hdf5_interface.c File Reference

HDF5 operations are accessed through here. More...

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <hdf5.h>
#include <hdf5_hl.h>
#include "ascot5.h"
#include "simulate.h"
#include "print.h"
#include "gitver.h"
#include "compiler_flags.h"
#include "hdf5_interface.h"
#include "hdf5io/hdf5_helpers.h"
#include "hdf5io/hdf5_options.h"
#include "hdf5io/hdf5_bfield.h"
#include "hdf5io/hdf5_plasma.h"
#include "hdf5io/hdf5_neutral.h"
#include "hdf5io/hdf5_efield.h"
#include "hdf5io/hdf5_wall.h"
#include "hdf5io/hdf5_boozer.h"
#include "hdf5io/hdf5_mhd.h"
#include "hdf5io/hdf5_marker.h"
#include "hdf5io/hdf5_state.h"
#include "hdf5io/hdf5_dist.h"
#include "hdf5io/hdf5_orbit.h"
#include "hdf5io/hdf5_transcoef.h"
#include "hdf5io/hdf5_asigma.h"
#include "hdf5io/hdf5_nbi.h"

Go to the source code of this file.

Functions
int	hdf5_get_active_qid (hid_t f, const char *group, char qid[11])
	Fetch active qid within the given group.
int	hdf5_interface_read_input (sim_offload_data *sim, int input_active, real **B_offload_array, real **E_offload_array, real **plasma_offload_array, real **neutral_offload_array, real **wall_offload_array, int **wall_int_offload_array, real **boozer_offload_array, real **mhd_offload_array, real **asigma_offload_array, real **nbi_offload_array, input_particle **p, int *n_markers)
	Read and initialize input data.
int	hdf5_interface_init_results (sim_offload_data *sim, char *qid, char *run)
	Initialize run group.
int	hdf5_interface_write_state (char *fn, char *state, integer n, particle_state *p)
	Write marker state to HDF5 output.
int	hdf5_interface_write_diagnostics (sim_offload_data *sim, real *diag_offload_array, char *out)
	Write diagnostics to HDF5 output.
void	hdf5_generate_qid (char *qid)
	Generate an identification number for a run.

Detailed Description

HDF5 operations are accessed through here.

This module handles IO operations to HDF5 file. Accessing HDF5 files from the main program should be done using this module.

Definition in file hdf5_interface.c.

Function Documentation

hdf5_get_active_qid()

int hdf5_get_active_qid	(	hid_t	f,
		const char *	group,
		char	qid[11] )

Fetch active qid within the given group.

Each input group (/bfield/, /options/, etc.) has qid string indicating which of the subgroups is active, i.e., meant to be used within this simulation.

This function fetches the active qid assuming the file is opened and closed outside of this function.

Parameters

f	HDF5 file identifier
group	group string including the "/"s on both sides e.g. /bfield/
qid	array where qid will be stored

Returns

Zero on success

Definition at line 712 of file hdf5_interface.c.

hdf5_interface_read_input()

int hdf5_interface_read_input	(	sim_offload_data *	sim,
		int	input_active,
		real **	B_offload_array,
		real **	E_offload_array,
		real **	plasma_offload_array,
		real **	neutral_offload_array,
		real **	wall_offload_array,
		int **	wall_int_offload_array,
		real **	boozer_offload_array,
		real **	mhd_offload_array,
		real **	asigma_offload_array,
		real **	nbi_offload_array,
		input_particle **	p,
		int *	n_markers )

Read and initialize input data.

This function reads input from HDF5 file, initializes it, and allocates offload arrays and returns the pointers to them.

Parameters

sim	pointer to simulation offload struct
input_active	bitflags for input types to read
B_offload_array	pointer to magnetic field offload array
E_offload_array	pointer to electric field offload array
plasma_offload_array	pointer to plasma data offload array
neutral_offload_array	pointer to neutral data offload array
wall_offload_array	pointer to wall offload array
wall_int_offload_array	pointer to wall integer offload array
boozer_offload_array	pointer to boozer offload array
mhd_offload_array	pointer to mhd offload array
asigma_offload_array	pointer to atomic offload array
nbi_offload_array	pointer to neutral beam injector data offload array
p	pointer to marker offload data
n_markers	pointer to integer notating how many markers were read

Returns

zero if reading and initialization succeeded

Definition at line 62 of file hdf5_interface.c.

hdf5_interface_init_results()

int hdf5_interface_init_results	(	sim_offload_data *	sim,
		char *	qid,
		char *	run )

Initialize run group.

This functions creates results group (if one does not already exist) and creates run group corresponding to this run. Run group is named as /results/<run>_XXXXXXXXXX/ where X's are the qid of current run and <run> is the type of the run: "run" for ascot5_main and "bbnbi" for bbnbi5.

The group is initialized by writing qids of all used inputs as string attributes in the run group. Also the date and empty "details" fields are written.

Parameters

sim	pointer to simulation offload struct
qid	qid of this run
run	type of this run

Returns

Zero if initialization succeeded

Definition at line 374 of file hdf5_interface.c.

hdf5_interface_write_state()

int hdf5_interface_write_state	(	char *	fn,
		char *	state,
		integer	n,
		particle_state *	p )

Write marker state to HDF5 output.

Parameters

fn	HDF5 output filename
state	name of the state to be written
n	number of markers in marker array
p	array of markers to be written

Returns

Zero if state was written succesfully

Definition at line 517 of file hdf5_interface.c.

hdf5_interface_write_diagnostics()

int hdf5_interface_write_diagnostics	(	sim_offload_data *	sim,
		real *	diag_offload_array,
		char *	out )

Write diagnostics to HDF5 output.

Parameters

sim	pointer to simulation offload data
diag_offload_array	diagnostics offload array
out	HDF5 output filename

Returns

Zero if diagnostics were written succesfully

Definition at line 577 of file hdf5_interface.c.

hdf5_generate_qid()

void hdf5_generate_qid

(

char *

qid

)

Generate an identification number for a run.

The identification number (QID) is a 32 bit unsigned integer represented in a string format, i.e., by ten characters. QID is a random integer between 0 and 4 294 967 295, and it is padded with leading zeroes in string representation.

Parameters

qid	a pointer to 11 chars wide array where generated QID is stored

Definition at line 730 of file hdf5_interface.c.