Enable eigenvalue ETKDG coordinate generation

[scal444]

Match RDKit eigen initialization and retry behavior, make the batched eigensolver padding- and stream-aware, and enable the default EmbedMolecules path with updated docs and tests.\n\nCloses #288

[greptile-apps]

Confidence Score: 5/5

The PR appears safe to merge because no accepted new actionable findings remain.

Summary

• Adds padded, per-system-dimension-aware eigensolver execution on caller-selected CUDA streams.
• Implements RDKit-compatible distance sampling, seeding, negative-eigenvalue handling, and retry behavior.
• Adds the 256-atom eigenvalue initialization limit and updates Python validation, documentation, examples, and tests.
• Preserves random-coordinate initialization when explicitly requested.

_{Reviews (10) · Last reviewed commit: "Allow small-system eigen coordinate gene..."}

[evasnow1992]

Thank you for addressing the comment. Changes look good to me.