| # Complete the edge-graph scientific capability |
|
|
| The source tree is a real intermediate snapshot from the development of an |
| atomistic-model backend. It contains the first public data contract for a |
| `NeighborGraph`, but the surrounding scientific capability is incomplete. |
|
|
| A downstream model must be able to start from atom coordinates and, for both |
| ordinary and periodic systems, construct a graph whose edges represent the |
| neighbor displacements used by the potential-energy model. The same graph must |
| remain usable when the number of edges is padded for a compiled/static backend. |
| Per-edge energy derivatives must then be transformed into per-atom forces, |
| per-atom virials, and one virial for each frame. Empty frames, isolated atoms, |
| virtual atoms, periodic-image neighbors, and padded guard edges are all valid |
| scientific situations rather than exceptional test-only cases. |
|
|
| Inspect the source context, run `python reproduce.py`, and |
| complete the reusable capability under `source/`. Preserve the public data |
| contract where it is already meaningful, and keep the implementation usable |
| with NumPy and the array-API style used by the source snapshot. |
|
|
| The package-level public API for the completed capability is explicit. Export |
| these names from `deepmd.dpmodel.utils` (the implementation may live in any |
| module under `deepmd/dpmodel/utils/`): |
|
|
| - `build_neighbor_graph` |
| - `from_dense_quartet` |
| - `node_validity_mask` |
| - `segment_sum` and `segment_mean` |
| - `edge_force_virial` |
|
|
| The file layout is your choice; hidden verification checks these public |
| behaviors through the package namespace rather than requiring a particular |
| internal module split. |
|
|
| The derivative contract is also part of the public behavior. For |
| `edge_vec = r_src - r_dst` and `g = dE / d(edge_vec)`, use |
|
|
| ```text |
| F_k = sum(g for edges with dst=k) - sum(g for edges with src=k) |
| edge_virial = -outer(g, edge_vec) |
| ``` |
|
|
| Attribute a complete edge virial to its source atom, ignore masked guard edges, |
| and return one `(3, 3)` virial per frame. Reject non-positive cutoffs and |
| inconsistent coordinate, type, or cell shapes with `ValueError` rather than |
| silently producing an empty or misaligned graph. |
|
|
| The result must be a coherent workflow, not a fixture-specific patch. It must |
| support more than the public coordinates, more than one frame, and more than |
| one edge count. Do not hard-code atom indices, distances, edge counts, force |
| values, or a particular periodic cell. Keep the sign and tensor-layout |
| conventions explicit in code and documentation so a downstream model can rely |
| on them. |
|
|
| The public reproduction is only a starting point. A successful solution must |
| also preserve ordinary non-periodic behavior while adding the missing general |
| scientific cases. |
|
|
