[backends] GPUMD support

[JaafarMehrez]

Summary

Add a GPUMD backend that enables PySAGES-enhanced sampling on GPUMD-accelerated simulations.

What changed

New backend (pysages/backends/gpumd.py)

• Sampler class that registers a per-step callback with GPUMD's C++ engine.
• Snapshot arrays are reconstructed from DLPack capsules every step so JAX sees updated GPU positions/forces.
• Constant data (ids, masses, box, dt) is cached during __init__ to avoid redundant Python to C++ calls.
• For NVT/NVE, sim.is_box_constant() returns True and the box is never refreshed.
• For NPT, the box is refreshed every 100 steps.
• Custom add_aos_bias_to_forces() kernel adds JAX-computed bias directly to GPUMD's SOA force buffer in a single CUDA operation.

Backend detection (pysages/backends/core.py)

• Auto-detects gpumd.Simulation contexts and routes to the GPUMD backend.

Examples (examples/gpumd/metad, new directory)

• ethane-metad.py — well-tempered metadynamics, H-C-C-H dihedral.

Dependency

This backend requires GPUMD with the Python wrapper support. refer to this PR

Author

Jaafar Mehrez

• Shanghai Jiao Tong University, Shanghai, China
• HPQC Labs, Waterloo, Canada
• jaafarmehrez@sjtu.edu.cn, jaafar@hpqc.org