Defining and Executing Simulations#

Executing Simulations#

`execute_DAG`	Locally execute a full `ProtocolDAG` in serial and in-process.
`setup_task_campaign`	Create a task database and FileSystemWarehouse from an alchemical network.
`Worker`	Execute protocol units from a task database.
`TaskStatusDB`	Database for managing execution and orchestration of tasks.
`get_task_df`	Create a pandas Dataframe from task_db.
`get_dependency_df`	Create a pandas Dataframe from task_db.
`update_max_tries`	Update the "max_tries" column to max_tries.
`storage.FileSystemWarehouse`	Warehouse implementation using local filesystem storage.

`ProtocolDAG`	An executable directed acyclic graph (DAG) of `ProtocolUnit` objects.
`ProtocolUnitResult`	Successful result of a single `ProtocolUnit` execution.
`ProtocolUnitFailure`	Failed result of a single `ProtocolUnit` execution.
`ProtocolDAGResult`	Result for a single execution of an entire `ProtocolDAG`.

These classes are abstract classes that are specialised (subclassed) for an individual Protocol.

`Protocol`	A method that via an alchemical transformation estimates free energy difference
`ProtocolUnit`	A unit of work within a ProtocolDAG.
`ProtocolResult`	Container for all results for a single `Transformation`.