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

ProtoMol::Output Class Reference

#include <Output.h>

Inheritance diagram for ProtoMol::Output:

List of all members.


Public Member Functions
	Output ()
	Output (int freq)
void	initialize (const Configuration config, const Integrator integrator, const GenericTopology topo, const Vector3DBlock pos, const Vector3DBlock vel, const ScalarStructure energies)
void	run (int step)
void	finalize (int step)
Output *	make (std::string &errMsg, const std::vector< Value > &values) const
virtual bool	isIdDefined (const Configuration *config) const
virtual bool	addDoKeyword () const
void	setCache (const OutputCache *cache)
int	getFirstStep () const
int	getLastStep () const
int	getOutputFreq () const
int	getNext () const
bool	first () const
virtual std::string	getScope () const
Static Public Attributes
const std::string	scope
Protected Attributes
int	myOutputFreq
const Configuration *	myConfig
const GenericTopology *	myTopology
const Integrator *	myIntegrator
const ScalarStructure *	myEnergies
const Vector3DBlock *	myPositions
const Vector3DBlock *	myVelocities
const OutputCache *	myCache
Private Member Functions
virtual void	doInitialize ()=0
virtual void	doRun (int step)=0
virtual void	doFinalize (int step)=0
virtual Output *	doMake (std::string &errMsg, const std::vector< Value > &values) const=0
Private Attributes
int	myFirstStep
int	myLastStep
int	myNextStep
bool	myFirst

Detailed Description

Base class of all Output classes to dump data at a given frequency. The actual output frequency is defined by global output frequency times the the frequency of the concrete class. The global output frequency is also used to define the number of steps to run the integrator. It keeps pointers to the topology, positions, velocities, integrator and to a cache object. The cache object provides method the retrieve values such that other output objects can reuse the values rather to recompute them again. Output objects are aggregated in OutputCollection, which invokes them one by one at application level. If you only need to print some output to a file you should rather inherit from OutputFile, then inherit directly from Output.

Constructor & Destructor Documentation

ProtoMol::Output::Output ( )

ProtoMol::Output::Output ( int freq )

Member Function Documentation

virtual bool ProtoMol::Output::addDoKeyword ( ) const [inline, virtual]

Defines if the output object supports do<getId()> to enable or disable the output.
Reimplemented in ProtoMol::OutputScreen.

virtual void ProtoMol::Output::doFinalize ( int step ) [private, pure virtual]

Hook method of finalize, implemented in the concrete class.

Implemented in ProtoMol::OutputDCDTrajectory, ProtoMol::OutputDihedrals, ProtoMol::OutputFile, ProtoMol::OutputFinalPDBPos, ProtoMol::OutputFinalXYZBinPos, ProtoMol::OutputFinalXYZBinVel, ProtoMol::OutputFinalXYZPos, ProtoMol::OutputFinalXYZVel, ProtoMol::OutputPDBFramePos, ProtoMol::OutputScreen, ProtoMol::OutputXYZTrajectoryForce, ProtoMol::OutputXYZTrajectoryPos, ProtoMol::OutputXYZTrajectoryVel, ProtoMol::OutputFinalPSF, and ProtoMol::OutputFinalXSC.

virtual void ProtoMol::Output::doInitialize ( ) [private, pure virtual]

Hook method of initialize, implemented in the concrete class.

Implemented in ProtoMol::OutputDCDTrajectory, ProtoMol::OutputDiffusion, ProtoMol::OutputDihedrals, ProtoMol::OutputEnergies, ProtoMol::OutputFinalPDBPos, ProtoMol::OutputFinalXYZBinPos, ProtoMol::OutputFinalXYZBinVel, ProtoMol::OutputFinalXYZPos, ProtoMol::OutputFinalXYZVel, ProtoMol::OutputMomentum, ProtoMol::OutputPaulTrap, ProtoMol::OutputPDBFramePos, ProtoMol::OutputScreen, ProtoMol::OutputTemperatures, ProtoMol::OutputXYZTrajectoryForce, ProtoMol::OutputXYZTrajectoryPos, ProtoMol::OutputXYZTrajectoryVel, ProtoMol::OutputFinalPSF, ProtoMol::OutputFinalXSC, and ProtoMol::OutputISGProperties.

virtual Output* ProtoMol::Output::doMake ( std::string & errMsg,

const std::vector< Value > & values

) const [private, pure virtual]

Implemented in ProtoMol::OutputDCDTrajectory, ProtoMol::OutputDiffusion, ProtoMol::OutputDihedrals, ProtoMol::OutputEnergies, ProtoMol::OutputFinalPDBPos, ProtoMol::OutputFinalXYZBinPos, ProtoMol::OutputFinalXYZBinVel, ProtoMol::OutputFinalXYZPos, ProtoMol::OutputFinalXYZVel, ProtoMol::OutputMomentum, ProtoMol::OutputPaulTrap, ProtoMol::OutputPDBFramePos, ProtoMol::OutputScreen, ProtoMol::OutputTemperatures, ProtoMol::OutputXYZTrajectoryForce, ProtoMol::OutputXYZTrajectoryPos, ProtoMol::OutputXYZTrajectoryVel, ProtoMol::OutputFinalPSF, ProtoMol::OutputFinalXSC, and ProtoMol::OutputISGProperties.

virtual void ProtoMol::Output::doRun ( int step ) [private, pure virtual]

Hook method of run, implemented in the concrete class.

Implemented in ProtoMol::OutputDCDTrajectory, ProtoMol::OutputFile, ProtoMol::OutputFinalPDBPos, ProtoMol::OutputFinalXYZBinPos, ProtoMol::OutputFinalXYZBinVel, ProtoMol::OutputFinalXYZPos, ProtoMol::OutputFinalXYZVel, ProtoMol::OutputPDBFramePos, ProtoMol::OutputScreen, ProtoMol::OutputXYZTrajectoryForce, ProtoMol::OutputXYZTrajectoryPos, ProtoMol::OutputXYZTrajectoryVel, ProtoMol::OutputFinalPSF, and ProtoMol::OutputFinalXSC.

void ProtoMol::Output::finalize ( int step )

bool ProtoMol::Output::first ( ) const [inline]

int ProtoMol::Output::getFirstStep ( ) const [inline]

int ProtoMol::Output::getLastStep ( ) const [inline]

int ProtoMol::Output::getNext ( ) const [inline]

int ProtoMol::Output::getOutputFreq ( ) const [inline]

virtual std::string ProtoMol::Output::getScope ( ) const [inline, virtual]

Implements ProtoMol::Makeable.

void ProtoMol::Output::initialize ( const Configuration * config,

const Integrator * integrator,

const GenericTopology * topo,

const Vector3DBlock * pos,

const Vector3DBlock * vel,

const ScalarStructure * energies

)

To initialize the object, before the simulation starts.

bool ProtoMol::Output::isIdDefined ( const Configuration * config ) const [virtual]

Should return true if the concrete object is defined/specified in Configuration by the user. Normally if gedId() has a valid value in Configuration.
Reimplemented in ProtoMol::OutputScreen.

Output* ProtoMol::Output::make ( std::string & errMsg,

const std::vector< Value > & values

) const

Factory method to create a complete output object from its prototype.

void ProtoMol::Output::run ( int step )

void ProtoMol::Output::setCache ( const OutputCache * cache )

Set the cache object, such that not each output object has to re-compute same values of interest. the cache object is shared among all output objects in OutputCollection.