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

ProtoMol::ShadowHMCIntegrator Class Reference

#include <ShadowHMCIntegrator.h>

Inheritance diagram for ProtoMol::ShadowHMCIntegrator:

List of all members.


Public Member Functions
	ShadowHMCIntegrator ()
	ShadowHMCIntegrator (int cycles, bool randomCycLen, Real initialTemperature, unsigned int shadowOrder, Real c, ForceGroup overloadedForces, StandardIntegrator nextIntegrator)
virtual	~ShadowHMCIntegrator ()
virtual std::string	getIdNoAlias () const
virtual unsigned int	getParameterSize () const
virtual void	getParameters (std::vector< Parameter > &parameters) const
virtual void	initialize (GenericTopology topo, Vector3DBlock positions, Vector3DBlock velocities, ScalarStructure energies)
virtual void	run (int numTimesteps)
Static Public Attributes
const std::string	keyword
Protected Member Functions
virtual void	perturbSystem ()
virtual void	saveValues ()
virtual void	restoreValues ()
Private Member Functions
void	updateBeta ()
void	pushShadowHistory ()
void	calculateShadow ()
Real	calcShadow4 ()
Real	calcShadow8 ()
void	runPreSteps (int numTimesteps)
void	runPostSteps (int numTimesteps)
void	resetHistory ()
void	disableBetaUpdate ()
void	enableBetaUpdate ()
virtual MTSIntegrator *	doMake (std::string &errMsg, const std::vector< Value > &values, ForceGroup fg, StandardIntegrator nextIntegrator) const
Private Attributes
unsigned int	myOrder
unsigned int	myShadowK
unsigned int	myShadowKover2
Real	myC
Real	myBeta
Real	sumTotalEnergy
std::deque< Vector3DBlock > *	myPrevVelocities
std::deque< Vector3DBlock > *	myPrevPositions
std::deque< Real > *	myPrevBeta
ModifierUpdateBeta *	myModifier1
ModifierUpdateBetaAndPush *	myModifier2
Vector3DBlock *	myOldForces
Friends
class	ModifierUpdateBeta
class	ModifierUpdateBetaAndPush

Constructor & Destructor Documentation

ProtoMol::ShadowHMCIntegrator::ShadowHMCIntegrator ( )

ProtoMol::ShadowHMCIntegrator::ShadowHMCIntegrator ( int cycles,

bool randomCycLen,

Real initialTemperature,

unsigned int shadowOrder,

Real c,

ForceGroup * overloadedForces,

StandardIntegrator * nextIntegrator

)

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

Member Function Documentation

Real ProtoMol::ShadowHMCIntegrator::calcShadow4 ( ) [private]

Real ProtoMol::ShadowHMCIntegrator::calcShadow8 ( ) [private]

void ProtoMol::ShadowHMCIntegrator::calculateShadow ( ) [private]

void ProtoMol::ShadowHMCIntegrator::disableBetaUpdate ( ) [private]

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

const std::vector< Value > & values,

ForceGroup * fg,

StandardIntegrator * nextIntegrator

) const [private, virtual]

Implements ProtoMol::MTSIntegrator.

void ProtoMol::ShadowHMCIntegrator::enableBetaUpdate ( ) [private]

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

Implements ProtoMol::Makeable.

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

retrieve all parameters

Reimplemented from ProtoMol::MCIntegrator.

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

number of parameters

Reimplemented from ProtoMol::MTSIntegrator.

void ProtoMol::ShadowHMCIntegrator::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::MCIntegrator.

void ProtoMol::ShadowHMCIntegrator::perturbSystem ( ) [protected, virtual]

Each class must implement its own system perturbation method.

Implements ProtoMol::MCIntegrator.

void ProtoMol::ShadowHMCIntegrator::pushShadowHistory ( ) [private]

void ProtoMol::ShadowHMCIntegrator::resetHistory ( ) [private]

void ProtoMol::ShadowHMCIntegrator::restoreValues ( ) [protected, virtual]

Implements ProtoMol::MCIntegrator.

void ProtoMol::ShadowHMCIntegrator::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.
Reimplemented from ProtoMol::MCIntegrator.

void ProtoMol::ShadowHMCIntegrator::runPostSteps ( int numTimesteps ) [private]

void ProtoMol::ShadowHMCIntegrator::runPreSteps ( int numTimesteps ) [private]

void ProtoMol::ShadowHMCIntegrator::saveValues ( ) [protected, virtual]

Save/restore state implementations (default pos, vel & energies).

Implements ProtoMol::MCIntegrator.