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

#include <MOLLYIntegrator.h>

Inheritance diagram for ProtoMol::MOLLYIntegrator:

ProtoMol::MTSIntegrator ProtoMol::StandardIntegrator ProtoMol::Integrator ProtoMol::Makeable ProtoMol::BSplineMOLLYIntegrator ProtoMol::EquilibriumMOLLYIntegrator List of all members.

Public Member Functions

 MOLLYIntegrator ()
 MOLLYIntegrator (int cycles, ForceGroup *overloadedForces, StandardIntegrator *nextIntegrator)
virtual ~MOLLYIntegrator ()
void averagingPositions ()
void mollification ()
virtual void initialize (GenericTopology *topo, Vector3DBlock *positions, Vector3DBlock *velocities, ScalarStructure *energies)

Protected Member Functions

virtual void addModifierBeforeInitialize ()

Private Member Functions

virtual Vector3DBlock * doAveragingPositions ()=0
virtual void doMollification (Vector3DBlock *doPreprocessedPositions)=0

Private Attributes

Vector3DBlock * mySwapPositions

Friends

class ModifierAveraging
class ModifierMollification

Constructor & Destructor Documentation

ProtoMol::MOLLYIntegrator::MOLLYIntegrator (   ) 
 

ProtoMol::MOLLYIntegrator::MOLLYIntegrator (  int  cycles,
ForceGroup *  overloadedForces,
StandardIntegrator *  nextIntegrator
) 
 

ProtoMol::MOLLYIntegrator::~MOLLYIntegrator (   )  [virtual]
 

Member Function Documentation

void ProtoMol::MOLLYIntegrator::addModifierBeforeInitialize (   )  [protected, virtual]
 

Added modifier to call averagingPositions() and mollification().

Reimplemented from ProtoMol::Integrator.

void ProtoMol::MOLLYIntegrator::averagingPositions (   ) 
 

virtual Vector3DBlock* ProtoMol::MOLLYIntegrator::doAveragingPositions (   )  [private, pure virtual]
 

Implemented in ProtoMol::BSplineMOLLYIntegrator, and ProtoMol::EquilibriumMOLLYIntegrator.

virtual void ProtoMol::MOLLYIntegrator::doMollification (  Vector3DBlock *  doPreprocessedPositions  )  [private, pure virtual]
 

Implemented in ProtoMol::BSplineMOLLYIntegrator, and ProtoMol::EquilibriumMOLLYIntegrator.

void ProtoMol::MOLLYIntegrator::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::MTSIntegrator.

Reimplemented in ProtoMol::BSplineMOLLYIntegrator, and ProtoMol::EquilibriumMOLLYIntegrator.

void ProtoMol::MOLLYIntegrator::mollification (   ) 
 

Friends And Related Function Documentation

friend class ModifierAveraging [friend]
 

friend class ModifierMollification [friend]
 

Member Data Documentation

Vector3DBlock* ProtoMol::MOLLYIntegrator::mySwapPositions [private]
 

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.