dg::file Namespace Reference

Namespace for Json and NetCDF I/O related classes and functions. More...

Classes
struct	LongNameAttribute
	Facilitate construction of CF attribute "long_name" in records lists. More...
struct	MPINcFile
	MPI NetCDF-4 file based on serial NetCDF. More...
struct	MPINcHyperslab
	A NetCDF Hyperslab for MPINcFile. More...
struct	NC_Error
	Class thrown by the NC_Error_Handle. More...
struct	NC_Error_Handle
	DEPRECATED Empty utitlity class that handles return values of netcdf functions and throws NC_Error(status) if( status != NC_NOERR) More...
struct	NcHyperslab
	A NetCDF Hyperslab for SerialNcFile. More...
struct	Probes
	Facilitate output at selected points. More...
struct	ProbesParams
	Parameter struct for probe values. More...
struct	Record
	A realisation of the Record concept. Helper to generate NetCDF variables. More...
struct	SerialNcFile
	Serial NetCDF-4 file. More...
struct	WrappedJsonValue
	Wrapped Access to Json values with error handling. More...

Typedefs
using	nc_att_t
	Utility type to simplify dealing with heterogeneous attribute types.
using	JsonType = Json::Value
	Json Type to use in dg::file functions and classes.
using	NcFile = MPINcFile
template<class Signature >
using	get_first_argument_type_t = std::decay_t<typename detail::get_first_argument_type<Signature>::type>
template<class Signature >
using	get_result_type_t = typename std::function<Signature>::result_type

Enumerations
enum class	error { error::is_throw , error::is_warning , error::is_silent }
	Switch between how to handle errors in a Json utitlity functions. More...
enum class	comments { comments::are_kept , comments::are_discarded , comments::are_forbidden }
	Switch how comments are treated in a json string or file. More...
enum	NcFileMode { nc_nowrite , nc_write , nc_clobber , nc_noclobber }
	NetCDF file format. More...

Functions
std::string	timestamp (int argc, char *argv[])
	Generate one line entry for the history global attribute.
template<class T >
bool	check_real_time (int ncid, const char *name, int *dimID, int *tvarID)
	DEPRECATED Check if an unlimited dimension exists as if define_real_time was called.
template<class T >
int	define_real_time (int ncid, const char *name, int *dimID, int *tvarID, bool full_check=false)
	DEPRECATED Define an unlimited time dimension and coordinate variable.
int	define_time (int ncid, const char *name, int *dimID, int *tvarID)
	DEPRECATED An alias for define_real_time<double>
int	define_limited_time (int ncid, const char *name, int size, int *dimID, int *tvarID)
	DEPRECATED Define a limited time dimension and coordinate variable.
template<class T >
bool	check_dimension (int ncid, int *dimID, const dg::RealGrid1d< T > &g, std::string name_dim="x", std::string axis="X")
	DEPRECATED Check if a dimension exists as if define_dimension was called.
template<class T >
int	define_dimension (int ncid, int *dimID, const dg::RealGrid1d< T > &g, std::string name_dim="x", std::string axis="X", bool full_check=false)
	DEPRECATED Define a 1d dimension and associated coordinate variable.
template<class Topology , std::enable_if_t< dg::is_vector_v< typename Topology::host_vector, dg::SharedVectorTag >, bool > = true>
int	define_dimensions (int ncid, int *dimsIDs, const Topology &g, std::vector< std::string > name_dims={}, bool full_check=false)
	DEPRECATED Define dimensions and associated coordiante variables.
template<class Topology , std::enable_if_t< dg::is_vector_v< typename Topology::host_vector, dg::SharedVectorTag >, bool > = true>
int	define_dimensions (int ncid, int *dimsIDs, int *tvarID, const Topology &g, std::vector< std::string > name_dims={}, bool full_check=false)
	DEPRECATED Define an unlimited time and grid dimensions together with their coordinate variables.
template<class Topology , std::enable_if_t< dg::is_vector_v< typename Topology::host_vector, dg::SharedVectorTag >, bool > = true>
bool	check_dimensions (int ncid, int *dimsIDs, const Topology &g, std::vector< std::string > name_dims={})
	DEPRECATED Check if dimensions exist as if define_dimensions was called.
template<class Topology , std::enable_if_t< dg::is_vector_v< typename Topology::host_vector, dg::SharedVectorTag >, bool > = true>
bool	check_dimensions (int ncid, int *dimsIDs, int *tvarID, const Topology &g, std::vector< std::string > name_dims={})
	DEPRECATED Check if dimensions exist as if define_dimensions was called.
template<class T >
int	define_limtime_xy (int ncid, int *dimsIDs, int size, int *tvarID, const dg::aRealTopology2d< T > &g, std::vector< std::string > name_dims={"time", "y", "x"})
	DEPRECATED Define a limited time and 2 dimensions and associated coordinate variables.
template<class MPITopology , std::enable_if_t< dg::is_vector_v< typename MPITopology::host_vector, dg::MPIVectorTag >, bool > = true>
int	define_dimensions (int ncid, int *dimsIDs, const MPITopology &g, std::vector< std::string > name_dims={}, bool full_check=false)
	DEPRECATED All processes may call this but only master process has to and will execute!! Convenience function that just calls the corresponding serial version with the global grid.
template<class MPITopology , std::enable_if_t< dg::is_vector_v< typename MPITopology::host_vector, dg::MPIVectorTag >, bool > = true>
int	define_dimensions (int ncid, int *dimsIDs, int *tvarID, const MPITopology &g, std::vector< std::string > name_dims={}, bool full_check=false)
	DEPRECATED All processes may call this but only master process has to and will execute!! Convenience function that just calls the corresponding serial version with the global grid.
template<class MPITopology , std::enable_if_t< dg::is_vector_v< typename MPITopology::host_vector, dg::MPIVectorTag >, bool > = true>
bool	check_dimensions (int ncid, int *dimsIDs, const MPITopology &g, std::vector< std::string > name_dims={})
	DEPRECATED All processes may call this and all will execute!! Convenience function that just calls the corresponding serial version with the global grid.
template<class MPITopology , std::enable_if_t< dg::is_vector_v< typename MPITopology::host_vector, dg::MPIVectorTag >, bool > = true>
bool	check_dimensions (int ncid, int *dimsIDs, int *tvarID, const MPITopology &g, std::vector< std::string > name_dims={})
	DEPRECATED All processes may call this and all will execute!! Convenience function that just calls the corresponding serial version with the global grid.
template<class host_vector , class Topology >
void	get_var (int ncid, int varid, const Topology &grid, host_vector &data, bool parallel=true)
	DEPRECATED Convenience wrapper around nc_get_var.
template<class host_vector , class Topology >
void	get_vara (int ncid, int varid, unsigned slice, const Topology &grid, host_vector &data, bool parallel=true)
	DEPRECATED Convenience wrapper around nc_get_vara()
template<class T , class real_type >
void	get_var (int ncid, int varid, const RealGrid0d< real_type > &grid, T &data, bool parallel=true)
	DEPRECATED Read a scalar from the netcdf file.
template<class T , class real_type >
void	get_vara (int ncid, int varid, unsigned slice, const RealGrid0d< real_type > &grid, T &data, bool parallel=true)
	DEPRECATED Read a scalar to the netcdf file.
template<class host_vector , class Topology >
void	put_var (int ncid, int varid, const Topology &grid, const host_vector &data, bool parallel=false)
	DEPRECATED Write an array to NetCDF file.
template<class host_vector , class Topology >
void	put_vara (int ncid, int varid, unsigned slice, const Topology &grid, const host_vector &data, bool parallel=false)
	DEPRECATED Write an array to NetCDF file.
template<class T , class real_type >
void	put_var (int ncid, int varid, const RealGrid0d< real_type > &grid, T data, bool parallel=false)
	DEPRECATED Write a scalar to the NetCDF file.
template<class T , class real_type >
void	put_vara (int ncid, int varid, unsigned slice, const RealGrid0d< real_type > &grid, T data, bool parallel=false)
	DEPRECATED Write a scalar to the NetCDF file.
ProbesParams	parse_probes (const dg::file::WrappedJsonValue &js, enum error probes_err=file::error::is_silent)
	Parse probe field in json file for use with Probes class.
JsonType	file2Json (std::string filename, enum comments comm=file::comments::are_discarded, enum error err=file::error::is_throw)
	Convenience wrapper to open a file and parse it into a JsonType.
void	file2Json (std::string filename, JsonType &js, enum comments comm=file::comments::are_discarded, enum error err=file::error::is_throw)
	Same as js = dg::file::file2Json( filename, comm, err)
JsonType	string2Json (std::string input, enum comments comm=file::comments::are_discarded, enum error err=file::error::is_throw)
	Convenience wrapper to parse a string into a JsonType.
void	string2Json (std::string input, JsonType &js, enum comments comm=file::comments::are_discarded, enum error err=file::error::is_throw)
	Same as js = string2Json( input, comm, err)
template<class ContainerType >
dg::file::JsonType	vec2json (const ContainerType &shared)
	convert a vector to a json arrray
template<class T >
dg::file::JsonType	vec2json (std::initializer_list< T > shared)
	Specialization for intitializer list.

Variables
const std::map< std::string, std::string >	version_flags
	Version compile time constants available as a map.

Detailed Description

Namespace for Json and NetCDF I/O related classes and functions.

The NetCDF files follow the CF-conventions and netCDF conventions

See also

Convert to Json and Utilities for the NcFile class