BALL::SnapShotManager Class Reference
[General Force Field Classes.]

#include <BALL/MOLMEC/COMMON/snapShotManager.h>

Classes
struct	Default
	Local class for handling default values for the options. More...
struct	Option
	Local class for handling options. More...
Public Member Functions
Constructors and Destructors

	SnapShotManager ()
	Default constructor.
	SnapShotManager (System my_system, TrajectoryFile my_snapshot_file=0)
	SnapShotManager (System my_system, const ForceField my_force_field, TrajectoryFile *my_snapshot_file)
	SnapShotManager (System my_system, const ForceField my_force_field, const Options &my_options, TrajectoryFile *file)
	SnapShotManager (const SnapShotManager &manager)
	Copy constructor.
virtual	~SnapShotManager ()
	Destructor.
Setup methods

bool	setup (System my_system, const ForceField my_forcefield, TrajectoryFile *my_snapshot_file)
bool	setup (System my_system, TrajectoryFile my_snapshot_file)
virtual bool	setup ()
Assignment

const SnapShotManager &	operator= (const SnapShotManager &manager)
virtual void	clear ()
	Clear method.
Debugging and diagnostics

virtual bool	isValid () const
Accessors

void	setSystem (System *my_system)
System *	getSystem () const
	get a const pointer to the system member
void	setForceField (const ForceField *my_ff)
	set the force field
const ForceField *	getForceField () const
	get a const pointer to the force field
void	setTrajectoryFile (TrajectoryFile *my_file)
	set the trajectory file
TrajectoryFile *	getTrajectoryFile () const
	get a pointer to the trajectory file
void	setFlushToDiskFrequency (Size number)
Size	getFlushToDiskFrequency () const
virtual void	takeSnapShot () throw (File::CannotWrite)
virtual bool	applySnapShot (Size number)
virtual bool	applyFirstSnapShot ()
virtual bool	applyNextSnapShot ()
virtual bool	applyLastSnapShot ()
virtual void	flushToDisk () throw (File::CannotWrite)
Size	getNumberOfSnapShotsInBuffer ()
Position	getCurrentSnapshotNumber () const
bool	readFromFile ()
void	clearBuffer ()
	Clear all currently loaded SnapShot 's.
Public Attributes
Public Attributes

Options	options
	The available options for this class.
Protected Member Functions
double	calculateKineticEnergy_ ()
Protected Attributes
System *	system_ptr_
const ForceField *	force_field_ptr_
vector< SnapShot >	snapshot_buffer_
TrajectoryFile *	trajectory_file_ptr_
Size	flush_to_disk_frequency_
Size	buffer_counter_
Position	current_snapshot_

Detailed Description

Snapshot management e.g. for MD simulations. This class manages a list of single SnapShot objects. Snapshots are numbered starting with 1.

Definition at line 33 of file snapShotManager.h.

Constructor & Destructor Documentation

BALL::SnapShotManager::SnapShotManager ( )

Default constructor.

BALL::SnapShotManager::SnapShotManager	(	System *	my_system,
		TrajectoryFile *	my_snapshot_file = `0`
	)

Constructor for a system and trajectory file. The internal reference to a force field will be set to NULL

Parameters:

	my_system	the system to bind this manager to
	my_snapshot_file	an optional file containing a trajectory for the my_system's atoms

BALL::SnapShotManager::SnapShotManager	(	System *	my_system,
		const ForceField *	my_force_field,
		TrajectoryFile *	my_snapshot_file
	)

This constructor expects a valid system, a valid force field and the name of a snapshot file. Any existing file of the given name will be overwritten.

Parameters:

	my_system	the system to bind this manager to
	my_force_field	the force field that is bound to the system
	my_snapshot_file	a file containing a trajectory for the my_system's atoms

BALL::SnapShotManager::SnapShotManager	(	System *	my_system,
		const ForceField *	my_force_field,
		const Options &	my_options,
		TrajectoryFile *	file
	)

This constructor expects a valid system, a valid force field and the name of a snapshot file. Any existing file of the given name will be overwritten.

Parameters:

	my_system	the system to bind this manager to
	my_force_field	the force field that is bound to the system
	my_options
	filename	the name of the snapshot file

BALL::SnapShotManager::SnapShotManager ( const SnapShotManager & manager )

Copy constructor.

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

Destructor.

Member Function Documentation

virtual bool BALL::SnapShotManager::applyFirstSnapShot ( ) [virtual]

Read a the first SnapShot from the associated TrajectoryFile.

Parameters:

snapshot

a buffer for returning the snapshot

Returns:: true if the snapshot could be read, false ow.

virtual bool BALL::SnapShotManager::applyLastSnapShot ( ) [virtual]

This method applies the last SnapShot of the associated file i. e. writes all available data (positions, forces, etc.) from the SnapShot to the System. Note that a SnapShot does not need to have all data.

virtual bool BALL::SnapShotManager::applyNextSnapShot ( ) [virtual]

Read a the next SnapShot from the associated TrajectoryFile and apply it to the system

Parameters:

snapshot

a buffer for returning the snapshot

Returns:: true if the snapshot could be read, false ow.

virtual bool BALL::SnapShotManager::applySnapShot ( Size number ) [virtual]

Read a certain SnapShot from a TrajectoryFile. This method tries to read SnapShot number number from the file

Parameters:

	number	the number of the snapshot we want to read
	snapshot	a buffer for returning the snapshot

Returns:: true if the snapshot could be read, false ow.

double BALL::SnapShotManager::calculateKineticEnergy_ ( ) [protected]

virtual void BALL::SnapShotManager::clear ( ) [virtual]

Clear method.

void BALL::SnapShotManager::clearBuffer ( )

Clear all currently loaded SnapShot 's.

virtual void BALL::SnapShotManager::flushToDisk ( ) throw (File::CannotWrite) [virtual]

This method writes all snapshots taken so far to hard disk

Exceptions:

File::CannotWrite

thrown if the snapshots could not be flushed to disk

Position BALL::SnapShotManager::getCurrentSnapshotNumber ( ) const [inline]

Definition at line 227 of file snapShotManager.h.

Size BALL::SnapShotManager::getFlushToDiskFrequency ( ) const

Get the current frequency for doing saves to hard disk

Returns:: the number of snapshots to take before flushing them to disk

const ForceField* BALL::SnapShotManager::getForceField ( ) const

get a const pointer to the force field

Size BALL::SnapShotManager::getNumberOfSnapShotsInBuffer ( ) [inline]

Definition at line 224 of file snapShotManager.h.

System* BALL::SnapShotManager::getSystem ( ) const

get a const pointer to the system member

TrajectoryFile* BALL::SnapShotManager::getTrajectoryFile ( ) const

get a pointer to the trajectory file

virtual bool BALL::SnapShotManager::isValid ( ) const [virtual]

Is the SnapshotManager ready for use?

const SnapShotManager& BALL::SnapShotManager::operator= ( const SnapShotManager & manager )

The assignment operator.

bool BALL::SnapShotManager::readFromFile ( )

Try to read all SnapShot 's from the TrajectoryFile into the memory.

void BALL::SnapShotManager::setFlushToDiskFrequency ( Size number )

Set the frequency for saving snapshots to hard disk. Every 'number' iterations, a save will be done.

Parameters:

number

the number of snapshots to take before flushing to disk

void BALL::SnapShotManager::setForceField ( const ForceField * my_ff )

set the force field

void BALL::SnapShotManager::setSystem ( System * my_system )

Set the system member

Parameters:

my_system

a const pointer to the system to which this SnapshotManager will be bound

void BALL::SnapShotManager::setTrajectoryFile ( TrajectoryFile * my_file )

set the trajectory file

virtual bool BALL::SnapShotManager::setup ( ) [virtual]

The setup method does all preparations necessary for using the SnapshotManager.

Returns:: true, if setup was succesful

bool BALL::SnapShotManager::setup	(	System *	my_system,
		TrajectoryFile *	my_snapshot_file
	)

This setup method sets all necessary members and calls setup afterwards. The internal force field reference is set to NULL.

Parameters:

	my_system	the System to which we want to bind this SnapShotManager
	my_snapshot_file	the trajectory file we want to use

Returns:: true, if the setup was succesful, false ow.

bool BALL::SnapShotManager::setup	(	System *	my_system,
		const ForceField *	my_forcefield,
		TrajectoryFile *	my_snapshot_file
	)

This setup method sets all necessary members and calls setup afterwards.

Parameters:

	my_system	the System to which we want to bind this SnapShotManager
	my_force_field	the respective forcefield
	my_snapshot_file	the trajectory file we want to use

Returns:: true, if the setup was succesful, false ow.

virtual void BALL::SnapShotManager::takeSnapShot ( ) throw (File::CannotWrite) [virtual]

This method takes a snapshot of the system's current state and stores it in main memory. If there is not sufficient space, the snapshots collected so far are flushed to hard disk. The first snapshot taken has index 1.

Exceptions:

File::CannotWrite

thrown if the snapshot could not be flushed to disk