Intermediate Examples

These examples assume familiarity with the basic tier and introduce the storage layer, performance monitoring, and more complex pipeline patterns.

01 — Multi-Stage Pipeline: FusedStage composition, LoggingHook CSV output, step-budget migration, fused hooks for global status monitoring.

02 — Trajectory I/O: Writing trajectories to Zarr, reading back with DataLoader, round-trip validation.

03 — NPT MD: Pressure-controlled dynamics with the MTK barostat, LJ stress computation, cell fluctuation monitoring.

04 — Inflight Batching: SizeAwareSampler, Mode 2 FusedStage run (batch=None), system_id tracking, ConvergedSnapshotHook collecting results.

05 — Safety and Monitoring: NaNDetectorHook, MaxForceClampHook, EnergyDriftMonitorHook, ProfilerHook — defensive MD patterns.

Multi-Stage Dynamics Pipelines with FusedStage

Multi-Stage Dynamics Pipelines with FusedStage

Writing and Replaying Trajectories with Zarr

Writing and Replaying Trajectories with Zarr

Pressure-Controlled (NPT) Molecular Dynamics

Pressure-Controlled (NPT) Molecular Dynamics

Processing Large Datasets with Inflight Batching

Processing Large Datasets with Inflight Batching

Defensive MD: Safety Hooks and Performance Monitoring

Defensive MD: Safety Hooks and Performance Monitoring