Read XYZ and EXTXYZ files. More...

#include <xyz.h>

Inheritance diagram for XYZ:

Collaboration diagram for XYZ:

Public Member Functions
	XYZ (std::filesystem::path path, bool blocking=false)
	Construct a new XYZ object to read from path.

Public Member Functions inherited from Structure
	Structure (std::filesystem::path path, bool blocking=false)

virtual uint64_t	atomCount () const
	Get the number of atoms in the file.

virtual void	readFrame (uint64_t frame)
	Read a single frame at position frame, and increment the current frame.

virtual	~Structure ()=default

uint64_t	frameCount () const
	Get the number of frames.

uint64_t	framePosition () const
	Get the current frame index.

bool	framePositionsLoaded () const
	Check if frames start positions have been loaded.

uint64_t	frameReadProgress () const
	Progress of the current frame read.

bool	frameReadComplete () const
	If the frame has been fully read into atoms.

glm::vec3	getCellA () const
	Get the a cell vector.

glm::vec3	getCellB () const
	Get the b cell vector.

glm::vec3	getCellC () const
	Get the c cell vector.

std::string	getPath ()
	Get the Path of the structure.

Additional Inherited Members
Public Attributes inherited from Structure
std::vector< Atom >	atoms
	The Atoms read in the current frame.

std::map< Element, glm::vec4 >	colourMap = CPK_COLOURS
	Colour map from Element to colour.

bool	updated = false

Protected Member Functions inherited from Structure
virtual void	beginning ()

void	skipFrame ()

virtual void	skipFrames (uint64_t count)

void	skipLine (std::ifstream &in)

void	scanPositions ()

void	cachePositions ()

void	countContentLinesInFile ()

void	checkRead (std::stringstream &ss, std::string lastInput, std::string context)

Protected Attributes inherited from Structure
std::filesystem::path	path

bool	blockingReads

std::ifstream	filestream

uint64_t	natoms

uint64_t	frames

uint64_t	linesPerFrame

uint64_t	timeStep

uint64_t	currentFrame

uint64_t	linesInFile

uint64_t	atomsRead

glm::vec3	cellA

glm::vec3	cellB

glm::vec3	cellC

bool	cacheComplete = false

std::map< uint64_t, uint64_t >	framePositions

Detailed Description

Read XYZ and EXTXYZ files.

Remarks

The file structure is nLine reads: ++line2 lines for nLine reads: +lineatoms.

Atom count [integer]
Comment line [string]
nLine reads: +lineentries of the form
- Symbol [string]
- Position [float, float, float]

A trajectory is a simple concatenation of multiple XYZ files.

EXTXYZ includes a more detail specification for the comment line.

Constructor & Destructor Documentation

inline

Construct a new XYZ object to read from path.

Parameters

path	the file path of the XYZ file.
blocking	if reads are blocking or detached.

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