McMd::TrajectoryReader Class Reference

Detailed Description

Trajectory file reader (base class).

Definition at line 30 of file mcMd/trajectory/TrajectoryReader.h.

#include <TrajectoryReader.h>

Inheritance diagram for McMd::TrajectoryReader:

Public Member Functions
	TrajectoryReader (System &system)
	Constructor. More...
virtual	~TrajectoryReader ()
	Destructor. More...
virtual void	open (std::string filename)=0
	Open trajectory file and read header, if any. More...
virtual bool	readFrame ()=0
	Read a single frame. More...
virtual void	close ()=0
	Close the trajectory file. More...

Protected Member Functions
System &	system () const
	Get a reference to the parent System. More...
Simulation &	simulation () const
	Get a reference to the parent Simulation. More...
Boundary &	boundary () const
	Get the Boundary. More...
virtual void	addMolecules ()
	Add all molecules to system. More...

Protected Attributes
int	nAtomTotal_
	Total number of atoms (all species) More...

Constructor & Destructor Documentation

McMd::TrajectoryReader::TrajectoryReader

(

System &

system

)

Constructor.

Definition at line 23 of file mcMd/trajectory/TrajectoryReader.cpp.

McMd::TrajectoryReader::~TrajectoryReader ( )

virtual

Destructor.

Definition at line 33 of file mcMd/trajectory/TrajectoryReader.cpp.

Member Function Documentation

virtual void McMd::TrajectoryReader::open ( std::string  filename )

pure virtual

Open trajectory file and read header, if any.

By convention, this function treats the trajectory filename as the name of an input file, and opens the file using the FileMaster:openInutFile function. This function prepends the input prefix (if any) to the file path. If compiled with MPI enabled, so that each processor simulates a different system, it also prepends a processor id prefix before the input prefix.

Parameters

filename

trajectory input file name.

Implemented in McMd::DCDTrajectoryReader, McMd::DdMdTrajectoryReader, and McMd::LammpsDumpReader.

Referenced by McMd::MdSimulation::analyzeTrajectory(), and McMd::McSimulation::analyzeTrajectory().

virtual bool McMd::TrajectoryReader::readFrame ( )

pure virtual

Read a single frame.

Frames are assumed to be read consecutively.

This function reads a frame from the trajectory file that was opened by the open() function.

Returns

true if a frame is avaiable, false if at end of file

Implemented in McMd::DCDTrajectoryReader, McMd::DdMdTrajectoryReader, and McMd::LammpsDumpReader.

Referenced by McMd::MdSimulation::analyzeTrajectory(), and McMd::McSimulation::analyzeTrajectory().

virtual void McMd::TrajectoryReader::close ( )

pure virtual

Close the trajectory file.

Implemented in McMd::DCDTrajectoryReader, McMd::DdMdTrajectoryReader, and McMd::LammpsDumpReader.

Referenced by McMd::MdSimulation::analyzeTrajectory(), and McMd::McSimulation::analyzeTrajectory().

System & McMd::TrajectoryReader::system ( ) const

inlineprotected

Get a reference to the parent System.

Definition at line 111 of file mcMd/trajectory/TrajectoryReader.h.

Referenced by addMolecules(), McMd::LammpsDumpReader::readFrame(), McMd::DdMdTrajectoryReader::readFrame(), and McMd::DCDTrajectoryReader::readFrame().

Simulation & McMd::TrajectoryReader::simulation ( ) const

inlineprotected

Get a reference to the parent Simulation.

Definition at line 120 of file mcMd/trajectory/TrajectoryReader.h.

Referenced by addMolecules(), McMd::LammpsDumpReader::open(), McMd::DdMdTrajectoryReader::open(), McMd::LammpsDumpReader::readFrame(), McMd::DdMdTrajectoryReader::readFrame(), and McMd::DCDTrajectoryReader::readFrame().

Boundary & McMd::TrajectoryReader::boundary ( ) const

inlineprotected

Get the Boundary.

Definition at line 129 of file mcMd/trajectory/TrajectoryReader.h.

Referenced by McMd::LammpsDumpReader::readFrame(), McMd::DdMdTrajectoryReader::readFrame(), and McMd::DCDTrajectoryReader::readFrame().

void McMd::TrajectoryReader::addMolecules ( )

protectedvirtual

Add all molecules to system.

Definition at line 39 of file mcMd/trajectory/TrajectoryReader.cpp.

References McMd::System::addMolecule(), Simp::Species::capacity(), McMd::Simulation::getMolecule(), Simp::Species::nAtom(), nAtomTotal_, McMd::Simulation::nSpecies(), simulation(), McMd::Simulation::species(), and system().

Referenced by McMd::LammpsDumpReader::open(), McMd::DdMdTrajectoryReader::open(), and McMd::DCDTrajectoryReader::open().

Member Data Documentation

int McMd::TrajectoryReader::nAtomTotal_

protected

Total number of atoms (all species)

Definition at line 77 of file mcMd/trajectory/TrajectoryReader.h.

Referenced by addMolecules(), McMd::LammpsDumpReader::open(), McMd::DdMdTrajectoryReader::open(), McMd::DCDTrajectoryReader::open(), McMd::LammpsDumpReader::readFrame(), and McMd::DdMdTrajectoryReader::readFrame().

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The documentation for this class was generated from the following files:

• mcMd/trajectory/TrajectoryReader.h
• mcMd/trajectory/TrajectoryReader.cpp