…sum)

…_graph

The dense path masks excluded type pairs; the graph path does not yet, so
raise NotImplementedError instead of silently diverging.

…pter (attn_layer=0)

…_sum)

…k kernel; sw to dense adapter

…nal dep)

…ph_method (Option B)

… in call_common

…orce_virial)

…gy_deriv) + parity

…d/pt_expt/model/)

…nterop

serialize roundtrip + dpmodel->pt_expt interop on the attn_layer=0 graph path
are already covered by test_dpa1.py::test_consistency (lines 86-113), which
routes through the graph forward via the Task-3 dense-call adapter.

…overage

…all back to dense

Task 3's adapter routed ALL attn_layer==0 through the graph, but the graph
only supports tebd_input_mode='concat', no exclude_types, and needs mapping
for ghosts. strip-mode / exclude / mapping-None-with-ghosts attn_layer=0
models raised/IndexError'd. uses_graph_lower() now encodes full eligibility
and ineligible configs fall back to the legacy dense body unchanged.
Fixes test_compressed_forward (attn_layer=0 strip).

…ping-ghosts) dense fallback

…(decision deepmodeling#17)

…pt graph mask key; legacy opt-out in Option-B test

- _resolve_graph_method/_call_common_graph use getattr(atomic_model,'descriptor',None)
  so Linear/ZBL models (no descriptor) fall back to dense instead of AttributeError
- pt_expt _call_common_graph override adds the all-ones mask key for dense parity
- test_dpa1_graph_model_energy dense refs use neighbor_graph_method='legacy'
  to opt out of the now-default carry-all graph (decision deepmodeling#17 default-flip)

…nse default

dpmodel/jax compute force/virial analytically inside call_common (energy_derv_r);
the energy-only graph lower drops it -> KeyError when force is requested. Only
pt_expt has the autograd graph force/virial path, so only pt_expt defaults
eligible models to the graph. dpmodel base _resolve_graph_method no longer
auto-routes; pt_expt overrides it to re-enable AUTO.

…nse call jit/export-traceable (decision deepmodeling#16)

…crptDPA1.call

…x int-sum, Array typing)

- swap dangling memory/spec_unified_edge_nlist.md refs -> public design
  discussion (#4) so the references resolve
- edge_force_virial: short-circuit n_out=int(node_capacity) when supplied so
  the static jax/export path never calls int() on a traced sum(n_node)
- derivatives.py: move Array import under TYPE_CHECKING (+ from __future__
  import annotations) for subpackage uniformity

…ph (align with .call) [review deepmodeling#5]

…; move dpmodel transform to edge_transform_output.py [review deepmodeling#8,deepmodeling#10]

- fit_output_to_model_output_graph now takes the NeighborGraph instead of
  n_node (dpmodel) / edge_vec+edge_index+edge_mask+n_node (pt_expt); the
  pt_expt autograd leaf is graph.edge_vec. Unifies the two signatures.
- dpmodel fit_output_to_model_output_graph moved transform_output.py ->
  new edge_transform_output.py (mirrors the pt_expt file layout).
- tighten pair-exclude non-vacuity tolerance (1e-9; the (0,1) effect is ~2e-6).

…per + alias) [review deepmodeling#6,deepmodeling#7,deepmodeling#9]

Mirror the dense lower structure for the graph path:
- NEW model-level forward_common_atomic_graph (builds NeighborGraph + atomic
  forward_common_atomic_graph + flat-N output transform) -- analogue of the
  dense forward_common_atomic; the graph build is no longer inlined in the
  lower [deepmodeling#6].
- call_lower_graph -> public call_common_lower_graph WITH _input/_output_type_cast
  (edge_vec is the geometry in place of coord), making it a directly-callable
  PRIMARY interface per spec decision deepmodeling#14 [deepmodeling#7].
- call_lower_graph = call_common_lower_graph alias (mirrors call_lower =
  call_common_lower) [deepmodeling#9].

The TestCompiledVaryingNatoms dpa1(attn_layer=0) case failed: the uncompiled
reference uses the pt_expt carry-all GRAPH forward (default-flip deepmodeling#17) while the
compiled forward_lower uses the sel-capped DENSE forward. Those are two
different force computations -- even at non-binding sel the forward matches to
~1e-16 but their backward gradients agree only to fp64 accumulation (~1e-12),
which the optimizer amplifies into a diverging training trajectory (weight
drift ~1e-3 after one step). It is NOT sel-binding and NOT a torch.compile
dynamic-shape bug.

Pin BOTH sides to the legacy dense env-mat path via force_legacy_descriptor=True
(monkeypatch descriptor.uses_graph_lower -> False, killing both the default-flip
and the _call_graph_adapter), so this stays a true compile-correctness check on
the path it actually compiles. Compiling the GRAPH lower so eager==compiled is
tracked for PR-B.

…tion

Add the missing Parameters/Returns sections (and fill incomplete ones) on the
NeighborGraph / graph-lower functions so they match the package numpydoc style:

- dpa1: _call_graph_adapter, _call_dense (Parameters+Returns)
- general_fitting.call_graph: add missing g2, h2 params
- neighbor_graph: pad_and_guard_edges, node_validity_mask (Parameters+Returns);
  from_dense_quartet, build_neighbor_graph_ase (Returns); edge_force_virial
  (add g_e/edge_vec/edge_index/edge_mask params)
- dpmodel/pt_expt make_model: _resolve_graph_method, _call_common_graph
  (Parameters+Returns); call_common_lower_graph (replace "Parameters mirror ..."
  cross-ref with an explicit Parameters section)
- pt_expt edge_transform_output: edge_energy_deriv (Parameters+Returns);
  fit_output_to_model_output_graph (Returns)

Docstring-only; no behavior change.

dpa1 does not consume charge_spin (get_dim_chg_spin()==0; the dense atomic model
passes None to the descriptor since add_chg_spin_ebd is False). charge_spin is
accepted on the graph lower only for ABI stability with charge/spin-conditioned
descriptors (dpa3/dpa4, PR-G). Pin that the dpa1 graph lower output is INVARIANT
to charge_spin:
- dpmodel call_common_lower_graph: energy/atom_energy/mask unchanged.
- pt_expt forward_common_lower_graph: energy/force/virial/atom_virial unchanged.

With the existing graph==dense parity at non-binding sel this gives the full
claim graph(charge_spin) == graph(None) == dense. Guards against a future
regression where charge_spin leaks into the dpa1 graph path.

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