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

ProtoMol::iSGIntegrator Class Reference

#include <iSGIntegrator.h>

Inheritance diagram for ProtoMol::iSGIntegrator:

List of all members.


Public Member Functions
	iSGIntegrator ()
	iSGIntegrator (Real timestep, unsigned int numComp, Real temperature, Real pressure, const std::vector< Real > &fugacityFrac, Real tauT, Real tauV, Real tauP, Real tauD, ForceGroup *overloadedForces)
XSC	getXSC () const
Real	getEpsilonVel () const
Real	getEtaVel () const
Real	getNumAtoms () const
Real	getAveDeltaMu (int NumSteps)
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)
virtual void	run (int numTimesteps)
virtual Modifier *	createRattleModifier (Real eps, int maxIter)
virtual Modifier *	createShakeModifier (Real eps, int maxIter)
Static Public Attributes
const std::string	keyword
Protected Member Functions
virtual void	addModifierBeforeInitialize ()
virtual void	addModifierAfterInitialize ()
virtual void	doDrift ()
virtual void	doHalfKick ()
void	modifyForces (const std::vector< iSGPAR::Bond > &, const std::vector< iSGPAR::Angle > &, const std::vector< iSGPAR::Dihedral > &, const std::vector< iSGPAR::Improper > &, const std::vector< iSGPAR::AtomType > &, const std::vector< ModifierISG::TransformMap > &)
void	checkForTransformation (const std::vector< iSGPAR::Bond > &, const std::vector< iSGPAR::Angle > &, const std::vector< iSGPAR::Dihedral > &, const std::vector< iSGPAR::Improper > &, const std::vector< iSGPAR::AtomType > &, const std::vector< ModifierISG::TransformMap > &)
Private Member Functions
void	do2ndHalfKick ()
void	PreForceThermostat ()
void	PostForceThermostat ()
void	PreForceBarostat ()
void	PostForceBarostat ()
void	PreForceChemostat ()
void	PostForceChemostat ()
virtual STSIntegrator *	doMake (std::string &, const std::vector< Value > &values, ForceGroup *fg) const
Private Attributes
const unsigned int	myNumComp
unsigned int	myNumStages
const Real	myTargetTemp
const Real	myTargetPres
std::vector< Real >	myTargetMu
const Real	myTauT
const Real	myTauV
const Real	myTauP
const Real	myTauD
const Real	kbT
Real	myLambda
unsigned int	NumAtoms
unsigned int	NumMols
unsigned int	myNumFree
int	T
int	thisStage
unsigned int	NumTransSteps
unsigned int	OldType
unsigned int	NewType
unsigned int	FinalType
bool	Transformed
Array< Real, 3 >	myDeltaMuIG
std::vector< Real >	myFugacityFrac
Real	myTargetDeltaMu
Real	mylnMassRatio
Real	myDMuIG
Real	myVolume
Real	myEpsilonVel
Real	Qo
Real	Qv
Real	W
Real	Qd
Real	myEta
Real	myEtaV
Real	myEtaVel
Real	myEtaVolVel
Real	myLambdaVel
std::vector< int >	N
Real	AveCQ
Real	AveCQSq
Real	AveDeltaMu
Friends
class	ModifierISG
class	ModifierPreForceThermostat
class	ModifierPostForceThermostat
class	ModifierPreForceBarostat
class	ModifierPostForceBarostat
class	iSGModifierPreForceChemostat
class	iSGModifierPostForceChemostat

Constructor & Destructor Documentation

ProtoMol::iSGIntegrator::iSGIntegrator ( )

ProtoMol::iSGIntegrator::iSGIntegrator ( Real timestep,

unsigned int numComp,

Real temperature,

Real pressure,

const std::vector< Real > & fugacityFrac,

Real tauT,

Real tauV,

Real tauP,

Real tauD,

ForceGroup * overloadedForces

)

Member Function Documentation

void ProtoMol::iSGIntegrator::addModifierAfterInitialize ( ) [protected, virtual]

Add modifiers which should not modify during initialize.

Reimplemented from ProtoMol::STSIntegrator.

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

Add modifiers which should modify during initialize.

Reimplemented from ProtoMol::Integrator.

void ProtoMol::iSGIntegrator::checkForTransformation ( const std::vector< iSGPAR::Bond > & ,

const std::vector< iSGPAR::Angle > & ,

const std::vector< iSGPAR::Dihedral > & ,

const std::vector< iSGPAR::Improper > & ,

const std::vector< iSGPAR::AtomType > & ,

const std::vector< ModifierISG::TransformMap > &

) [protected]

Modifier * ProtoMol::iSGIntegrator::createRattleModifier ( Real eps,

int maxIter

) [virtual]

Create a Rattle modifier.

Reimplemented from ProtoMol::Integrator.

Modifier * ProtoMol::iSGIntegrator::createShakeModifier ( Real eps,

int maxIter

) [virtual]

Create a Shake modifier.

Reimplemented from ProtoMol::Integrator.

void ProtoMol::iSGIntegrator::do2ndHalfKick ( ) [private]

void ProtoMol::iSGIntegrator::doDrift ( ) [protected, virtual]

Reimplemented from ProtoMol::STSIntegrator.

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

Reimplemented from ProtoMol::StandardIntegrator.

virtual STSIntegrator* ProtoMol::iSGIntegrator::doMake ( std::string & ,

const std::vector< Value > & values,

ForceGroup * fg

) const [private, virtual]

Implements ProtoMol::STSIntegrator.

Real ProtoMol::iSGIntegrator::getAveDeltaMu ( int NumSteps ) [inline]

Real ProtoMol::iSGIntegrator::getEpsilonVel ( ) const [inline]

Real ProtoMol::iSGIntegrator::getEtaVel ( ) const [inline]

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

Implements ProtoMol::Makeable.

Real ProtoMol::iSGIntegrator::getNumAtoms ( ) const [inline]

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

retrieve all parameters

Reimplemented from ProtoMol::STSIntegrator.

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

number of parameters

Implements ProtoMol::Makeable.

XSC ProtoMol::iSGIntegrator::getXSC ( ) const

void ProtoMol::iSGIntegrator::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::STSIntegrator.

void ProtoMol::iSGIntegrator::modifyForces ( const std::vector< iSGPAR::Bond > & ,

const std::vector< iSGPAR::Angle > & ,

const std::vector< iSGPAR::Dihedral > & ,

const std::vector< iSGPAR::Improper > & ,

const std::vector< iSGPAR::AtomType > & ,

const std::vector< ModifierISG::TransformMap > &

) [protected]

void ProtoMol::iSGIntegrator::PostForceBarostat ( ) [private]

void ProtoMol::iSGIntegrator::PostForceChemostat ( ) [private]

void ProtoMol::iSGIntegrator::PostForceThermostat ( ) [private]

void ProtoMol::iSGIntegrator::PreForceBarostat ( ) [private]

void ProtoMol::iSGIntegrator::PreForceChemostat ( ) [private]

void ProtoMol::iSGIntegrator::PreForceThermostat ( ) [private]

void ProtoMol::iSGIntegrator::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::StandardIntegrator.