ProtoMol - an object-oriented component based framework for Molecular Dynamics simulations.
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ProtoMol::StandardIntegrator Class Reference

#include <StandardIntegrator.h>

Inheritance diagram for ProtoMol::StandardIntegrator:

ProtoMol::Integrator ProtoMol::Makeable ProtoMol::MTSIntegrator ProtoMol::STSIntegrator ProtoMol::DihedralHMCIntegrator ProtoMol::ImpulseIntegrator ProtoMol::MCIntegrator ProtoMol::MOLLYIntegrator ProtoMol::UmbrellaIntegrator ProtoMol::BBKIntegrator ProtoMol::DMDLeapfrogIntegrator ProtoMol::iSGIntegrator ProtoMol::LangevinImpulseIntegrator ProtoMol::LeapfrogIntegrator ProtoMol::NoseNVTLeapfrogIntegrator ProtoMol::NPTVerletIntegrator ProtoMol::NVTVerletIntegrator ProtoMol::PaulTrapIntegrator ProtoMol::PLeapfrogIntegrator List of all members.

Public Member Functions

 StandardIntegrator ()
 StandardIntegrator (ForceGroup *forceGroup)
virtual void run (int numTimesteps)
virtual void initialize (GenericTopology *topo, Vector3DBlock *positions, Vector3DBlock *velocities, ScalarStructure *energies)
virtual Integrator * previous ()
virtual const Integrator * previous () const

Protected Member Functions

virtual void doHalfKick ()
virtual void doKick ()
virtual void initializeForces ()
virtual void doDriftOrNextIntegrator ()=0
virtual void calculateForces ()

Protected Attributes

StandardIntegrator * myPreviousIntegrator

Friends

class MTSIntegrator

Constructor & Destructor Documentation

ProtoMol::StandardIntegrator::StandardIntegrator (   ) 
 

ProtoMol::StandardIntegrator::StandardIntegrator (  ForceGroup *  forceGroup  ) 
 

Member Function Documentation

void ProtoMol::StandardIntegrator::calculateForces (   )  [protected, virtual]
 

Reimplemented in ProtoMol::STSIntegrator.

virtual void ProtoMol::StandardIntegrator::doDriftOrNextIntegrator (   )  [protected, pure virtual]
 

Implemented in ProtoMol::MTSIntegrator, and ProtoMol::STSIntegrator.

void ProtoMol::StandardIntegrator::doHalfKick (   )  [protected, virtual]
 

Reimplemented in ProtoMol::DMDLeapfrogIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::NVTVerletIntegrator, and ProtoMol::iSGIntegrator.

void ProtoMol::StandardIntegrator::doKick (   )  [protected, virtual]
 

void ProtoMol::StandardIntegrator::initialize (  GenericTopology *  topo,
Vector3DBlock *  positions,
Vector3DBlock *  velocities,
ScalarStructure *  energies
)  [virtual]
 

Set the integrator up. This method can be called at any time, and should perform any starting force evaluations the integrator needs in order to run correctly. The simulation data should be kept in the given structures.

Reimplemented from ProtoMol::Integrator.

Reimplemented in ProtoMol::BBKIntegrator, ProtoMol::BSplineMOLLYIntegrator, ProtoMol::DihedralHMCIntegrator, ProtoMol::DLMCIntegrator, ProtoMol::DMDLeapfrogIntegrator, ProtoMol::EquilibriumMOLLYIntegrator, ProtoMol::HMCIntegrator, ProtoMol::ImpulseIntegrator, ProtoMol::LangevinImpulseIntegrator, ProtoMol::LeapfrogIntegrator, ProtoMol::MCIntegrator, ProtoMol::MOLLYIntegrator, ProtoMol::MTSIntegrator, ProtoMol::NoseNVTLeapfrogIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::PaulTrapIntegrator, ProtoMol::PLeapfrogIntegrator, ProtoMol::ShadowHMCIntegrator, ProtoMol::STSIntegrator, ProtoMol::UmbrellaIntegrator, and ProtoMol::iSGIntegrator.

void ProtoMol::StandardIntegrator::initializeForces (   )  [protected, virtual]
 

const Integrator * ProtoMol::StandardIntegrator::previous (   )  const [virtual]
 

Implements ProtoMol::Integrator.

Integrator * ProtoMol::StandardIntegrator::previous (   )  [virtual]
 

Implements ProtoMol::Integrator.

void ProtoMol::StandardIntegrator::run (  int  numTimesteps  )  [virtual]
 

Run the integrator for the certain number of timesteps. It can be assumed that the topology and forces have not changed since the last time the integrator was initialized.

Implements ProtoMol::Integrator.

Reimplemented in ProtoMol::BBKIntegrator, ProtoMol::DihedralHMCIntegrator, ProtoMol::DMDLeapfrogIntegrator, ProtoMol::LeapfrogIntegrator, ProtoMol::MCIntegrator, ProtoMol::NPTVerletIntegrator, ProtoMol::NVTVerletIntegrator, ProtoMol::PLeapfrogIntegrator, ProtoMol::ShadowHMCIntegrator, ProtoMol::UmbrellaIntegrator, and ProtoMol::iSGIntegrator.

Friends And Related Function Documentation

friend class MTSIntegrator [friend]
 

Member Data Documentation

StandardIntegrator* ProtoMol::StandardIntegrator::myPreviousIntegrator [protected]
 

The documentation for this class was generated from the following files: Last update: . GNU GENERAL PUBLIC LICENSE, copyrighted by the University of Notre Dame and the University of Bergen, Norway.