hdf_common.hpp File Reference

Common functionality for writing VTK HDF files.

#include <vector>
#include <cstddef>
#include <numeric>
#include <string>
#include <optional>
#include <ranges>
#include <array>
#include <gridformat/common/hdf5.hpp>
#include <gridformat/common/field.hpp>
#include <gridformat/common/precision.hpp>
#include <gridformat/common/lazy_field.hpp>
#include <gridformat/common/range_field.hpp>
#include <gridformat/common/field_transformations.hpp>
#include <gridformat/common/multi_string.hpp>
#include <gridformat/common/string_conversion.hpp>
#include <gridformat/common/exceptions.hpp>
#include <gridformat/parallel/communication.hpp>
#include <gridformat/parallel/helpers.hpp>

Go to the source code of this file.

Classes
struct	GridFormat::VTK::HDFTransientOptions
	Options for transient vtk-hdf file formats. More...
struct	GridFormat::VTKHDF::IOContext
	Helper class to store processor offsets in parallel writes. More...
class	GridFormat::VTKHDF::DataSetField< C >
	Field implementation that draws values from an open HDF5 file upon request. More...

Functions
void	GridFormat::VTKHDF::check_array_name (const std::string &name)
	Throw if the given name cannot be used as a vtk-hdf array name.
bool	GridFormat::VTKHDF::is_string_field (const Field &field)
	Return true if the given field holds strings (i.e. is a flat array of characters, see MultiString).
std::vector< std::string >	GridFormat::VTKHDF::extract_strings (const Field &field)
	Return the strings stored in the given character field (see MultiString).
template<typename C>
	GridFormat::VTKHDF::DataSetField (const HDF5::File< C > &, std::string) -> DataSetField< C >
template<typename C, typename CB>
	GridFormat::VTKHDF::DataSetField (const HDF5::File< C > &, MDLayout, DynamicPrecision, CB &&) -> DataSetField< C >
template<typename C>
std::string	GridFormat::VTKHDF::get_file_type (const HDF5::File< C > &file)
	Read the vtk-hdf file type from an hdf5 file.
template<typename C>
void	GridFormat::VTKHDF::check_version_compatibility (const HDF5::File< C > &file, const std::array< std::size_t, 2 > &supported)
FieldPtr	GridFormat::VTKHDF::as_field_data_tuples (FieldPtr field)
	Return the given field data in the shape of tuples, i.e. (tuples) or (tuples, components).
void	GridFormat::VTKHDF::write_field_data (HDF5::File<> &file, const std::string &name, FieldPtr field)
	Write a field data array into a file that is not transient.
void	GridFormat::VTKHDF::write_field_data_step (HDF5::File<> &file, const std::string &name, FieldPtr field)
	Append a time step to a field data array of a transient file.
void	GridFormat::VTKHDF::write_field_data_step_referencing (std::size_t step_index, HDF5::File<> &file, const std::string &name)
	Append a time step to a field data array of a transient file, referring to the data of an earlier step.
template<typename C>
FieldPtr	GridFormat::VTKHDF::read_field_data (const HDF5::File< C > &file, const std::string &name, std::optional< std::size_t > step)
	Read the field data array with the given name, at the given step for transient files.
template<Concepts::Communicator C, std::invocable< HDF5::File<> & > Write>
void	GridFormat::VTKHDF::write_on_root (const std::string &filename, const C &comm, int root, Write &&write)
	Open the given file with the default (non-MPI) driver on the root rank and pass it to write.

Function Documentation

check_version_compatibility()

template<typename C>

void GridFormat::VTKHDF::check_version_compatibility	(	const HDF5::File< C > &	file,
		const std::array< std::size_t, 2 > &	supported )

Check that the version stated in the file is supported

Note

Only the major version is checked, since the specification guarantees that files can be read correctly by implementations for a different minor version of the same major.

write_field_data_step()

void GridFormat::VTKHDF::write_field_data_step ( HDF5::File<> & file, const std::string & name, FieldPtr field )

inline

Uses the layout written by VTK: the tuples of all steps are concatenated, and the offset (in tuples) and the sizes (number of components and tuples) of each step are stored in the "Steps" group. Strings are stored as one tuple per string.

write_on_root()

template<Concepts::Communicator C, std::invocable< HDF5::File<> & > Write>

void GridFormat::VTKHDF::write_on_root	(	const std::string &	filename,
		const C &	comm,
		int	root,
		Write &&	write )

Must be called collectively once all ranks have closed the file. If write throws, the exception is rethrown on the root rank, and an IOError is thrown on all other ranks.