ProtoMol - an object-oriented component based framework for Molecular Dynamics simulations.

ProtoMol::BSplineMOLLYIntegrator Class Reference

#include <BSplineMOLLYIntegrator.h>

Inheritance diagram for ProtoMol::BSplineMOLLYIntegrator:

List of all members.


Public Member Functions
	BSplineMOLLYIntegrator ()
	BSplineMOLLYIntegrator (int cycles, const BSplineType &typeOfBSpline, Real mollyStepsize, ForceGroup overloadedForces, StandardIntegrator nextIntegrator)
virtual	~BSplineMOLLYIntegrator ()
virtual std::string	getIdNoAlias () const
virtual void	getParameters (std::vector< Parameter > &parameters) const
virtual unsigned int	getParameterSize () const
virtual void	initialize (GenericTopology topo, Vector3DBlock positions, Vector3DBlock velocities, ScalarStructure energies)
Static Public Attributes
const std::string	keyword
Private Member Functions
virtual Vector3DBlock *	doAveragingPositions ()
virtual void	doMollification (Vector3DBlock *preprocessedPositions)
virtual void	doUncache ()
virtual MTSIntegrator *	doMake (std::string &errMsg, const std::vector< Value > &values, ForceGroup fg, StandardIntegrator nextIntegrator) const
void	calcMOLLYForcesHalfKickOneDrift ()
void	calcMOLLYForcesOneKickOneDrift ()
void	calculateMOLLYForcesBonded ()
void	calculateMOLLYForcesHBonded ()
void	setMyNumIterMOLLYStepsize ()
void	updateXx ()
void	updateB_Bx_Px_for1Kick ()
void	updateB_Bx ()
void	updateB_Bx_Px_for1stHalfKick ()
void	calcHessiansBondsAnglesHBonds ()
void	init ()
Private Attributes
bool	myCached
ForceGroup *	myMOLLYForcesBonded
ForceGroup *	myMOLLYForcesHBonded
ForceGroup *	myHBondForces
Vector3DBlock *	myMOLLYPositions
Vector3DBlock *	myMOLLYVelocities
Vector3DBlock *	myMOLLYForces
ScalarStructure *	myMOLLYEnergies
Vector3DBlock *	myB
std::vector< ReducedHessAngle > *	myAngleFilter
std::vector< ReducedHessAngle > *	myPxAngle
std::vector< ReducedHessAngle > *	myXxAngle
std::vector< ReducedHessAngle > *	myBxAngle
BSplineType	myTypeOfBSpline
Real	myMOLLYStepsize
Real	myMOLLYStepsizeP
Real	myMOLLYStepsizeSquare
unsigned int	myNumIter
bool	myBond
bool	myAngle
bool	myCoulomb
bool	myLennardJones
std::vector< AngleIndex >	myAngleIndexes

Detailed Description

This integrator is developped using an approximation to the dynamics: let the heavy atoms always be fixed in their position such that we could use the reduced forms of Hessians. This is a physically and mathematically correct approximation.

Constructor & Destructor Documentation

ProtoMol::BSplineMOLLYIntegrator::BSplineMOLLYIntegrator ( )

ProtoMol::BSplineMOLLYIntegrator::BSplineMOLLYIntegrator ( int cycles,

const BSplineType & typeOfBSpline,

Real mollyStepsize,

ForceGroup * overloadedForces,

StandardIntegrator * nextIntegrator

)

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

Member Function Documentation

void ProtoMol::BSplineMOLLYIntegrator::calcHessiansBondsAnglesHBonds ( ) [private]

void ProtoMol::BSplineMOLLYIntegrator::calcMOLLYForcesHalfKickOneDrift ( ) [private]

void ProtoMol::BSplineMOLLYIntegrator::calcMOLLYForcesOneKickOneDrift ( ) [private]

void ProtoMol::BSplineMOLLYIntegrator::calculateMOLLYForcesBonded ( ) [private]

void ProtoMol::BSplineMOLLYIntegrator::calculateMOLLYForcesHBonded ( ) [private]

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

Implements ProtoMol::MOLLYIntegrator.

MTSIntegrator * ProtoMol::BSplineMOLLYIntegrator::doMake ( std::string & errMsg,

const std::vector< Value > & values,

ForceGroup * fg,

StandardIntegrator * nextIntegrator

) const [private, virtual]

Implements ProtoMol::MTSIntegrator.

void ProtoMol::BSplineMOLLYIntegrator::doMollification ( Vector3DBlock * preprocessedPositions ) [private, virtual]

Implements ProtoMol::MOLLYIntegrator.

void ProtoMol::BSplineMOLLYIntegrator::doUncache ( ) [private, virtual]

Integrator specific details of uncache.

Reimplemented from ProtoMol::Integrator.

virtual std::string ProtoMol::BSplineMOLLYIntegrator::getIdNoAlias ( ) const [inline, virtual]

Implements ProtoMol::Makeable.

void ProtoMol::BSplineMOLLYIntegrator::getParameters ( std::vector< Parameter > & parameters ) const [virtual]

retrieve all parameters

Reimplemented from ProtoMol::MTSIntegrator.

virtual unsigned int ProtoMol::BSplineMOLLYIntegrator::getParameterSize ( ) const [inline, virtual]

number of parameters

Reimplemented from ProtoMol::MTSIntegrator.

void ProtoMol::BSplineMOLLYIntegrator::init ( ) [private]

void ProtoMol::BSplineMOLLYIntegrator::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::MOLLYIntegrator.