Package etomica.action

Define elementary actions that can be performed on simulation elements. Examples include classes that move an Atom, or that change the density of a Box. Classes defining such actions implement the Action interface. Interfaces extending IAction define actions for different simulation elements, such as Box, Atom, and so on.

Activity implements Action and is an abstract class appropriate to encapsulate more complex, time-consuming tasks. Classes extending Activity are collected in the subpackage etomica.action.activity. Whereas Actions must be completed before further processing continues, Activity instances generally operate on a different thread than the one that calls them, and can be paused, resumed or halted before they complete. Classes extending Activity are collected in the subpackage etomica.action.activity.

Interface Summary

Interface	Description
ActionGroup	An action formed from a set of other actions.
AtomAction	Performs an action on an atom.
BoxAction	Elementary action performed on a Box.
IAction	General interface for performing an action, allowing the defined behavior to be separated from the driver that causes it.
IntegratorAction	Elementary action performed on an integrator.
MoleculeAction	Interface for a class that can perform an action on an atom.
Undoable	Interface for an action that can be "undone", such that its effect is reversed if the undo() method is invoked immediately after the actionPerformed().

Class Summary

Class	Description
ActionGroupSeries	A set of Action instances grouped and performed in series as if a single action.
ActionIntegrate	Action that repeatedly invokes an Integrator's doStep method.
ActionMinimizeEnergy
ActionMinimizeEnergy.MyForceTorque
ActionToggle	Action that toggles a boolean value.
AtomActionRandomizeVelocity	Action that sets the velocity vector of a given atom to a randomly chosen value sampled from a Boltzmann distribution.
AtomActionRotateBy	Performs RIGHT-HANDED rotations of an atom about the x-, y-, and z-axes by the specified angles (roll, pitch, and yaw angles, respectively) in radians.
AtomActionTransformed	Moves (translates) an atom by a specified vector amount.
AtomActionTranslateBy	Moves (translates) an atom by a specified vector amount.
BoxActionAdapter	Convenience class used to define a BoxAction.
BoxDeleteMolecules	Deletes molecules from a box as determined by an AtomTest.
BoxImposePbc	Action that imposes the central-image effect of a box having periodic boundaries.
BoxInflate	Performs actions that cause volume of system to expand or contract, with molecule positions scaled to keep them in the same relative positions.
BoxInflateAnisotropic	Class that perform anisotropic angle fluctuation
BoxInflateDeformable	Performs actions that cause volume of a deformable system to expand, with molecule positions scaled to keep them in the same relative positions.
BoxQuench	Scales all velocities of a box so that its kinetic temperature is equal to a given value.
BoxRandomizeMomenta	Randomizes the velocities of all the leaf atoms in a Box based on the Maxwell-Boltzmann distribution.
BoxScaleMomenta	Scales the momenta of all the leaf atoms in a Box such that the kinetic temperature matches some value.
CalcVibrationalModes	Calculates the eigenvalues of an NxN matrix.
IntegratorActionAdapter	Convenience class used to define a IntegratorAction.
IntegratorDimerApproach
IntegratorReset	Action that calls the reset method of an integrator.
MoleculeActionTranslateTo	Moves (translates) an atom to a specified position.
MoleculeChildAtomAction	Wraps an AtomAction, and performs the wrapped action on the atom only if it is a leaf atom; if given an atom group (as indicated by the atom's node), performs action instead on all the atom's child atoms.
PDBWriter	Action that dumps a box's configuration to an PDB file.
ResetAccumulators
ResetAccumulatorsAveraged
SimulationDataAction	Action that performs a call to the reset() method of a set of accumulators, as specified via a list of AccumulatorManager instances.
SimulationRestart	Action that invokes reset method of all registered simulation elements, effectively initializing the entire simulation.
WriteConfiguration	Dumps a box's configuration to a file.
WriteConfigurationBinary	Dumps a box's configuration to a file.
WriteConfigurationDLPOLY	Dumps a box's configuration to a file.
WriteConfigurationOriented	WriteConfiguration subclass capable of handling oriented atoms.
WriteConfigurationP2DLPOLY	Dumps a box's configuration to a file.
XYZWriter	Action that dumps a box's configuration to an XYZ file.