)
Han Wang
committed
7526989
feat(dpmodel): add mask-aware segment_sum/segment_mean reduction toolkit
Han Wang
committed
2b681a2
feat(dpmodel): pad_and_guard_edges (compact layout, capacity, edge_mask)
Han Wang
committed
f62cf5f
feat(dpmodel): NumpyNeighborList reference builder (coords -> NeighborGraph)
Han Wang
committed
608d379
feat(dpmodel): edge force/virial assembly (full-to-src atom virial)
Han Wang
committed
0fb91f7
feat(dpmodel): export NeighborGraph foundation symbols
Han Wang
committed
9c6cc80
fix(dpmodel): sort __all__ (RUF022) + cast edge mask to g dtype
Han Wang
committed
341a408
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot]
committed
a7e4382
refactor(dpmodel): build NeighborGraph from existing nlist; drop NumpyNeighborList
Han Wang
committed
52ca488
fix(dpmodel): drop stale numpy_neighbor_list import (rebase leftover)
Han Wang
committed
28a3627
refactor(dpmodel): group NeighborGraph into a subpackage
Han Wang
committed
8077877
fix(dpmodel): honor int sel in build_neighbor_graph; strengthen padding test
Han Wang
committed
2d9fd98
fix(dpmodel): per-frame virial in edge_force_virial; clarify legacy sel contract
Han Wang
committed
a2c5da8
test(dpmodel): general multi-frame coverage (ragged nodes/edges + padding)
Han Wang
committed
04d49fb
test(dpmodel): drop redundant single-frame/square-multiframe edge_force_virial tests
Han Wang
committed
675a781
test(dpmodel): cover empty frame (n_node has a 0) in edge_force_virial
Han Wang
committed
a641355
test(dpmodel): cover all-empty graph (zero real edges) in edge_force_virial
Han Wang
committed
dd76bd6

Commits on Jun 25, 2026

feat(dpmodel): make build_neighbor_graph a carry-all search; rename converter to from_dense_quartet
Han Wang
committed
014a9d5
test(dpmodel): cover min_edges guard, flat coord input, virtual-center exclusion in build_neighbor_graph
Han Wang
committed
83f12c2
refactor(dpmodel): vectorize build_neighbor_graph and from_dense_quartet over frames
Han Wang
committed
6a3c5c4
test(dpmodel): add discriminating cross-periodic-boundary neighbor case
Han Wang
committed
1a97db9
test(dpmodel): add torch-namespace smoke test for graph builders
Han Wang
committed
0eed16e
test(dpmodel): drop the torch-namespace smoke test
Han Wang
committed
f32efc8

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feat(dpmodel): NeighborGraph foundation — contract, segment toolkit, numpy builder, edge force/virial - #5581

feat(dpmodel): NeighborGraph foundation — contract, segment toolkit, numpy builder, edge force/virial#5581
wanghan-iapcm merged 24 commits into
deepmodeling:masterfrom
wanghan-iapcm:feat-dpmodel-neighbor-graph

Commits on Jun 24, 2026

feat(dpmodel): add NeighborGraph/GraphLayout contract dataclasses

feat(dpmodel): derive node validity mask from n_node (compact-prefix)

feat(dpmodel): add mask-aware segment_sum/segment_mean reduction toolkit

feat(dpmodel): pad_and_guard_edges (compact layout, capacity, edge_mask)

feat(dpmodel): NumpyNeighborList reference builder (coords -> NeighborGraph)

feat(dpmodel): edge force/virial assembly (full-to-src atom virial)

feat(dpmodel): export NeighborGraph foundation symbols

fix(dpmodel): sort all (RUF022) + cast edge mask to g dtype

[pre-commit.ci] auto fixes from pre-commit.com hooks

refactor(dpmodel): build NeighborGraph from existing nlist; drop NumpyNeighborList

fix(dpmodel): drop stale numpy_neighbor_list import (rebase leftover)

refactor(dpmodel): group NeighborGraph into a subpackage

fix(dpmodel): honor int sel in build_neighbor_graph; strengthen padding test

fix(dpmodel): per-frame virial in edge_force_virial; clarify legacy sel contract

test(dpmodel): general multi-frame coverage (ragged nodes/edges + padding)

test(dpmodel): drop redundant single-frame/square-multiframe edge_force_virial tests

test(dpmodel): cover empty frame (n_node has a 0) in edge_force_virial

test(dpmodel): cover all-empty graph (zero real edges) in edge_force_virial

Commits on Jun 25, 2026

feat(dpmodel): make build_neighbor_graph a carry-all search; rename converter to from_dense_quartet

test(dpmodel): cover min_edges guard, flat coord input, virtual-center exclusion in build_neighbor_graph

refactor(dpmodel): vectorize build_neighbor_graph and from_dense_quartet over frames

test(dpmodel): add discriminating cross-periodic-boundary neighbor case

test(dpmodel): add torch-namespace smoke test for graph builders

test(dpmodel): drop the torch-namespace smoke test