Stage 1: generic two-center model (overlap S = I + 2C)#5
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Implements the linear two-center overlap model end-to-end: - blocks.jl: OrbitalBasis (per-species shells) and global matrix block bookkeeping (OrbitalLayout, shell_range). - overlap.jl: OverlapModel + assemble_S. On-site S_ii = identity; off-site S_ij is a bond-harmonic expansion recoupled via transform_Λ, summing only proper-parity (l+l'+Λ even) channels since a single bond vector is a proper tensor. Hermiticity by post-hoc symmetrization ½(S+Sᵀ). - Bond radial basis via ACEpotentials.Models.ace_learnable_Rnlrzz; angular basis via Polynomials4ML real spherical harmonics. Adds ACEpotentials / Polynomials4ML / Random deps and the §12 symmetry suite restricted to S: rotation, inversion (+parity), Hermiticity, permutation, cutoff smoothness (311 tests total).
A single bond vector supplies only even-(l+l'+Λ) channels, which is complete for a two-center quantity (the count matches Slater-Koster). Reword the comments accordingly; :proper -> :even. No behaviour change.
Follow-up to the BlockCoupling refactor on #4: the parities field is gone, so the overlap model computes the even-(l+l'+L) check via channel_parity at the point it selects channels.
Design revision: the overlap and Hamiltonian models are independent structs with independent hypers, parameters, and forward passes. Rationale: initial focus is experimentation with possibly unrelated forms of S and H, and S is much cheaper than H. Shared building blocks (coupling, embeddings, block bookkeeping) remain at the code level. Stage 1's OverlapModel already follows this design.
- Rename overlap.jl -> twocenter.jl, OverlapModel -> TwoCenterModel, assemble_S -> assemble: the model is a generic linear bond-only two-center model (generalized Slater-Koster table), not overlap- specific. It now assembles the purely off-site matrix; callers add their on-site term (overlap: S = I + assemble(model, ...)). - Graph input per plan sec 3.3: graph(model, sys) and assemble(model, G::ETGraph, W) via ET.Atoms.interaction_graph (NeighbourLists-backed, PBC incl. self-image bonds, Gamma-point). bondlist retained as the brute-force free-cluster cross-check. - New deps: NeighbourLists, Unitful (both already in the dep tree); test extras AtomsBase, AtomsBuilder. - Tests: renamed to test_twocenter.jl; new graph+PBC testset (free- cluster cross-check, PBC Hermiticity, translation-with-wrap, rotation of positions and cell). Plan/design docs updated.
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On hold. This staged implementation has become hard to review and will be restarted from scratch. The PR stays open for reference, but it should not be merged or updated for now. |
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Stage 1 of the linear 2-center model (plan in
agents/plan_lin2c.md, design §8). Base:main(#4 merged).What this adds
src/linear2c/blocks.jl—OrbitalBasis(per-species shell lists) and global matrix block bookkeeping (OrbitalLayout,shell_range,species_norb,maxL).src/linear2c/twocenter.jl—TwoCenterModel+assemble: a generic linear bond-only two-center model (a generalized Slater–Koster table), of which the overlap matrix is the first instantiation:Λ, bond harmonicsφ^b_{nΛ}(r_ji) = R^b_{nΛ}(r) Y_{Λ}(r̂)are contracted with learnable per-(species-pair, shell-pair, Λ) coefficients and recoupled to the(m,m')block viatransform_Λ(Stage 0). Callers add their own on-site term — overlap:S = I + assemble(model, …).l+l'+Λ) channels contribute — complete for any single-bond quantity.X ← ½(X+Xᵀ).graph(model, sys)/assemble(model, G::ETGraph, W)viaET.Atoms.interaction_graph(NeighbourLists-backed). Periodic-image bonds — including self-images — accumulate into the same block (Γ-point convention). A brute-forcebondlistis retained as the free-cluster cross-check.ACEpotentials.Models.ace_learnable_Rnlrzz(the decided dependency; species asIntatomic numbers); angular basis fromPolynomials4MLreal spherical harmonics.NeighbourLists,Unitful(both already in the dependency tree); test extrasAtomsBase,AtomsBuilder.Notes / decisions in play
SandHare separate, independent models — no single model producing the pair(H, S). The initial focus is experimentation with possibly unrelated forms ofSandH, andSis much cheaper; they share building blocks only (agents/plan_lin2c.md§3.6,docs/src/twocenter.md§§1, 8, 10, 11, 14).OverlapModel/assemble_S→ genericTwoCenterModel/assemble; on-site handling moved to the caller.ET.EdgeEmbed(whose pooled layout targets the env basis) — recorded as a deviation in the plan. Lux-layer glue is Stage-5 scope.Polynomials4MLreal-SH ordering (degree-lblock at(l²+1):(l+1)², ascendingm) is equivariant withO3.D_from_angles(·,real), consistent with the coupling from Stage 0.Tests (351 total)
§12 suite restricted to the 2C model: rotational equivariance, inversion equivariance + parity signs, Hermiticity, permutation equivariance, cutoff smoothness (
C¹envelope, vanishing beyondr_cut), plus the new graph + PBC set: free-cluster graph path ≡ brute-force bondlist, PBC Hermiticity (self-image bonds), translation invariance under wrap, rotational equivariance with rotated cell.🤖 Generated with Claude Code