Writer::H5md Namespace Reference

Classes
class	File
	Class for writing H5MD files. More...
struct	H5MD_Specification
	Layout information for H5MD files. More...
struct	incompatible_h5mdfile
struct	left_backupfile

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 >

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 void	backup_file (const std::string &from, const std::string &to)
template<typename extent_type >
static void	extend_dataset (h5xx::dataset &dataset, extent_type const &change_extent)
template<typename value_type , typename extent_type >
static void	write_dataset (value_type const &data, h5xx::dataset &dataset, extent_type const &change_extent, extent_type const &offset, extent_type const &count)
static void	write_script (std::string const &target, boost::filesystem::path const &script_path)
static std::vector< hsize_t >	create_dims (hsize_t rank, hsize_t data_dim)
static std::vector< hsize_t >	create_chunk_dims (hsize_t rank, hsize_t data_dim)
static void	write_attributes (h5xx::file &h5md_file)
template<std::size_t dim, typename Op >
void	write_td_particle_property (hsize_t prefix, hsize_t n_part_global, ParticleRange const &particles, h5xx::dataset &dataset, Op op)
static void	write_box (BoxGeometry const &box_geo, h5xx::dataset &dataset)
static void	write_le_off (LeesEdwardsBC const &lebc, h5xx::dataset &dataset)
static void	write_le_dir (LeesEdwardsBC const &lebc, h5xx::dataset &dataset)
static void	write_le_normal (LeesEdwardsBC const &lebc, h5xx::dataset &dataset)
auto	fields_list_to_bitfield (std::vector< std::string > const &fields)

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 49 of file h5md_core.cpp.

Vector1hs

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

Definition at line 50 of file h5md_core.cpp.

Vector2hs

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

Definition at line 51 of file h5md_core.cpp.

Vector3hs

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

Definition at line 52 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 56 of file h5md_core.hpp.

Function Documentation

backup_file()

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

static

Definition at line 54 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  )

static

Definition at line 166 of file h5md_core.cpp.

create_dims()

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

static

Definition at line 152 of file h5md_core.cpp.

extend_dataset()

template<typename extent_type >

static void Writer::H5md::extend_dataset ( h5xx::dataset &  dataset, extent_type const &  change_extent  )

static

Definition at line 69 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()

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

inline

Definition at line 89 of file h5md_core.hpp.

References fields_map, and H5MD_OUT_NONE.

write_attributes()

static void Writer::H5md::write_attributes ( h5xx::file &  h5md_file )

static

Definition at line 200 of file h5md_core.cpp.

write_box()

static void Writer::H5md::write_box ( BoxGeometry const &  box_geo, h5xx::dataset &  dataset  )

static

Definition at line 326 of file h5md_core.cpp.

References extend_dataset(), and BoxGeometry::length().

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

write_dataset()

template<typename value_type , typename extent_type >

static void Writer::H5md::write_dataset ( value_type const &  data, h5xx::dataset &  dataset, extent_type const &  change_extent, extent_type const &  offset, extent_type const &  count  )

static

Definition at line 81 of file h5md_core.cpp.

References extend_dataset().

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

write_le_dir()

static void Writer::H5md::write_le_dir ( LeesEdwardsBC const &  lebc, h5xx::dataset &  dataset  )

static

Definition at line 340 of file h5md_core.cpp.

References extend_dataset(), and LeesEdwardsBC::shear_direction.

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

write_le_normal()

static void Writer::H5md::write_le_normal ( LeesEdwardsBC const &  lebc, h5xx::dataset &  dataset  )

static

Definition at line 348 of file h5md_core.cpp.

References extend_dataset(), and LeesEdwardsBC::shear_plane_normal.

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

write_le_off()

static void Writer::H5md::write_le_off ( LeesEdwardsBC const &  lebc, h5xx::dataset &  dataset  )

static

Definition at line 333 of file h5md_core.cpp.

References extend_dataset(), and LeesEdwardsBC::pos_offset.

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

write_script()

static void Writer::H5md::write_script ( std::string const &  target, boost::filesystem::path const &  script_path  )

static

Definition at line 89 of file h5md_core.cpp.

write_td_particle_property()

template<std::size_t dim, typename Op >

void Writer::H5md::write_td_particle_property	(	hsize_t	prefix,
		hsize_t	n_part_global,
		ParticleRange const &	particles,
		h5xx::dataset &	dataset,
		Op	op
	)

Definition at line 309 of file h5md_core.cpp.

References extend_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 73 of file h5md_core.hpp.

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