BALL::CanonicalMD Class Reference
[Molecular Dynamics Simulation]

#include <BALL/MOLMEC/MDSIMULATION/canonicalMD.h>

Inheritance diagram for BALL::CanonicalMD:

Classes
struct	AuxFactors
	Helper class containing auxiliary factors. More...
Public Member Functions
Constructors and Destructor

	CanonicalMD ()
	CanonicalMD (ForceField &myforcefield)
	CanonicalMD (ForceField &force_field, SnapShotManager *ssm)
	CanonicalMD (ForceField &myforcefield, SnapShotManager *ssm, const Options &options)
	CanonicalMD (const CanonicalMD &rhs)
	Copy constructor.
virtual	~CanonicalMD ()
	Destructor.
Assignment

CanonicalMD &	operator= (const CanonicalMD &rhs)
	Assignment operator.
Setup methods

virtual bool	setup (ForceField &force_field, SnapShotManager *ssm=0)
virtual bool	setup (ForceField &force_field, SnapShotManager *ssm, const Options &options)
virtual bool	specificSetup ()
Accessors

void	setBathRelaxationTime (double time)
double	getBathRelaxationTime () const
virtual void	setTimeStep (double time)
virtual bool	simulateIterations (Size number, bool restart=false)
Protected Member Functions
Protected methods

void	calculateFactors_ ()
Protected Attributes
Protected Attributes

double	bath_relaxation_time_
	The coupling parameter to the heat bath.
std::vector< AuxFactors >	mass_factor_
	This vector contains special precomputed factors.

Detailed Description

A MD simulation in the canoncial ensemble. A class for doing molecular dynamics simulations according to the principle of a canonical ensemble (NVT), i.e., the temperature is kept constant. This is achieved via the velocity rescaling proposed by Berendsen et al., J. Chem. Physics, 81:3684, 1984. Note that this approach does not give all properties of a true canonical system. In particular, the heat capacity cannot be calculated!

: The temperature is set through the MDSimulation::setReferenceTemperature method.

Definition at line 30 of file canonicalMD.h.

Constructor & Destructor Documentation

BALL::CanonicalMD::CanonicalMD ( )

BALL::CanonicalMD::CanonicalMD ( ForceField & myforcefield )

This constructor expects a force field . The force field's options are used and no saving of snapshots is done.

Parameters:

myforcefield

the forcefield we need for the simulation

BALL::CanonicalMD::CanonicalMD	(	ForceField &	force_field,
		SnapShotManager *	ssm
	)

This constructor expects a force field and a snapshot manager. The force field's options are used.

Parameters:

	myforcefield	the forcefield to use in the simulation
	ssm	a pointer to the SnapShotManager which will be used to create trajectory files

BALL::CanonicalMD::CanonicalMD	(	ForceField &	myforcefield,
		SnapShotManager *	ssm,
		const Options &	options
	)

This constructor wants a force field, a snapshot manager and new options.

Parameters:

	myforcefield	the forcefield which is to be used in the simulation
	ssm	a pointer to the SnapShotManager used for creating trajectory files
	myoptions	arbitrary options that are to be used by this instance instead of those defined therein

BALL::CanonicalMD::CanonicalMD ( const CanonicalMD & rhs )

Copy constructor.

virtual BALL::CanonicalMD::~CanonicalMD ( ) [virtual]

Destructor.

Member Function Documentation

void BALL::CanonicalMD::calculateFactors_ ( ) [protected]

A protected method for calculating some factors that are needed all the time.

double BALL::CanonicalMD::getBathRelaxationTime ( ) const

This method gets the current value for heat bath coupling.

Returns:: the bath relaxation time in ps

CanonicalMD& BALL::CanonicalMD::operator= ( const CanonicalMD & rhs )

Assignment operator.

void BALL::CanonicalMD::setBathRelaxationTime ( double time )

This method sets a new relaxation time for the coupling to an external heat bath. The readjustment to the external bath is not done after every step in order to save compute time. Instead, it is coupled periodically after the time specified here has elapsed.

Parameters:

time

the time in ps

virtual void BALL::CanonicalMD::setTimeStep ( double time ) [virtual]

Set a new time step for the numerical integration.

Reimplemented from BALL::MolecularDynamics.

virtual bool BALL::CanonicalMD::setup	(	ForceField &	force_field,
		SnapShotManager *	ssm,
		const Options &	options
	)			`[virtual]`

This method does general setup things. This method also allows the assignment of options for the setup.

Reimplemented from BALL::MolecularDynamics.

virtual bool BALL::CanonicalMD::setup	(	ForceField &	force_field,
		SnapShotManager *	ssm = `0`
	)			`[virtual]`

This method does general setup things

Parameters:

	ssm	if no snapshots during the simulations are required, leave this at the default (NULL pointer)
	force_field	the forcefield, which has to be bound to a system

Reimplemented from BALL::MolecularDynamics.

virtual bool BALL::CanonicalMD::simulateIterations	(	Size	number,
		bool	restart = `false`
	)			`[virtual]`

This method does the actual simulation stuff. It runs for the indicated number of iterations. If restart is true, the counting of iterations starts with the number of the last iteration in the previous run.

Parameters: