#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. More...

virtual	~CanonicalMD ()
	Destructor. More...

Assignment
CanonicalMD &	operator= (const CanonicalMD &rhs)
	Assignment operator. More...

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)

Public Member Functions inherited from BALL::MolecularDynamics
	MolecularDynamics ()

	MolecularDynamics (ForceField &force_field)

	MolecularDynamics (const MolecularDynamics &rhs)

virtual	~MolecularDynamics ()

const MolecularDynamics &	operator= (const MolecularDynamics &rhs)

void	set (const MolecularDynamics &rhs)

bool	isValid () const

void	setNumberOfIteration (Size number)

void	setMaximalNumberOfIterations (Size number)

void	setMaximalSimulationTime (double time)

void	setReferenceTemperature (double temperature)

void	setCurrentTime (double time)

void	setEnergyOutputFrequency (Size number)

void	setSnapShotFrequency (Size number)

Size	getEnergyOutputFrequency () const

Size	getNumberOfIterations () const

Size	getMaximalNumberOfIterations () const

double	getMaximalSimulationTime () const

double	getTimeStep () const

Size	getSnapShotFrequency () const

double	getTemperature () const

double	getTime () const

double	getTotalEnergy () const

double	getPotentialEnergy () const

double	getKineticEnergy () const

ForceField *	getForceField () const

bool	simulate (bool restart=false)

bool	simulateTime (double simulation_time, bool restart=false)

void	enableEnergyAbortCondition (bool state)

bool	energyAbortConditionEnabled () const
	Query if the MDSimulation aborts if the Energy is greater than abort_energy_. More...

void	setEnergyToAbort (float value)

float	getEnergyToAbort () const

Protected Member Functions
Protected methods
void	calculateFactors_ ()

Protected Member Functions inherited from BALL::MolecularDynamics
void	updateInstantaneousTemperature ()

Protected Attributes
Protected Attributes
double	bath_relaxation_time_
	The coupling parameter to the heat bath. More...

std::vector< AuxFactors >	mass_factor_
	This vector contains special precomputed factors. More...

Protected Attributes inherited from BALL::MolecularDynamics
bool	valid_

ForceField *	force_field_ptr_

System *	system_ptr_

AtomVector	atom_vector_

Size	number_of_iteration_

Size	maximal_number_of_iterations_

double	time_step_

double	reference_temperature_

double	current_temperature_

double	kinetic_energy_

double	total_energy_

double	current_time_

Size	energy_output_frequency_

Size	snapshot_frequency_

SnapShotManager *	snapshot_manager_ptr_

bool	abort_by_energy_enabled_

float	abort_energy_

Additional Inherited Members
Public Attributes inherited from BALL::MolecularDynamics
Options	options

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 = `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::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::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

number	the number of iterations that have to be simulated
restart	flag for restarting the simulation

Reimplemented from BALL::MolecularDynamics.

virtual bool BALL::CanonicalMD::specificSetup ( )

virtual

This method is meant for additional preparations apart from those done in setup.

Returns: bool, true if specificSetup() was successful

Reimplemented from BALL::MolecularDynamics.

Member Data Documentation

double BALL::CanonicalMD::bath_relaxation_time_

protected

The coupling parameter to the heat bath.

Definition at line 160 of file canonicalMD.h.

std::vector<AuxFactors> BALL::CanonicalMD::mass_factor_

protected

This vector contains special precomputed factors.

Definition at line 163 of file canonicalMD.h.

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation