SBSimulator#

This class describes a simulator, which combines a dynamical model, an interaction model, and a state updater into a runnable simulation workflow.

Initialize and add simulator in the active document

To add a simulator in SAMSON you need to create and add a dynamical model, an interaction model, and a state updater. In the following example we will apply a simulator to a molecular system in the active document using the Brenner interaction model and the Interactive modeling state updater.

# Apply a simulator to a molecule in the active document

# get a node indexer of all structural models in the active document
nodeIndexer = SAMSON.getNodes('n.t sm')

# make an instance of a simulator by providing class names of an interaction model and a state updater
simulator = SAMSON.makeSimulator(
        nodeIndexer = nodeIndexer,
        # the name of the interaction model class
        interactionModelClassName = 'SMMBrennerInteractionModel',
        # the UUID of the Brenner SAMSON Extension
        interactionModelExtensionUUID = SBUUID('AD608CB6-6971-7CD4-6FCC-34531998E743'),
        # no parameters for the Brenner interaction model
        interactionModelParameterMap = SBValueMap(),
        # the name of the state updater class
        stateUpdaterClassName = 'SESInteractiveModelingUpdater',
        # the UUID of the State Updater pack SAMSON Extension
stateUpdaterExtensionUUID = SBUUID('F912F119-7CBB-B5BD-972A-0A02DFCF683D')
        )

# now we need to create a dynamical model, an interaction model, and a state updater

# get the dynamical model from the simulator
dynamicalModel = simulator.getDynamicalModel()
# create the dynamical model
dynamicalModel.create()

# get the interaction model from the simulator
interactionModel = simulator.getInteractionModel()
# create the interaction model
interactionModel.create()
# show a window with interaction model properties
SAMSON.showProperties(interactionModel)
# initialize interaction model
interactionModel.initializeInteractions()

# get the state updater from the simulator
stateUpdater = simulator.getStateUpdater()
# create the state updater
stateUpdater.create()
# show a window with state updater properties
SAMSON.showProperties(stateUpdater)

# create the simulator
simulator.create()

# get the active document
document = SAMSON.getActiveDocument()

# turn the undo system on
with SAMSON.holding('Add simulator'):
        # hold an object for undo/redo
        SAMSON.hold(dynamicalModel)
        # add the dynamical model to the active document
        document.addChild(dynamicalModel)

        # hold an object for undo/redo
        SAMSON.hold(interactionModel)
        # add the interaction model to the active document in SAMSON
        document.addChild(interactionModel)

        # hold an object for undo/redo
        SAMSON.hold(simulator)
        # add the simulator to the active document
        document.addChild(simulator)

You can start and stop simulation using the SAMSON Facade (samson.SAMSON):

# start simulation
SAMSON.startSimulation()

# check until the simulation is done
# ...

# stop simulation
SAMSON.stopSimulation()

SBSimulator

Contents

SBSimulator#