Defining and Executing Simulations

Executing Simulations

execute_DAG

Locally execute a full ProtocolDAG in serial and in-process.

General classes

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.

Specialised classes

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.