#!/bin/bash

#SBATCH --job-name=jorek
#SBATCH --nodes=1
#SBATCH --ntasks=2
#SBATCH --cpus-per-task=24
#SBATCH --time=00:10:00
#SBATCH --partition=gw

export OMP_NUM_THREADS=24

srun /pfs/work/$USER/jorek/jorek_model303 < ./inxflow > logfile.out

#SBATCH --partition=gwdbg

sbatch  submit.sh

squeue -u $USER

  jorek-namelist/
    jorek.git/                  # the source code
    intear_ntor3/               # run directory

cd jorek-namelist/
git clone ssh://git@git.iter.org/stab/jorek.git jorek.git

  cd jorek.git/
  ./util/config.sh model=199 n_tor=3 n_period=1 n_plane=4     # run with toroidal mode numbers n=0,1
  make clean
  make -j 8
  make -j 8 jorek2vtk jorek2_postproc

  cp jorek_model199 jorek2vtk jorek2_postproc namelist/model199/intear ../intear_ntor3
  cd ../intear_ntor3

  tstep = 3000.
  nstep = 0

$ cd jorek/util/nmlist2h5

Requirements:
HDF5 version >= 1.12

To use the provided Makefile, be sure that:
- The HDF5_HOME environment variable is defined in order to find the HDF5 header files
- The HDF5 lib directory is referenced by the LD_LIBRARY_PATH variable, for linking
- BOOST library is available in your system

Compiling:
$ make -f Makefile_namelist

Example:
[nmlist2h5]$ make -f Makefile_namelist
gcc -c -o namelist2h5.o namelist2h5.c
gcc -c -o h5_2_namelist.o h5_2_namelist.c
gcc -c -o h5_utils.o h5_utils.c
gcc -c -o namelist_api.o namelist_api.c
g++ -pthread -Wl,--no-undefined -o namelist_api namelist2h5.o h5_2_namelist.o h5_utils.o namelist_api.o -L/Applications/libraries/hdf5/1.12.0/gcc/6.4.0/lib -lhdf5

Namelist to HDF5 Converter API:
//---------------------------------------------------------------------
int new_simulation(const char* h5_namelist_folder, const char* nml_file_name);
int restart(const char* h5_namelist_folder, const char* nml_file_name, const char* jorek_restart_file_name, const char* time_index);
int write_restart_file (const char* h5_namelist_folder, const char* jorek_restart_file);
int extract_from_h5_namelist (const char* h5_namelist_folder, const char* nml_file, const char* time_index);
int extract_from_jorek_restart_file (const char* h5_namelist_folder, const char* jorek_restart_file_name, const char* nml_file_name, const char* time_index);
//---------------------------------------------------------------------


NEW SIMULATION:

int new_simulation(const char* h5_namelist_folder, const char* nml_file_name);

/** Creates a new HDF5 namelist file from an existing JOREK parameters file in CSV format. Parameters are written in the '00000' HDF5 group which will be created.
* Inputs:
* h5_namelist_folder (string) : directory path in which the new HDF5 namelist file will be created
* nml_file_name (string) : name of the JOREK namelist file in CSV format, the file must be supplied in the 'h5_namelist_folder', an error will occur otherwise.
* Returns:
* 0 if the operation is successfull or a code status < 0 otherwise.
**/


RESTART:

int restart(const char* h5_namelist_folder, const char* nml_file_name, const char* jorek_restart_file_name, const char* time_index);

/** If the HDF5 namelist file already exists in the folder specified by 'h5_namelist_folder', 'restart' will update this file from the specified JOREK restart file 'jorek_restart_file_name':
* - all HDF5 groups YYYYY >= time_index=XXXXX are removed from the HDF5 namelist file
* - the parameters from the file 'nml_file_name' (in CSV format) are added to the HDF5 namelist file in the HDF5 group XXXXX
* If the HDF5 namelist does not exist in the folder specified by 'h5_namelist_folder', 'restart' will create a new HDF5 namelist file in the folder 'h5_namelist_folder':
* - all parameters of the JOREK restart file specified by 'jorek_restart_file_name' are added to the HDF5 namelist file
* - the parameters located in the file 'nml_file_name' (in CSV format) are added to the HDF5 namelist file in the HDF5 group time_index=XXXXX
* Inputs:
* h5_namelist_folder (string) : directory path in which the HDF5 file is located. If the file does not exist, it will be created in this directory.
* nml_file_name (string) : name of the JOREK parameters file in CSV format, the file must be supplied in the 'h5_namelist_folder', an error will occur otherwise.
* jorek_restart_file_name (string) : name of the JOREK restart file in HDF5 format, the file must be supplied in the 'h5_namelist_folder' if the HDF5 namelist file does not exist, an error will occur otherwise.
* time_index (string) : name of the HDF5 group of the HDF5 namelist file where the namelist parameters from the file 'nml_file_name' will be added
* Returns:
* 0 if the operation is successfull or a code status < 0 otherwise.
**/


WRITE RESTART FILE:

/** Creates a new HDF5 JOREK restart file. All parameters from the existing HDF5 namelist file are written in the 'namelist' HDF5 group.
* If the HDF5 namelist file does not exist in the specified 'h5_namelist_folder' directory, an error will occur.
* Inputs:
* h5_namelist_folder (string) : directory path in which the new HDF5 JOREK restart file will be created
* jorek_restart_file_name (string) : name of the JOREK restart file in HDF5 format
* Returns:
* 0 if the operation is successfull or a code status < 0 otherwise.
**/

EXTRACT FROM H5 NAMELIST:

/** Creates a new namelist parameters file in CSV format. All parameters from the supplied HDF5 namelist file are extracted from the HDF5 group 'time_index' and copied to the CSV namelist parameters file.
* Inputs:
* h5_namelist_folder (string) : directory path in which the CSV namelist file will be created. This directory should contain the supplied HDF5 namelist file, an error will occur otherwise.
* nml_file_name (string) : name of the CSV namelist file to be created
* time_index (string) : time index with format 'XXXXX'
* Returns:
* 0 if the operation is successfull or a code status < 0 otherwise.
**/

EXTRACT FROM JOREK RESTART FILE:

/** Creates a new namelist parameters file in CSV format. All parameters from the existing JOREK HDF5 restart file are extracted from the HDF5 group 'namelist/time_index' and copied to the CSV namelist file.
* Inputs:
* h5_namelist_folder (string) : directory path in which the CSV namelist file will be created. This directory should contain the supplied HDF5 namelist file, an error will occur otherwise.
* jorek_restart_file_name (string) : name of the JOREK restart file
* nml_file_name (string) : name of the CSV namelist file to be created
* time_index (string) : time index with format 'XXXXX'
* Returns:
* 0 if the operation is successfull or a code status < 0 otherwise.
**/

NEW SIMULATION

./namelist_api new_simulation /Home/LF218007/jorek out711.nml
analysing file, 13453 line(s) found with identifier, (n_line=15864)
File analysis ended.
Number of identifiers=13453.
Number of parameters=301.
HDF5 dataset for parameter GRID_TO_WALL already previously defined, ignoring new definition
HDF5 dataset for parameter FIX_AXIS_NODES already previously defined, ignoring new definition


Checking the file with h5dump:

h5dump namelist.h5 |less

HDF5 "namelist.h5" {
GROUP "/" {
GROUP "00000" {
DATASET "ADAPTIVE_TIME" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
DATA {
(0): "F
"
}
}
DATASET "AKI_NEO_CONST" {
…


RESTART

./namelist_api restart /Home/LF218007/jorek out711.nml jorek_restart.h5 00001
copying time index: 00001...
analysing file, 13453 line(s) found with identifier, (n_line=15864)
File analysis ended.
Number of identifiers=13453.
Number of parameters=301.
HDF5 dataset for parameter GRID_TO_WALL already previously defined, ignoring new definition
HDF5 dataset for parameter FIX_AXIS_NODES already previously defined, ignoring new definition

Checking the file with h5ls:

$ h5ls namelist.h5
00000 Group
00001 Group


WRITE RESTART FILE:

./namelist_api write_restart_file /Home/LF218007/jorek/jorek_repo/jorek/util jorek_restart.h5


Checking the file with h5ls:

h5ls -r jorek_restart.h5

/ Group
/namelist Group
/namelist/00000 Group
/namelist/00000/ADAPTIVE_TIME Dataset {SCALAR}
/namelist/00000/AKI_NEO_CONST Dataset {SCALAR}
/namelist/00000/AMIN Dataset {SCALAR}
/namelist/00000/AMIX Dataset {SCALAR}
...
/namelist/00001 Group
/namelist/00001/ADAPTIVE_TIME Dataset {SCALAR}
/namelist/00001/AKI_NEO_CONST Dataset {SCALAR}
/namelist/00001/AMIN Dataset {SCALAR}
/namelist/00001/AMIX Dataset {SCALAR}
...
/namelist/00001/Z_LIMITER Dataset {1000/Inf}


EXTRACT FROM H5 NAMELIST:

./namelist_api extract_from_h5_namelist /Home/LF218007/jorek test.nml 00001
found group 00001
matched group 00001
Converting HDF5 file /Home/LF218007/jorek/jorek_repo/jorek/util/namelist.h5 ...


more test.nml

&IN1
ADAPTIVE_TIME = F
,
AKI_NEO_CONST = 0.000000e+00,
AMIN = 1.000000e+00,
AMIX = 0.000000e+00,
AMIX_FREEB = 8.500000e-01,
AMU_NEO_CONST = 0.000000e+00,
AUTODISTRIBUTE_MODES = T
,
…


EXTRACT FROM JOREK RESTART FILE:

./namelist_api extract_from_jorek_restart_file /Home/LF218007/jorek jorek_restart.h5 test2.nml 00001
found group 00001
matched group 00001
Converting HDF5 file /Home/LF218007/jorek/jorek_repo/jorek/util/jorek_restart.h5 ...


more test2.nml

&IN1
ADAPTIVE_TIME = F
,
AKI_NEO_CONST = 0.000000e+00,
AMIN = 1.000000e+00,
AMIX = 0.000000e+00,
AMIX_FREEB = 8.500000e-01,
AMU_NEO_CONST = 0.000000e+00,
AUTODISTRIBUTE_MODES = T
,
…