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 step, Random &rng)
	Update the input vectors with the position and the box of the frame.
void	frame (View< Vector > posToUpdate, View< double, 9 > 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() [1/2]

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

inherited

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

frame() [2/2]

void PLMD::fileTraj::frame ( View< Vector > posToUpdate, View< double, 9 > box, unsigned step, Random & rng )

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.

This is used principally in the benchmark. All the atoms distributions usually acts all the atoms passed by the vector of positions, so this does not change the input

But the "reading file" ones will only work if the number of atoms is the same of the one in the file, so this set the input to that number

And in case of the ones that replicate the trajectory this multiplies the input by the number of replicated "systems" this this is needed to inform benchmark that if you asked for replicating N atoms X*Y*Z times it will need an array of N*X*Y*Z atoms Outside of the specific usecase of the benchmark this is less important, because replicate will generate the inner trjectory on a limited number of atoms and the it will replicate it

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