class for reading H5MD trajectory. More...

#include <h5mdtrajectoryreader.h>

Inheritance diagram for votca::csg::H5MDTrajectoryReader:

Collaboration diagram for votca::csg::H5MDTrajectoryReader:

[legend]

Public Member Functions
	H5MDTrajectoryReader ()

	~H5MDTrajectoryReader () override

bool	Open (const std::string &file) override
	Opens original trajectory file.

void	Initialize (Topology &top)
	Initialize data structures.

bool	FirstFrame (Topology &conf) override
	Reads in the first frame.

bool	NextFrame (Topology &conf) override
	Reads in the next frame.

void	Close () override
	Closes original trajectory file.

Public Member Functions inherited from votca::csg::TrajectoryReader
virtual	~TrajectoryReader ()=default

virtual bool	Open (const std::string &file)=0
	open a trejectory file

virtual void	Close ()

virtual bool	FirstFrame (Topology &top)=0
	read in the first frame

virtual bool	NextFrame (Topology &top)=0
	read in the next frame

Private Types
enum	DatasetState { NONE , STATIC , TIMEDEPENDENT }

Private Member Functions
template<typename T1 >
T1 *	ReadVectorData (hid_t ds, hid_t ds_data_type, Index row)
	Reads dataset that contains vectors.

template<typename T1 >
T1 *	ReadScalarData (hid_t ds, hid_t ds_data_type, Index row)
	Reads dataset with scalar values.

template<typename T1 >
void	ReadStaticData (hid_t ds, hid_t ds_data_type, std::unique_ptr< T1 > &outbuf)

void	ReadBox (hid_t ds, hid_t ds_data_type, Index row, std::unique_ptr< double[]> &data_out)

double	ReadScaleFactor (const hid_t &ds, const std::string &unit_type)

void	CheckError (hid_t hid, std::string error_message)

bool	GroupExists (hid_t file_id, std::string path)

Private Attributes
hid_t	file_id_

hid_t	ds_atom_position_

hid_t	ds_atom_force_

hid_t	ds_atom_velocity_

hid_t	ds_atom_id_

hid_t	ds_edges_group_

hid_t	particle_group_

hid_t	atom_position_group_

hid_t	atom_force_group_

hid_t	atom_velocity_group_

hid_t	atom_id_group_

hid_t	edges_group_

Index	rank_

std::string	fname_

bool	first_frame_

DatasetState	has_velocity_

DatasetState	has_force_

DatasetState	has_id_group_

DatasetState	has_box_

bool	file_opened_

Index	idx_frame_

Index	max_idx_frame_

Index	N_particles_

int	vec_components_

bool	unit_module_enabled_ = false

double	length_scaling_ = 1.0

double	velocity_scaling_ = 1.0

double	force_scaling_ = 1.0

std::unordered_map< std::string, double >	votca_units_scaling_factors

boost::regex	suffix_units = boost::regex("^([a-z]+)([0-9+-]+)")

Eigen::Matrix3d	m

Additional Inherited Members
Static Public Member Functions inherited from votca::csg::TrajectoryReader
static void	RegisterPlugins (void)

Detailed Description

class for reading H5MD trajectory.

This class implements the H5MD trajectory reading function. The format of the H5MD file is defined in Pierre de Buyl, Peter H. Colberg, Felix Höfling, H5MD: A structured, efficient, and portable file format for molecular data, http://dx.doi.org/10.1016/j.cpc.2014.01.018 The current reference is available here: http://nongnu.org/h5md/

Definition at line 48 of file h5mdtrajectoryreader.h.

Member Enumeration Documentation

◆ DatasetState

enum votca::csg::H5MDTrajectoryReader::DatasetState

private

Enumerator
NONE
STATIC
TIMEDEPENDENT

Definition at line 69 of file h5mdtrajectoryreader.h.

Constructor & Destructor Documentation

◆ H5MDTrajectoryReader()

votca::csg::H5MDTrajectoryReader::H5MDTrajectoryReader ( )

Definition at line 36 of file h5mdtrajectoryreader.cc.

◆ ~H5MDTrajectoryReader()

votca::csg::H5MDTrajectoryReader::~H5MDTrajectoryReader ( )

override

Definition at line 43 of file h5mdtrajectoryreader.cc.

Member Function Documentation

◆ CheckError()

void votca::csg::H5MDTrajectoryReader::CheckError	(	hid_t	hid,
		std::string	error_message
	)

inlineprivate

Definition at line 135 of file h5mdtrajectoryreader.h.

◆ Close()

void votca::csg::H5MDTrajectoryReader::Close ( )

overridevirtual

Closes original trajectory file.

Reimplemented from votca::csg::TrajectoryReader.

Definition at line 107 of file h5mdtrajectoryreader.cc.

◆ FirstFrame()

bool votca::csg::H5MDTrajectoryReader::FirstFrame ( Topology & conf )

overridevirtual

Reads in the first frame.

Implements votca::csg::TrajectoryReader.

Definition at line 234 of file h5mdtrajectoryreader.cc.

◆ GroupExists()

bool votca::csg::H5MDTrajectoryReader::GroupExists	(	hid_t	file_id,
		std::string	path
	)

inlineprivate

Definition at line 142 of file h5mdtrajectoryreader.h.

◆ Initialize()

void votca::csg::H5MDTrajectoryReader::Initialize ( Topology & top )

Initialize data structures.

Definition at line 114 of file h5mdtrajectoryreader.cc.

◆ NextFrame()

bool votca::csg::H5MDTrajectoryReader::NextFrame ( Topology & conf )

overridevirtual

Reads in the next frame.

Reading the data.

Implements votca::csg::TrajectoryReader.

Definition at line 245 of file h5mdtrajectoryreader.cc.

◆ Open()

bool votca::csg::H5MDTrajectoryReader::Open ( const std::string & file )

overridevirtual

Opens original trajectory file.

Implements votca::csg::TrajectoryReader.

Definition at line 50 of file h5mdtrajectoryreader.cc.

◆ ReadBox()

void votca::csg::H5MDTrajectoryReader::ReadBox	(	hid_t	ds,
		hid_t	ds_data_type,
		Index	row,
		std::unique_ptr< double[]> &	data_out
	)

private

Definition at line 351 of file h5mdtrajectoryreader.cc.

◆ ReadScalarData()

template<typename T1 >

T1 * votca::csg::H5MDTrajectoryReader::ReadScalarData	(	hid_t	ds,
		hid_t	ds_data_type,
		Index	row
	)

inlineprivate

Reads dataset with scalar values.

Definition at line 99 of file h5mdtrajectoryreader.h.

◆ ReadScaleFactor()

double votca::csg::H5MDTrajectoryReader::ReadScaleFactor	(	const hid_t &	ds,
		const std::string &	unit_type
	)

private

Definition at line 370 of file h5mdtrajectoryreader.cc.

◆ ReadStaticData()

template<typename T1 >

void votca::csg::H5MDTrajectoryReader::ReadStaticData	(	hid_t	ds,
		hid_t	ds_data_type,
		std::unique_ptr< T1 > &	outbuf
	)

inlineprivate

Definition at line 121 of file h5mdtrajectoryreader.h.

◆ ReadVectorData()

template<typename T1 >

T1 * votca::csg::H5MDTrajectoryReader::ReadVectorData	(	hid_t	ds,
		hid_t	ds_data_type,
		Index	row
	)

inlineprivate

Reads dataset that contains vectors.

Definition at line 73 of file h5mdtrajectoryreader.h.

Member Data Documentation

◆ atom_force_group_

hid_t votca::csg::H5MDTrajectoryReader::atom_force_group_

private

Definition at line 160 of file h5mdtrajectoryreader.h.

◆ atom_id_group_

hid_t votca::csg::H5MDTrajectoryReader::atom_id_group_

private

Definition at line 162 of file h5mdtrajectoryreader.h.

◆ atom_position_group_

hid_t votca::csg::H5MDTrajectoryReader::atom_position_group_

private

Definition at line 159 of file h5mdtrajectoryreader.h.

◆ atom_velocity_group_

hid_t votca::csg::H5MDTrajectoryReader::atom_velocity_group_

private

Definition at line 161 of file h5mdtrajectoryreader.h.

◆ ds_atom_force_

hid_t votca::csg::H5MDTrajectoryReader::ds_atom_force_

private

Definition at line 153 of file h5mdtrajectoryreader.h.

◆ ds_atom_id_

hid_t votca::csg::H5MDTrajectoryReader::ds_atom_id_

private

Definition at line 155 of file h5mdtrajectoryreader.h.

◆ ds_atom_position_

hid_t votca::csg::H5MDTrajectoryReader::ds_atom_position_

private

Definition at line 152 of file h5mdtrajectoryreader.h.

◆ ds_atom_velocity_

hid_t votca::csg::H5MDTrajectoryReader::ds_atom_velocity_

private

Definition at line 154 of file h5mdtrajectoryreader.h.

◆ ds_edges_group_

hid_t votca::csg::H5MDTrajectoryReader::ds_edges_group_

private

Definition at line 156 of file h5mdtrajectoryreader.h.

◆ edges_group_

hid_t votca::csg::H5MDTrajectoryReader::edges_group_

private

Definition at line 163 of file h5mdtrajectoryreader.h.

◆ file_id_

hid_t votca::csg::H5MDTrajectoryReader::file_id_

private

Definition at line 151 of file h5mdtrajectoryreader.h.

◆ file_opened_

bool votca::csg::H5MDTrajectoryReader::file_opened_

private

Definition at line 176 of file h5mdtrajectoryreader.h.

◆ first_frame_

bool votca::csg::H5MDTrajectoryReader::first_frame_

private

Definition at line 168 of file h5mdtrajectoryreader.h.

◆ fname_

std::string votca::csg::H5MDTrajectoryReader::fname_

private

Definition at line 167 of file h5mdtrajectoryreader.h.

◆ force_scaling_

double votca::csg::H5MDTrajectoryReader::force_scaling_ = 1.0

private

Definition at line 191 of file h5mdtrajectoryreader.h.

◆ has_box_

DatasetState votca::csg::H5MDTrajectoryReader::has_box_

private

Definition at line 174 of file h5mdtrajectoryreader.h.

◆ has_force_

DatasetState votca::csg::H5MDTrajectoryReader::has_force_

private

Definition at line 172 of file h5mdtrajectoryreader.h.

◆ has_id_group_

DatasetState votca::csg::H5MDTrajectoryReader::has_id_group_

private

Definition at line 173 of file h5mdtrajectoryreader.h.

◆ has_velocity_

DatasetState votca::csg::H5MDTrajectoryReader::has_velocity_

private

Definition at line 171 of file h5mdtrajectoryreader.h.

◆ idx_frame_

Index votca::csg::H5MDTrajectoryReader::idx_frame_

private

Definition at line 179 of file h5mdtrajectoryreader.h.

◆ length_scaling_

double votca::csg::H5MDTrajectoryReader::length_scaling_ = 1.0

private

Definition at line 189 of file h5mdtrajectoryreader.h.

◆ m

Eigen::Matrix3d votca::csg::H5MDTrajectoryReader::m

private

Definition at line 204 of file h5mdtrajectoryreader.h.

◆ max_idx_frame_

Index votca::csg::H5MDTrajectoryReader::max_idx_frame_

private

Definition at line 180 of file h5mdtrajectoryreader.h.

◆ N_particles_

Index votca::csg::H5MDTrajectoryReader::N_particles_

private

Definition at line 183 of file h5mdtrajectoryreader.h.

◆ particle_group_

hid_t votca::csg::H5MDTrajectoryReader::particle_group_

private

Definition at line 158 of file h5mdtrajectoryreader.h.

◆ rank_

Index votca::csg::H5MDTrajectoryReader::rank_

private

Definition at line 165 of file h5mdtrajectoryreader.h.

◆ suffix_units

boost::regex votca::csg::H5MDTrajectoryReader::suffix_units = boost::regex("^([a-z]+)([0-9+-]+)")

private

Definition at line 201 of file h5mdtrajectoryreader.h.

◆ unit_module_enabled_

bool votca::csg::H5MDTrajectoryReader::unit_module_enabled_ = false

private

Definition at line 188 of file h5mdtrajectoryreader.h.

◆ vec_components_

int votca::csg::H5MDTrajectoryReader::vec_components_

private

Definition at line 185 of file h5mdtrajectoryreader.h.

◆ velocity_scaling_

double votca::csg::H5MDTrajectoryReader::velocity_scaling_ = 1.0

private

Definition at line 190 of file h5mdtrajectoryreader.h.

◆ votca_units_scaling_factors

std::unordered_map<std::string, double> votca::csg::H5MDTrajectoryReader::votca_units_scaling_factors

private

Initial value:

=
      std::unordered_map<std::string, double>({{"fm", 0.000001},
                                               {"pm", 0.001},
                                               {"nm", 1.0},
                                               {"A", 0.1},
                                               {"um", 1000.0}})

Definition at line 194 of file h5mdtrajectoryreader.h.

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

csg/src/libcsg/modules/io/h5mdtrajectoryreader.h
csg/src/libcsg/modules/io/h5mdtrajectoryreader.cc

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ DatasetState

Constructor & Destructor Documentation

◆ H5MDTrajectoryReader()

◆ ~H5MDTrajectoryReader()

Member Function Documentation

◆ CheckError()

◆ Close()

◆ FirstFrame()

◆ GroupExists()

◆ Initialize()

◆ NextFrame()

◆ Open()

◆ ReadBox()

◆ ReadScalarData()

◆ ReadScaleFactor()

◆ ReadStaticData()

◆ ReadVectorData()

Member Data Documentation

◆ atom_force_group_

◆ atom_id_group_

◆ atom_position_group_

◆ atom_velocity_group_

◆ ds_atom_force_

◆ ds_atom_id_

◆ ds_atom_position_

◆ ds_atom_velocity_

◆ ds_edges_group_

◆ edges_group_

◆ file_id_

◆ file_opened_

◆ first_frame_

◆ fname_

◆ force_scaling_

◆ has_box_

◆ has_force_

◆ has_id_group_

◆ has_velocity_

◆ idx_frame_

◆ length_scaling_

◆ m

◆ max_idx_frame_

◆ N_particles_

◆ particle_group_

◆ rank_

◆ suffix_units

◆ unit_module_enabled_

◆ vec_components_

◆ velocity_scaling_

◆ votca_units_scaling_factors