MDManager module

class MDManager.MDManager(sim_list, atomic_structure)

Bases: object

Run a configured sequence of MD simulation stages.

The manager iterates through a simulation list produced by preprocessing and dispatches to the corresponding run class: - "Equilibrium" -> MDClasses.EquilibriumRun - "Stretch" -> MDClasses.StretchRun - "Sample" -> MDClasses.SampleRun

Parameters:

• sim_list (iterable) – Iterable of (simulation_name, settings) pairs describing what to run.

• atomic_structure – Initial structure object passed into the first stage and updated by stages that return a modified structure.

run(store_traj=False)

Execute the configured MD workflow.

Iterates through sim_list and runs each stage in order. The internal atomic_structure is updated when stages return an updated structure (e.g., equilibration).

Parameters:

store_traj (bool, optional) – If True, enable writing ASE trajectory files for stages that support it.

Return type:

None