PLMD::fileTraj Class Reference

atomic distribution from a trajectory file More...

#include <AtomDistribution.h>

Inheritance diagram for PLMD::fileTraj:

Public Member Functions
	fileTraj (std::string_view fmt, std::string_view fname, bool useMolfile, int command_line_natoms)
void	frame (std::vector< Vector > &posToUpdate, std::vector< double > &box, unsigned, Random &) override
	Update the input vectors with the position and the box of the frame.
bool	overrideNat (unsigned &natoms) override
	If necessary changes the number of atoms, returns true if that number has been changed.

Static Public Member Functions
static std::unique_ptr< AtomDistribution >	getAtomDistribution (std::string_view atomicDistr)

Private Member Functions
void	rewind ()
void	step (bool doRewind=true)

Private Attributes
std::vector< double >	cell
std::vector< double >	charges {}
std::vector< Vector >	coordinates {}
bool	dont_read_pbc =false
std::vector< double >	masses {}
TrajectoryParser	parser
bool	read =false

Detailed Description

atomic distribution from a trajectory file

Constructor & Destructor Documentation

fileTraj()

PLMD::fileTraj::fileTraj	(	std::string_view	fmt,
		std::string_view	fname,
		bool	useMolfile,
		int	command_line_natoms )

Member Function Documentation

frame()

void PLMD::fileTraj::frame ( std::vector< Vector > & posToUpdate, std::vector< double > & box, unsigned , Random &  )

overridevirtual

Update the input vectors with the position and the box of the frame.

Implements PLMD::AtomDistribution.

getAtomDistribution()

std::unique_ptr< AtomDistribution > PLMD::AtomDistribution::getAtomDistribution ( std::string_view atomicDistr )

staticinherited

overrideNat()

bool PLMD::fileTraj::overrideNat ( unsigned & )

overridevirtual

If necessary changes the number of atoms, returns true if that number has been changed.

Reimplemented from PLMD::AtomDistribution.

rewind()

void PLMD::fileTraj::rewind ( )

private

step()

void PLMD::fileTraj::step ( bool doRewind = true )

private

Member Data Documentation

cell

std::vector<double> PLMD::fileTraj::cell

private

Initial value:

{0.0,0.0,0.0,
        0.0,0.0,0.0,
        0.0,0.0,0.0}

charges

std::vector<double> PLMD::fileTraj::charges {}

private

coordinates

std::vector<Vector> PLMD::fileTraj::coordinates {}

private

dont_read_pbc

bool PLMD::fileTraj::dont_read_pbc =false

private

masses

std::vector<double> PLMD::fileTraj::masses {}

private

parser

TrajectoryParser PLMD::fileTraj::parser

private

read

bool PLMD::fileTraj::read =false

private

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

• tools/AtomDistribution.h
• tools/AtomDistribution.cpp