Fix GraphConverter three-body index batching

[Lingyu-Kong]

Summary

Fix GraphConverter.convert() to return M3GNetData instead of plain PyG Data.

three_body_indices stores edge indices, so PyG needs M3GNetData.__inc__ to offset those indices by num_bonds when batching multiple graphs. Returning plain Data leaves three_body_indices local to each graph for batch_size > 1, while the current M3GNet forward path expects already-global batched edge indices.

Validation

• Added a regression test checking that the second graph's three_body_indices are offset by the first graph's num_bonds after Batch.from_data_list.
• Ran py_compile on the modified files.
• Ran git diff --check.

[Lingyu-Kong]

@microsoft-github-policy-service agree