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

ProtoMol::NPTVerletIntegrator Class Reference

#include <NPTVerletIntegrator.h>

Inheritance diagram for ProtoMol::NPTVerletIntegrator:

List of all members.


Public Member Functions
	NPTVerletIntegrator ()
	NPTVerletIntegrator (Real timestep, Real temperature, Real pressure, Real omegaTo, Real omegaTv, Real tauP, ForceGroup *overloadedForces)
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)
virtual STSIntegrator *	doMake (std::string &errMsg, const std::vector< Value > &values, ForceGroup *fg) const
Real	getEpsilonVel () const
Real	getEtaVel () const
Real	getNumAtoms () const
Static Public Attributes
const std::string	keyword
Protected Member Functions
virtual void	addModifierAfterInitialize ()
virtual void	doDrift ()
virtual void	doHalfKick ()
Private Member Functions
void	do2ndHalfKick ()
void	PreForceThermostat ()
void	PostForceThermostat ()
void	PreForceBarostat ()
void	PostForceBarostat ()
Private Attributes
const Real	myTargetTemp
const Real	myTargetPres
const Real	myOmegaTo
const Real	myOmegaTv
const Real	myTauP
const Real	kbT
unsigned int	NumAtoms
unsigned int	myNumFree
Real	myVolume
Real	myEpsilonVel
Real	Qo
Real	Qv
Real	W
Real	myEta
Real	myEtaV
Real	myEtaVel
Real	myEtaVolVel
Friends
class	ModifierPreForceThermostat
class	ModifierPostForceThermostat
class	ModifierPreForceBarostat
class	ModifierPostForceBarostat

Constructor & Destructor Documentation

ProtoMol::NPTVerletIntegrator::NPTVerletIntegrator ( )

ProtoMol::NPTVerletIntegrator::NPTVerletIntegrator ( Real timestep,

Real temperature,

Real pressure,

Real omegaTo,

Real omegaTv,

Real tauP,

ForceGroup * overloadedForces

)

Member Function Documentation

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

Add modifiers which should not modify during initialize.

Reimplemented from ProtoMol::STSIntegrator.

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

int maxIter

) [virtual]

Create a Rattle modifier.

Reimplemented from ProtoMol::Integrator.

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

int maxIter

) [virtual]

Create a Shake modifier.

Reimplemented from ProtoMol::Integrator.

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

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

Reimplemented from ProtoMol::STSIntegrator.

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

Reimplemented from ProtoMol::StandardIntegrator.

virtual STSIntegrator* ProtoMol::NPTVerletIntegrator::doMake ( std::string & errMsg,

const std::vector< Value > & values,

ForceGroup * fg

) const [virtual]

Implements ProtoMol::STSIntegrator.

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

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

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

Implements ProtoMol::Makeable.

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

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

retrieve all parameters

Reimplemented from ProtoMol::STSIntegrator.

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

number of parameters

Implements ProtoMol::Makeable.

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

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

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

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

void ProtoMol::NPTVerletIntegrator::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.