Classes
struct	Dataset

class	File
	Class for writing H5MD files. More...

struct	incompatible_h5mdfile

struct	left_backupfile

struct	Specification
	Layout information for H5MD files. More...

Typedefs
using	MultiArray3i = boost::multi_array< int, 3 >

using	Vector1hs = Utils::Vector< hsize_t, 1 >

using	Vector2hs = Utils::Vector< hsize_t, 2 >

using	Vector3hs = Utils::Vector< hsize_t, 3 >

using	Vector1s = Utils::Vector< std::size_t, 1 >

using	Vector2s = Utils::Vector< std::size_t, 2 >

using	Vector3s = Utils::Vector< std::size_t, 3 >

Enumerations
enum	H5MDOutputFields : unsigned int { H5MD_OUT_NONE = 0u , H5MD_OUT_TYPE = 1u , H5MD_OUT_POS = 2u , H5MD_OUT_IMG = 4u , H5MD_OUT_VEL = 8u , H5MD_OUT_FORCE = 16u , H5MD_OUT_MASS = 32u , H5MD_OUT_CHARGE = 16u , H5MD_OUT_BONDS = 128u , H5MD_OUT_BOX_L = 256u , H5MD_OUT_LE_OFF = 512u , H5MD_OUT_LE_DIR = 1024u , H5MD_OUT_LE_NORMAL = 2048u , H5MD_OUT_ALL = 0b1111111111111111u }
	Constants which indicate what to output. More...

Functions
static auto	fields_list_to_bitfield (std::vector< std::string > const &fields)

static void	backup_file (std::filesystem::path const &from, std::filesystem::path const &to)

template<typename extent_type >
static void	extend_dataset (HighFive::DataSet &dataset, extent_type const &change_extent)

template<typename value_type , typename extent_type >
static void	write_dataset (value_type const &data, HighFive::DataSet &dataset, extent_type const &offset, extent_type const &count)

template<typename value_type , typename extent_type >
static void	write_dataset (value_type const &data, HighFive::DataSet &dataset, extent_type const &change_extent, extent_type const &offset, extent_type const &count)

static void	write_script (HighFive::File &h5md_file, std::filesystem::path const &script_path)

static std::vector< std::size_t >	create_dims (hsize_t rank, hsize_t data_dim)

static std::vector< std::size_t >	create_maxdims (hsize_t rank, hsize_t data_dim, hsize_t max_dim)

static std::vector< hsize_t >	create_chunk_dims (hsize_t rank, hsize_t data_dim, hsize_t size)

static void	write_attributes (HighFive::File &h5md_file)

template<std::size_t dim, typename Serializer >
void	write_td_particle_property (hsize_t prefix, hsize_t n_part_global, ParticleRange const &particles, HighFive::DataSet &dataset, Serializer serializer)

static void	write_box (BoxGeometry const &box_geo, HighFive::DataSet &dataset)

static void	write_le_off (LeesEdwardsBC const &lebc, HighFive::DataSet &dataset)

static void	write_le_dir (LeesEdwardsBC const &lebc, HighFive::DataSet &dataset)

static void	write_le_normal (LeesEdwardsBC const &lebc, HighFive::DataSet &dataset)

Variables
static std::unordered_map< std::string, H5MDOutputFields > const	fields_map

Typedef Documentation

◆ MultiArray3i

using Writer::H5md::MultiArray3i = typedef boost::multi_array<int, 3>

Definition at line 61 of file h5md_core.cpp.

◆ Vector1hs

using Writer::H5md::Vector1hs = typedef Utils::Vector<hsize_t, 1>

Definition at line 62 of file h5md_core.cpp.

◆ Vector1s

using Writer::H5md::Vector1s = typedef Utils::Vector<std::size_t, 1>

Definition at line 65 of file h5md_core.cpp.

◆ Vector2hs

using Writer::H5md::Vector2hs = typedef Utils::Vector<hsize_t, 2>

Definition at line 63 of file h5md_core.cpp.

◆ Vector2s

using Writer::H5md::Vector2s = typedef Utils::Vector<std::size_t, 2>

Definition at line 66 of file h5md_core.cpp.

◆ Vector3hs

using Writer::H5md::Vector3hs = typedef Utils::Vector<hsize_t, 3>

Definition at line 64 of file h5md_core.cpp.

◆ Vector3s

using Writer::H5md::Vector3s = typedef Utils::Vector<std::size_t, 3>

Definition at line 67 of file h5md_core.cpp.

Enumeration Type Documentation

◆ H5MDOutputFields

enum Writer::H5md::H5MDOutputFields : unsigned int

Constants which indicate what to output.

To indicate the output of multiple fields, OR the corresponding values.

Enumerator
H5MD_OUT_NONE
H5MD_OUT_TYPE
H5MD_OUT_POS
H5MD_OUT_IMG
H5MD_OUT_VEL
H5MD_OUT_FORCE
H5MD_OUT_MASS
H5MD_OUT_CHARGE
H5MD_OUT_BONDS
H5MD_OUT_BOX_L
H5MD_OUT_LE_OFF
H5MD_OUT_LE_DIR
H5MD_OUT_LE_NORMAL
H5MD_OUT_ALL

Definition at line 55 of file h5md_core.hpp.

Function Documentation

◆ backup_file()

static void Writer::H5md::backup_file	(	std::filesystem::path const &	from,
		std::filesystem::path const &	to
	)

static

Definition at line 96 of file h5md_core.cpp.

◆ create_chunk_dims()

static std::vector< hsize_t > Writer::H5md::create_chunk_dims	(	hsize_t	rank,
		hsize_t	data_dim,
		hsize_t	size
	)

static

Definition at line 229 of file h5md_core.cpp.

◆ create_dims()

static std::vector< std::size_t > Writer::H5md::create_dims	(	hsize_t	rank,
		hsize_t	data_dim
	)

static

Definition at line 206 of file h5md_core.cpp.

◆ create_maxdims()

static std::vector< std::size_t > Writer::H5md::create_maxdims	(	hsize_t	rank,
		hsize_t	data_dim,
		hsize_t	max_dim
	)

static

Definition at line 217 of file h5md_core.cpp.

◆ extend_dataset()

template<typename extent_type >

static void Writer::H5md::extend_dataset	(	HighFive::DataSet &	dataset,
		extent_type const &	change_extent
	)

static

Definition at line 111 of file h5md_core.cpp.

Referenced by write_box(), write_dataset(), write_le_dir(), write_le_normal(), write_le_off(), and write_td_particle_property().

◆ fields_list_to_bitfield()

static auto Writer::H5md::fields_list_to_bitfield ( std::vector< std::string > const & fields )

static

Definition at line 85 of file h5md_core.cpp.

References fields_map, and H5MD_OUT_NONE.

◆ write_attributes()

static void Writer::H5md::write_attributes ( HighFive::File & h5md_file )

static

Definition at line 274 of file h5md_core.cpp.

◆ write_box()

static void Writer::H5md::write_box	(	BoxGeometry const &	box_geo,
		HighFive::DataSet &	dataset
	)

static

Definition at line 506 of file h5md_core.cpp.

References Utils::Vector< T, N >::as_vector(), extend_dataset(), BoxGeometry::length(), and write_dataset().

Referenced by Writer::H5md::File::write().

◆ write_dataset() [1/2]

template<typename value_type , typename extent_type >

static void Writer::H5md::write_dataset	(	value_type const &	data,
		HighFive::DataSet &	dataset,
		extent_type const &	change_extent,
		extent_type const &	offset,
		extent_type const &	count
	)

static

Definition at line 132 of file h5md_core.cpp.

References extend_dataset(), and write_dataset().

◆ write_dataset() [2/2]

template<typename value_type , typename extent_type >

static void Writer::H5md::write_dataset	(	value_type const &	data,
		HighFive::DataSet &	dataset,
		extent_type const &	offset,
		extent_type const &	count
	)

static

Definition at line 123 of file h5md_core.cpp.

Referenced by Writer::H5md::File::write(), write_box(), write_dataset(), write_le_dir(), write_le_normal(), write_le_off(), and write_td_particle_property().

◆ write_le_dir()

static void Writer::H5md::write_le_dir	(	LeesEdwardsBC const &	lebc,
		HighFive::DataSet &	dataset
	)

static

Definition at line 527 of file h5md_core.cpp.

References extend_dataset(), LeesEdwardsBC::shear_direction, and write_dataset().

Referenced by Writer::H5md::File::write().

◆ write_le_normal()

static void Writer::H5md::write_le_normal	(	LeesEdwardsBC const &	lebc,
		HighFive::DataSet &	dataset
	)

static

Definition at line 539 of file h5md_core.cpp.

References extend_dataset(), LeesEdwardsBC::shear_plane_normal, and write_dataset().

Referenced by Writer::H5md::File::write().

◆ write_le_off()

static void Writer::H5md::write_le_off	(	LeesEdwardsBC const &	lebc,
		HighFive::DataSet &	dataset
	)

static

Definition at line 516 of file h5md_core.cpp.

References extend_dataset(), LeesEdwardsBC::pos_offset, and write_dataset().

Referenced by Writer::H5md::File::write().

◆ write_script()

static void Writer::H5md::write_script	(	HighFive::File &	h5md_file,
		std::filesystem::path const &	script_path
	)

static

Definition at line 140 of file h5md_core.cpp.

◆ write_td_particle_property()

template<std::size_t dim, typename Serializer >

void Writer::H5md::write_td_particle_property	(	hsize_t	prefix,
		hsize_t	n_part_global,
		ParticleRange const &	particles,
		HighFive::DataSet &	dataset,
		Serializer	serializer
	)

Definition at line 488 of file h5md_core.cpp.

References extend_dataset(), ParticleRange::size(), and write_dataset().

Variable Documentation

◆ fields_map

std::unordered_map<std::string, H5MDOutputFields> const Writer::H5md::fields_map

static

Initial value:

= {
    {"all", H5MD_OUT_ALL},
    {"particle.type", H5MD_OUT_TYPE},
    {"particle.position", H5MD_OUT_POS},
    {"particle.image", H5MD_OUT_IMG},
    {"particle.velocity", H5MD_OUT_VEL},
    {"particle.force", H5MD_OUT_FORCE},
    {"particle.bonds", H5MD_OUT_BONDS},
    {"particle.charge", H5MD_OUT_CHARGE},
    {"particle.mass", H5MD_OUT_MASS},
    {"box.length", H5MD_OUT_BOX_L},
    {"lees_edwards.offset", H5MD_OUT_LE_OFF},
    {"lees_edwards.direction", H5MD_OUT_LE_DIR},
    {"lees_edwards.normal", H5MD_OUT_LE_NORMAL},
}

Definition at line 69 of file h5md_core.cpp.

Referenced by fields_list_to_bitfield(), and Writer::H5md::File::valid_fields().

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

◆ MultiArray3i

◆ Vector1hs

◆ Vector1s

◆ Vector2hs

◆ Vector2s

◆ Vector3hs

◆ Vector3s

Enumeration Type Documentation

◆ H5MDOutputFields

Function Documentation

◆ backup_file()

◆ create_chunk_dims()

◆ create_dims()

◆ create_maxdims()

◆ extend_dataset()

◆ fields_list_to_bitfield()

◆ write_attributes()

◆ write_box()

◆ write_dataset() [1/2]

◆ write_dataset() [2/2]

◆ write_le_dir()

◆ write_le_normal()

◆ write_le_off()

◆ write_script()

◆ write_td_particle_property()

Variable Documentation

◆ fields_map