Structure Class Reference

Specification for the structure file interface. More...

#include <structure.h>

Inheritance diagram for Structure:

Public Member Functions
	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.

Public Attributes
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.

Protected Member Functions
virtual void	beginning ()
virtual void	getFrame ()=0
virtual void	getCell ()=0
void	skipFrame ()
virtual void	skipFrames (uint64_t count)
void	skipLine (std::ifstream &in)
virtual void	initialise ()=0
void	scanPositions ()
void	cachePositions ()
void	countContentLinesInFile ()
void	checkRead (std::stringstream &ss, std::string lastInput, std::string context)

Protected Attributes
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

Specification for the structure file interface.

Remarks

See also

XYZ for an XYZ/EXTXYZ implementation.

Remarks

See also

CONFIG for a CONFIG implementation.

Remarks

Implementors must set:

• atoms: the atom count.
• frames: the frame count.
• linesPerFrame: the (constant) lines in each frame.

Constructor & Destructor Documentation

Structure()

Structure::Structure ( std::filesystem::path  path, bool  blocking = false  )

inline

~Structure()

virtual Structure::~Structure ( )

virtualdefault

Member Function Documentation

atomCount()

virtual uint64_t Structure::atomCount ( ) const

inlinevirtual

Get the number of atoms in the file.

Returns

uint64_t the number of atoms.

beginning()

virtual void Structure::beginning ( )

inlineprotectedvirtual

cachePositions()

void Structure::cachePositions ( )

inlineprotected

checkRead()

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

inlineprotected

countContentLinesInFile()

void Structure::countContentLinesInFile ( )

inlineprotected

frameCount()

uint64_t Structure::frameCount ( ) const

inline

Get the number of frames.

Returns

uint64_t the frame count.

framePosition()

uint64_t Structure::framePosition ( ) const

inline

Get the current frame index.

Returns

uint64_t the current frame index.

framePositionsLoaded()

bool Structure::framePositionsLoaded ( ) const

inline

Check if frames start positions have been loaded.

Remarks

Frame start position offsets are loaded in a detached I/O thread. The result of this method indicates whether the I/O read has completed.

Structure::frameCount will be update while the detached read is progressing.

Structure::readFrame will only allow reads up to Structure::framePosition.

Returns

true if all frame start offsets have been loaded.

false frame start positions are still being read.

frameReadComplete()

bool Structure::frameReadComplete ( ) const

inline

If the frame has been fully read into atoms.

Returns

true if all Atoms in the frame have been read.

false if reading is in progress.

frameReadProgress()

uint64_t Structure::frameReadProgress ( ) const

inline

Progress of the current frame read.

Returns

uint64_t count of Atom read into atoms.

getCell()

virtual void Structure::getCell ( )

protectedpure virtual

getCellA()

glm::vec3 Structure::getCellA ( ) const

inline

Get the a cell vector.

Returns

glm::vec3 cell vector a.

getCellB()

glm::vec3 Structure::getCellB ( ) const

inline

Get the b cell vector.

Returns

glm::vec3 cell vector b.

getCellC()

glm::vec3 Structure::getCellC ( ) const

inline

Get the c cell vector.

Returns

glm::vec3 cell vector c.

getFrame()

virtual void Structure::getFrame ( )

protectedpure virtual

initialise()

virtual void Structure::initialise ( )

protectedpure virtual

readFrame()

virtual void Structure::readFrame ( uint64_t  frame )

inlinevirtual

Read a single frame at position frame, and increment the current frame.

Remarks

Structure::frameCount is the maximum readable frame. If frame is larger it will be 'd.

See also

framePosition for the status of detached frame caching.

getAtoms for accessing the read data.

Parameters

frame

the frame position.

scanPositions()

void Structure::scanPositions ( )

inlineprotected

skipFrame()

void Structure::skipFrame ( )

inlineprotected

skipFrames()

virtual void Structure::skipFrames ( uint64_t  count )

inlineprotectedvirtual

skipLine()

void Structure::skipLine ( std::ifstream &  in )

inlineprotected

Member Data Documentation

atoms

std::vector<Atom> Structure::atoms

The Atoms read in the current frame.

atomsRead

uint64_t Structure::atomsRead

protected

blockingReads

bool Structure::blockingReads

protected

cacheComplete

bool Structure::cacheComplete = false

protected

cellA

glm::vec3 Structure::cellA

protected

cellB

glm::vec3 Structure::cellB

protected

cellC

glm::vec3 Structure::cellC

protected

colourMap

std::map<Element, glm::vec4> Structure::colourMap = CPK_COLOURS

Colour map from Element to colour.

currentFrame

uint64_t Structure::currentFrame

protected

filestream

std::ifstream Structure::filestream

protected

framePositions

std::map<uint64_t, uint64_t> Structure::framePositions

protected

frames

uint64_t Structure::frames

protected

linesInFile

uint64_t Structure::linesInFile

protected

linesPerFrame

uint64_t Structure::linesPerFrame

protected

natoms

uint64_t Structure::natoms

protected

path

std::filesystem::path Structure::path

protected

timeStep

uint64_t Structure::timeStep

protected

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

• include/structure.h