Base data structure for native XTC format as used in Gromacs and supported by the C library. More...

#include <io.h>

Public Member Functions
	XTCTrajectoryFrame (int number_of_atoms)
	Creates an empty XTC trajectory frame for given number of coordinates (atoms). More...

	XTCTrajectoryFrame (const TrajectoryFrame &frame)
	Creates an XTC trajectory frame from TrajectoryFrame and converts data accordingly. More...

template<RequirePointIterator begin_iterator, class end_iterator >
	XTCTrajectoryFrame (int step, float time, const Point &box, begin_iterator coordinates_begin, end_iterator coordinates_end)
	Creates an XTC trajectory frame from scalar parameters and input iterator and converts data accordingly. More...

XTCTrajectoryFrame &	operator= (const TrajectoryFrame &frame)
	Copies TrajectoryFrame and converts data. More...

void	importFrame (const TrajectoryFrame &frame)
	Imports data from a TrajectoryFrame. More...

template<RequirePointIterator begin_iterator, class end_iterator >
void	importFrame (const int step, const float time, const Point &box, begin_iterator coordinates_begin, end_iterator coordinates_end)
	Imports data from scalar parameters and an input iterator over coordinates. More...

void	exportFrame (TrajectoryFrame &frame) const
	Exports data from a TrajectoryFrame. More...

template<RequirePointIterator begin_iterator, RequirePointIterator end_iterator>
void	exportFrame (int &step, float &time, Point &box, begin_iterator coordinates_begin, end_iterator coordinates_end) const
	Exports data to scalar paramers and output iterator over atomic coordinates. More...

Public Attributes
XdrFile::matrix	xtc_box
	box tensor; only diagonal elements are used

std::unique_ptr< XdrFile::rvec[]>	xtc_coordinates
	C-style array of particle coordinates.

int	xtc_step = 0
	current frame number

float	xtc_time = 0.0
	current time (unit?)

int	number_of_atoms = 0
	number of coordinates (atoms) in each frame

float	precision = 1000.0
	output precision

Protected Types
using	XTCFloat = float

using	XTCMatrix = Eigen::Matrix< XTCFloat, 3, 3, Eigen::RowMajor >

using	XTCVector = Eigen::Matrix< XTCFloat, 3, 1 >

Protected Member Functions
void	importTimestamp (int step, float time)
	Imports and converts step and timestamp. More...

void	importBox (const Point &box)
	Imports and converts simulation box dimensions. More...

void	importCoordinates (const PointVector &coordinates, const Point &offset)
	Imports and converts atomic coordinates. More...

template<RequirePointIterator begin_iterator, typename end_iterator >
void	importCoordinates (begin_iterator begin, end_iterator end, const Point &offset) const
	Imports and converts atomic coordinates. More...

void	exportTimestamp (int &step, float &time) const
	Exports and converts step and timestamp. More...

void	exportBox (Point &box) const
	Exports and converts simulation box dimensions. More...

void	exportCoordinates (PointVector &coordinates, const Point &offset) const
	Exports and converts atomic coordinates. More...

template<RequirePointIterator begin_iterator, typename end_iterator >
void	exportCoordinates (begin_iterator begin, end_iterator end, const Point &offset) const
	Exports and converts atomic coordinates. More...

Detailed Description

Base data structure for native XTC format as used in Gromacs and supported by the C library.

Import methods do the data conversion from the Faunus native format to the XTC format, and export methods do the oposite.

By convention, XTC has coordinates' origin in a corner (main box's coordinates are always positive), while Faunus has coordinates' origin in the center of the simulation box. During conversion the corresponding offset is subtracted, or added, respectively.

XTC format uses floats (Faunus doubles) and dimensions are in nanometers (Faunus ångströms). XTC library requires raw 2D C-style arrays for coordinates in row-major format. XTC tensor of the simulation box is converted to an XYZ point pressuming orthogonal geometry bacause of current limitation of Faunus. XTC format does not support variable number of coordinates (atoms) between frames.

Constructor & Destructor Documentation

◆ XTCTrajectoryFrame() [1/3]

Faunus::XTCTrajectoryFrame::XTCTrajectoryFrame ( int number_of_atoms )

Creates an empty XTC trajectory frame for given number of coordinates (atoms).

Parameters

number_of_atoms number of coordinates (atoms)

◆ XTCTrajectoryFrame() [2/3]

Faunus::XTCTrajectoryFrame::XTCTrajectoryFrame ( const TrajectoryFrame & frame )

Creates an XTC trajectory frame from TrajectoryFrame and converts data accordingly.

Parameters

frame source trajectory frame

◆ XTCTrajectoryFrame() [3/3]

template<RequirePointIterator begin_iterator, class end_iterator >

Faunus::XTCTrajectoryFrame::XTCTrajectoryFrame	(	int	step,
		float	time,
		const Point &	box,
		begin_iterator	coordinates_begin,
		end_iterator	coordinates_end
	)

inline

Creates an XTC trajectory frame from scalar parameters and input iterator and converts data accordingly.

Template Parameters

begin_iterator
end_iterator

Parameters

[in]	step	frame step
[in]	time	timestamp in picoseconds
[in]	box	box dimensions (xyz) in nanometers
[in]	coordinates_begin	input iterator with coordinates in nanometers
[in]	coordinates_end	input iterator's end

Member Function Documentation

◆ exportBox()

void Faunus::XTCTrajectoryFrame::exportBox ( Point & box ) const

protected

Exports and converts simulation box dimensions.

Parameters

[out] box simulation box dimensions in nanometers (xyz)

◆ exportCoordinates() [1/2]

void Faunus::XTCTrajectoryFrame::exportCoordinates	(	PointVector &	coordinates,
		const Point &	offset
	)		const

protected

Exports and converts atomic coordinates.

Offset is subtracted from all coordinates to account different coordinates' origin.

Parameters

[out]	coordinates	atomic coordinates in nanometers
[in]	offset	offset in nanometers to subtract from all coordinates upon conversion

Exceptions

std::runtime_error when the source box is not orthogonal

◆ exportCoordinates() [2/2]

template<RequirePointIterator begin_iterator, typename end_iterator >

void Faunus::XTCTrajectoryFrame::exportCoordinates	(	begin_iterator	begin,
		end_iterator	end,
		const Point &	offset
	)		const

inlineprotected

Exports and converts atomic coordinates.

Offset is subtracted to all coordinates to account different coordinates' origin.

Template Parameters

begin_iterator
end_iterator

Parameters

[out]	begin	output iterator with coordinates in nanometers
[out]	end	output iterator's end
[in]	offset	offset in nanometers to subtract from all coordinates upon conversion

◆ exportFrame() [1/2]

void Faunus::XTCTrajectoryFrame::exportFrame ( TrajectoryFrame & frame ) const

Exports data from a TrajectoryFrame.

Parameters

frame target frame

Exceptions

std::runtime_error when the number of coordinates does not match

◆ exportFrame() [2/2]

template<RequirePointIterator begin_iterator, RequirePointIterator end_iterator>

void Faunus::XTCTrajectoryFrame::exportFrame	(	int &	step,
		float &	time,
		Point &	box,
		begin_iterator	coordinates_begin,
		end_iterator	coordinates_end
	)		const

inline

Exports data to scalar paramers and output iterator over atomic coordinates.

Template Parameters

begin_iterator
end_iterator

Parameters

[out]	step	frame step
[out]	time	frame timestamp
[out]	box	box dimensions (xyz) in nanometers
[out]	coordinates_begin	output iterator with coordinates in nanometers
[out]	coordinates_end	output iterator's end

Exceptions

std::runtime_error when the number of coordinates does not match

◆ exportTimestamp()

void Faunus::XTCTrajectoryFrame::exportTimestamp	(	int &	step,
		float &	time
	)		const

protected

Exports and converts step and timestamp.

Parameters

[out]	step	frame step
[out]	time	frame timestamp

◆ importBox()

void Faunus::XTCTrajectoryFrame::importBox ( const Point & box )

protected

Imports and converts simulation box dimensions.

Parameters

[in] box simulation box dimensions in nanometers (xyz)

◆ importCoordinates() [1/2]

void Faunus::XTCTrajectoryFrame::importCoordinates	(	const PointVector &	coordinates,
		const Point &	offset
	)

protected

Imports and converts atomic coordinates.

Offset is added to all coordinates to account different coordinates' origin.

Parameters

[in]	coordinates	atomic coordinates in nanometers
[in]	offset	offset in nanometers to add to all coordinates upon conversion

◆ importCoordinates() [2/2]

template<RequirePointIterator begin_iterator, typename end_iterator >

void Faunus::XTCTrajectoryFrame::importCoordinates	(	begin_iterator	begin,
		end_iterator	end,
		const Point &	offset
	)		const

inlineprotected

Imports and converts atomic coordinates.

Offset is added to all coordinates to account different coordinates' origin.

Template Parameters

begin_iterator
end_iterator

Parameters

[in]	begin	input iterator with coordinates in nanometers
[in]	end	input iterator's end
[in]	offset	offset in nanometers to add to all coordinates upon conversion

◆ importFrame() [1/2]

void Faunus::XTCTrajectoryFrame::importFrame ( const TrajectoryFrame & frame )

Imports data from a TrajectoryFrame.

Parameters

frame source frame

Exceptions

std::runtime_error when the number of coordinates does not match

◆ importFrame() [2/2]

template<RequirePointIterator begin_iterator, class end_iterator >

void Faunus::XTCTrajectoryFrame::importFrame	(	const int	step,
		const float	time,
		const Point &	box,
		begin_iterator	coordinates_begin,
		end_iterator	coordinates_end
	)

inline

Imports data from scalar parameters and an input iterator over coordinates.

Template Parameters

begin_iterator
end_iterator

Parameters

[in]	step	frame step
[in]	time	frame timestamp
[in]	box	box dimensions (xyz) in nanometers
[in]	coordinates_begin	input iterator with coordinates in nanometers
[in]	coordinates_end	input iterator's end

Exceptions

std::runtime_error when the number of coordinates does not match

◆ importTimestamp()

void Faunus::XTCTrajectoryFrame::importTimestamp	(	int	step,
		float	time
	)

protected

Imports and converts step and timestamp.

Parameters

[in]	step	frame step
[in]	time	frame timestamp

◆ operator=()

XTCTrajectoryFrame & Faunus::XTCTrajectoryFrame::operator= ( const TrajectoryFrame & frame )

Copies TrajectoryFrame and converts data.

Calls importFrame.

The number of coordinates is immutable to prevent mistakes.

Parameters

frame source frame

Exceptions

std::runtime_error when the number of coordinates does not match

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

src/io.h
src/io.cpp

Public Member Functions

Public Attributes

Protected Types

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ XTCTrajectoryFrame() [1/3]

◆ XTCTrajectoryFrame() [2/3]

◆ XTCTrajectoryFrame() [3/3]

Member Function Documentation

◆ exportBox()

◆ exportCoordinates() [1/2]

◆ exportCoordinates() [2/2]

◆ exportFrame() [1/2]

◆ exportFrame() [2/2]

◆ exportTimestamp()

◆ importBox()

◆ importCoordinates() [1/2]

◆ importCoordinates() [2/2]

◆ importFrame() [1/2]

◆ importFrame() [2/2]

◆ importTimestamp()

◆ operator=()