Package etomica.integrator

Provides Integrator classes that implement different molecular simulation algorithms.

See:
Description

Interface Summary

Integrator.Forcible	Integrator agent that holds a force vector.
Integrator.Torquable	Integrator agent that holds a torque vector.
IntegratorHard.CollisionListener
IntegratorPT.MCMoveSwap	Interface for a move that swaps two boxes.
IntegratorPT.MCMoveSwapFactory	Interface for a class that can make a MCMove that will swap the configurations of two boxes.

Class Summary

Integrator	Integrator implements the algorithm used to move the atoms around and generate new configurations in one or more boxs.
IntegratorAnalytic	Integrator that generates atom trajectories from an analytic formula.
IntegratorAnalytic.AtomTimeAction	Extends AtomAction class to add a method to set the time.
IntegratorBox	Integrator implements the algorithm used to move the atoms around and generate new configurations in one or more boxs.
IntegratorConNVT	Constant NVT Molecular Dynamics Integrator-Constraint Method Uses a modified version of the Leap Frog Algorithm.
IntegratorConNVT.Agent
IntegratorEvent	Event object given to registered listeners when an integrator fires any type event.
IntegratorEvent.Type
IntegratorEventManager
IntegratorGear4	Gear 4th-order predictor-corrector integrator.
IntegratorGear4.Agent
IntegratorGear4NPH	Gear 4th-order predictor-corrector integrator for constant enthalphy, pressure.
IntegratorGear4NPH.EnsembleToggler
IntegratorGear4NPH.ForceSumNPH
IntegratorGear4NPH.MeterEnthalpy
IntegratorGEMC	Simple Gibbs-ensemble Monte Carlo integrator.
IntegratorHard	Integrator for hard potentials.
IntegratorHard.Agent	Agent defined by this integrator.
IntegratorHard.CollisionHandlerUp
IntegratorHardField	Extension of IntegratorHard for case where a constant external force field is applied.
IntegratorHardField.HardFieldAgent	Extends IntegratorHard.Agent to hold a force vector.
IntegratorHardField.PotentialCalculationForceSum	Sums the force on each iterated atom and adds it to the integrator agent associated with the atom.
IntegratorManagerMC	Integrator manages other Integrators which either act on a Box, or manager still other Integrators.
IntegratorMC	Integrator to perform Metropolis Monte Carlo sampling.
IntegratorMD	Superclass of all molecular-dynamics integrators.
IntegratorMD.ThermostatType
IntegratorNonintervalEvent	Event thrown by integrator when it announces reaching special points in the simulation process, such as its beginning and end.
IntegratorNonintervalEvent.NonintervalEventType
IntegratorPT	Parallel-tempering integrator.
IntegratorPT.BoxTracker	Meter that tracks the swapping of the boxes in parallel-tempering simulation.
IntegratorRigidIterative
IntegratorRigidIterative.MoleculeAgent
IntegratorRigidMatrixIterative	Integrator implementation of Omelyan's leapfrog integrator for rotational motion.
IntegratorRigidMatrixIterative.AtomAgent
IntegratorRigidMatrixIterative.BoxImposePbcMolecule
IntegratorRigidMatrixIterative.MoleculeAgent
IntegratorVelocityVerlet
IntegratorVelocityVerlet.MyAgent
IntegratorVelocityVerletRattle	Integrator implementing RATTLE algorithm.
IntegratorVelocityVerletShake	Integrator implementing SHAKE algorithm.
IntegratorVelocityVerletShake.BondConstraints
IntegratorVerlet
IntegratorVerlet.Agent

Package etomica.integrator Description

Provides Integrator classes that implement different molecular simulation algorithms. The Integrator moves the simulated atoms around, generating configurations and thereby conducting the simulation. All integrator techniques, such as molecular dynamics or Monte Carlo, are implemented via subclasses of the Integrator class. Repeated calls to the Integrator's doStep method generate successive configurations. This process is typically performed by an ActivityIntegrate instance.

The Integrator maintains a list of IntegratorListeners, which are notified when the Integrator starts, is reset, and finishes or, for IntegratorIntervalListeners, when the integrators completes a specified number of doStep calls. Although the listeners are kept by the Integrator, firing of the event is performed by the Activity running the Integrator. Arbitrary Actions can be performed in response to an IntegratorEvent through the use of an IntervalActionAdapter.

The general categories of Integrator are IntegratorMD, for molecular dynamics, and IntegratorMC, for Monte Carlo. Molecular dynamics integration of hard potentials requires the use of a special integrator, IntegratorHard. IntegratorMC holds a set of MCMove instances which define the types of Monte Carlo trials that are performed in the simulation.

To use an Integrator, add the instance to a new ActivityIntegrate instance, and add the ActivityIntegrate to the Simulation's Controller. The Box upon which the Integrator acts must be set before beginning the simulation. Some Integrators require the specification of multiple boxs. It can also be helpful to invoke the register method in the governing Simulation, passing the Integrator instance; this will cause the Integrator to be reset when the Simulation is reset to a new (or initial) condition.