#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. More...

	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. More...

virtual	~SnapShotManager ()
	Destructor. More...

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. More...

Debugging and diagnostics
virtual bool	isValid () const

Accessors
void	setSystem (System *my_system)

System *	getSystem () const
	get a const pointer to the system member More...

void	setForceField (const ForceField *my_ff)
	set the force field More...

const ForceField *	getForceField () const
	get a const pointer to the force field More...

void	setTrajectoryFile (TrajectoryFile *my_file)
	set the trajectory file More...

TrajectoryFile *	getTrajectoryFile () const
	get a pointer to the trajectory file More...

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. More...

Public Attributes
Public Attributes
Options	options
	The available options for this class. More...

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

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.

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.

virtual bool BALL::SnapShotManager::setup ( )

virtual

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

Returns: true, if setup was succesful

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

Member Data Documentation

Size BALL::SnapShotManager::buffer_counter_

protected

Definition at line 267 of file snapShotManager.h.

Position BALL::SnapShotManager::current_snapshot_

protected

Definition at line 270 of file snapShotManager.h.

Size BALL::SnapShotManager::flush_to_disk_frequency_

protected

Definition at line 264 of file snapShotManager.h.

const ForceField* BALL::SnapShotManager::force_field_ptr_

protected

Definition at line 253 of file snapShotManager.h.

Options BALL::SnapShotManager::options

The available options for this class.

Definition at line 241 of file snapShotManager.h.

vector<SnapShot> BALL::SnapShotManager::snapshot_buffer_

protected

Definition at line 256 of file snapShotManager.h.

System* BALL::SnapShotManager::system_ptr_

protected

Definition at line 250 of file snapShotManager.h.

TrajectoryFile* BALL::SnapShotManager::trajectory_file_ptr_

protected

Definition at line 259 of file snapShotManager.h.

Classes

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation