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$ 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 |
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API
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Namelist to HDF5 Converter API: |
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//--------------------------------------------------------------------- |
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int new_simulation(const char* h5_namelist_folder, const char* nml_file_name); |
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int restart(const char* h5_namelist_folder, const char* nml_file_name, const char* jorek_restart_file_name, const char* time_index); |
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int write_restart_file (const char* h5_namelist_folder, const char* jorek_restart_file); |
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int extract_from_h5_namelist (const char* h5_namelist_folder, const char* nml_file, const char* time_index); |
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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); |
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//--------------------------------------------------------------------- |
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NEW SIMULATION: |
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int new_simulation(const char* h5_namelist_folder, const char* nml_file_name); |
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/** 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. |
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* Inputs: |
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* h5_namelist_folder (string) : directory path in which the new HDF5 namelist file will be created |
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* 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. |
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* Returns: |
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* 0 if the operation is successfull or a code status < 0 otherwise. |
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**/ |
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RESTART: |
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int restart(const char* h5_namelist_folder, const char* nml_file_name, const char* jorek_restart_file_name, const char* time_index); |
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/** 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': |
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* - all HDF5 groups YYYYY >= time_index=XXXXX are removed from the HDF5 namelist file |
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* - the parameters from the file 'nml_file_name' (in CSV format) are added to the HDF5 namelist file in the HDF5 group XXXXX |
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* 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': |
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* - all parameters of the JOREK restart file specified by 'jorek_restart_file_name' are added to the HDF5 namelist file |
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* - 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 |
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* Inputs: |
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* 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. |
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* 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. |
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* 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. |
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* 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 |
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* Returns: |
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* 0 if the operation is successfull or a code status < 0 otherwise. |
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**/ |
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WRITE RESTART FILE: |
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/** Creates a new HDF5 JOREK restart file. All parameters from the existing HDF5 namelist file are written in the 'namelist' HDF5 group. |
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* If the HDF5 namelist file does not exist in the specified 'h5_namelist_folder' directory, an error will occur. |
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* Inputs: |
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* h5_namelist_folder (string) : directory path in which the new HDF5 JOREK restart file will be created |
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* jorek_restart_file_name (string) : name of the JOREK restart file in HDF5 format |
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* Returns: |
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* 0 if the operation is successfull or a code status < 0 otherwise. |
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**/ |
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EXTRACT FROM H5 NAMELIST: |
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/** 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. |
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* Inputs: |
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* 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. |
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* nml_file_name (string) : name of the CSV namelist file to be created |
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* time_index (string) : time index with format 'XXXXX' |
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* Returns: |
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* 0 if the operation is successfull or a code status < 0 otherwise. |
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**/ |
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EXTRACT FROM JOREK RESTART FILE: |
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/** 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. |
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* Inputs: |
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* 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. |
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* jorek_restart_file_name (string) : name of the JOREK restart file |
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* nml_file_name (string) : name of the CSV namelist file to be created |
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* time_index (string) : time index with format 'XXXXX' |
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* Returns: |
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* 0 if the operation is successfull or a code status < 0 otherwise. |
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**/ |
1. EXAMPLES
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NEW SIMULATION |
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./namelist_api new_simulation /Home/LF218007/jorek out711.nml |
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analysing file, 13453 line(s) found with identifier, (n_line=15864) |
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File analysis ended. |
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Number of identifiers=13453. |
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Number of parameters=301. |
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HDF5 dataset for parameter GRID_TO_WALL already previously defined, ignoring new definition |
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HDF5 dataset for parameter FIX_AXIS_NODES already previously defined, ignoring new definition |
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Checking the file with h5dump: |
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h5dump namelist.h5 |less |
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HDF5 "namelist.h5" { |
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GROUP "/" { |
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GROUP "00000" { |
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DATASET "ADAPTIVE_TIME" { |
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DATATYPE H5T_STRING { |
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STRSIZE H5T_VARIABLE; |
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STRPAD H5T_STR_NULLTERM; |
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CSET H5T_CSET_ASCII; |
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CTYPE H5T_C_S1; |
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} |
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DATASPACE SCALAR |
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DATA { |
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(0): "F |
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" |
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} |
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} |
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DATASET "AKI_NEO_CONST" { |
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… |
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RESTART ./namelist_api restart /Home/LF218007/jorek out711.nml jorek_restart.h5 00001 |
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copying time index: 00001... |
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analysing file, 13453 line(s) found with identifier, (n_line=15864) |
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File analysis ended. |
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Number of identifiers=13453. |
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Number of parameters=301. |
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HDF5 dataset for parameter GRID_TO_WALL already previously defined, ignoring new definition |
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HDF5 dataset for parameter FIX_AXIS_NODES already previously defined, ignoring new definition |
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Checking the file with h5ls: |
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$ h5ls namelist.h5 |
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00000 Group |
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00001 Group |
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WRITE RESTART FILE: |
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./namelist_api write_restart_file /Home/LF218007/jorek/jorek_repo/jorek/util jorek_restart.h5 |
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Checking the file with h5ls: |
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h5ls -r jorek_restart.h5 |
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/ Group |
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/namelist Group |
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/namelist/00000 Group |
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/namelist/00000/ADAPTIVE_TIME Dataset {SCALAR} |
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/namelist/00000/AKI_NEO_CONST Dataset {SCALAR} |
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/namelist/00000/AMIN Dataset {SCALAR} |
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/namelist/00000/AMIX Dataset {SCALAR} |
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... |
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/namelist/00001 Group |
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/namelist/00001/ADAPTIVE_TIME Dataset {SCALAR} |
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/namelist/00001/AKI_NEO_CONST Dataset {SCALAR} |
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/namelist/00001/AMIN Dataset {SCALAR} |
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/namelist/00001/AMIX Dataset {SCALAR} |
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/namelist/00001/Z_LIMITER Dataset {1000/Inf} |
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EXTRACT FROM H5 NAMELIST: |
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./namelist_api extract_from_h5_namelist /Home/LF218007/jorek test.nml 00001 |
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found group 00001 |
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matched group 00001 |
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Converting HDF5 file /Home/LF218007/jorek/jorek_repo/jorek/util/namelist.h5 ... |
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more test.nml |
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&IN1 |
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ADAPTIVE_TIME = F |
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, |
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AKI_NEO_CONST = 0.000000e+00, |
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AMIN = 1.000000e+00, |
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AMIX = 0.000000e+00, |
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AMIX_FREEB = 8.500000e-01, |
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AMU_NEO_CONST = 0.000000e+00, |
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AUTODISTRIBUTE_MODES = T |
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, |
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… |
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EXTRACT FROM JOREK RESTART FILE: |
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./namelist_api extract_from_jorek_restart_file /Home/LF218007/jorek jorek_restart.h5 test2.nml 00001 |
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found group 00001 |
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matched group 00001 |
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Converting HDF5 file /Home/LF218007/jorek/jorek_repo/jorek/util/jorek_restart.h5 ... |
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more test2.nml |
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&IN1 |
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ADAPTIVE_TIME = F |
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, |
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AKI_NEO_CONST = 0.000000e+00, |
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AMIN = 1.000000e+00, |
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AMIX = 0.000000e+00, |
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AMIX_FREEB = 8.500000e-01, |
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AMU_NEO_CONST = 0.000000e+00, |
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AUTODISTRIBUTE_MODES = T |
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, |
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… |