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1. Introduction
2. Files provided
3. Running a test example
4. Structure of the parameter command files
5. Storing the EIRENE triangular grids in IMAS
   
   1. Structure of EIRENE files keeping the grid
   2. Presentation of EIRENE grid in GGD
   3. Module  triangular_grid_modile 
      1. Data types
      2. Methods
   4. Module  triangular_grid_ids_io
      1. Data types
      2. Methods
6. EIRENE input wrapper
   1. Structure of EIRENE input files
   2. Module eirene_data_io
      1. Data types
      2. Methods
   3. Module imas_data_io
      1. Constants
      2. Methods
   4. Module edge_profiles_io
      1. Data types
      2. Methods
   5. Module equilibrium_io
      1. Data types
      2. Methods
   6. Module global_objects
      1. Constants
      2. Methods
      ???
   7. Module imas_controls_for_input
      1. Data types
      2. Methods
   8. Main program files  save_input_main.f90  and  provide_input_main.f90
7. Known issues
8. Things to be done

Introduction

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The structure of this document is as follows. Section 2 lists the files provided. Section 3 describes how to run a test example. Section 4 presents the parameter files controlling the wrapper programs. Section 5 describes the organization of the grid storage. In Section 6, the wrapper for the EIRENE input is described. Finally, the things to be done are outlined in Section 7.

Files provided

This document can be found at EIRENE IMASification - Scientific Worfklows - PCSS Confluence (psnc.pl), https://docs.psnc.pl/display/WFMS/EIRENE+IMASification.

The repository folder of the current version is The files listed below can be found in the public directory ~g2yyakov/public/eirene/version0.910.!!! To be updated

Files provided

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1. Copy the files to your directory. 
2. If you wish to test the programs with your own files, copy them to the same directory. Do not forget to put the correct names to the command file save_input.par.
3. Load the IMAS library by typing:
   module load imasenv/3.37.0    
4. Create the IMAS database entry:
   imasdb eirene 
5. Now you can compile the examples. Type
   make clean 
make save_input 
6. Run the program:
   ./save_input.exe 
   The program puts the grid stored in the files soledge3x.* and the content of the dat-files into the IMAS database  eirene .
7. Type
   make provide_input 
8. Run the program:
   ./provide_input.exe 
9. Compare the new files  eirene.*   with the original files  soledge3x.* and the original data files with the new files (their names end with the suffix '_input.dat').

Structure of the

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command files

The program save_input.exe takes parameters that control the work of the program from the file save_input.par. A template of this file is given below. 

! Parameters that control saving the EIRENE input to IMAS.

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! Use '!' when inserting comment lines.

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! You can add comments at the end of each line unless this line holds a text that may contain blanks (e.g., a description field).
! Do not change the order of the parameters.
!

! Parameters that control saving the EIRENE input to IMAS.
! Use '!' when inserting comment lines.
! You can add comments at the end of each line unless this line holds a text that may contain blanks (e.g., a description field).
! Do not change the order of the parameters.
!
eirene                                         <= IMAS database
10003                                         <= shot
1                                                <= run
'IDS created to test EIRENE input storage'     <= IDS comment
'Yurii Yakovenko'                          <= input provider
'once upon a time'                       <= creation date
!!! grid data
"SN"                                         <= grid name
4                                              <= grid index in dictionary (single null)
"EIRENE grid for single null configuration"  <= grid description
"primary_standard"                 <= poloidal space name
"primary poloidal triangular grid" <= poloidal space description
soledge3x.npco_char                <= grid node file
soledge3x.elemente                 <= grid triangle file
soledge3x.neighbors                <= grid neighbor file
!!! Physical quantities
bx.dat       <= bx file
by.dat       <= by file
bz.dat       <= bz file
Btotal.dat   <= Btotal file
vx.dat       <= vx file
vy.dat       <= vy file
vz.dat      <= vz file
Te.dat       <= Te file
!!! Ion physical quantities
2           <= Number of ion species
! Ion species 1
D  2  1  1  <= label, mass, Z_ion, Z_element
TD.dat      <= temperature file
nD.dat      <= density file
! Ion species 2
T  3  1  1  <= label, mass, Z_ion, Z_element
TT.dat      <= temperature file
nT.dat      <= density file

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• read_next_line
  Return the next file record not starting with '!'.
• get_imas_version
  Get the versions of IMAS and IMAS Access Layer from the system environment.

??????????????

Module imas_controls_for_input

????????????

Main files  save_input_main.f90   and  provide_input_main .f90 

The wrapper program contained in the file  save_input_main .f90  performs the following actions:

• ????????      Initializes an instance of the  edge_profiles   IDS in the code memory with writing some mandatory fields.
• Writes some labels to the IDS.
• Allocates the  grid_ggd  AOS with only one element.
• Reads information about the grid from files and establishes grid edges, using the  read_eirene_grid  function (module  triangular_grid_module).
• Puts the grid information into the IDS, using the  put_triangular_grid_to_ids  subroutine (module  triangular_grid_ids_io).
• Creates the corresponding IDS in an IMAS database.
• Writes the IDS prepared in the code memory to the IMAS database and closes the database.

The program contained in the file  recover_grid.f90  performs the following actions:

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function read_next_line (io_unit, label) result (line)

Return the next file record not starting with '!' (the function is used for reading only meaningful records, skipping the comment lines).

function get_imas_version () result (version)

Get the versions of IMAS and IMAS Access Layer from the system environment. The function result is a structure with the type 'ids_version_dd_al' (the type used in IMAS for holding this information).

An example of the environment variable used by the function is as follows:
IMAS_PREFIX=/gw/swimas/core/IMAS/3.37.0/AL/4.11.0/intel/2020

Module imas_controls_for_input

The module contains the tools that permit to control the wrappers via the content of the command file.

 Data types

type imas_control_panel
    character(len=16) :: database          !! Name of the database/machine
                                           !! Note: the database must exist
                                           !! before running the wrapper
    integer :: shot, run
    character(len=4) :: imas_major_version = '3'
    character(len=16) :: username             !! current login username;
                                              !! to be provided with
                                              !! getlog() Fortran routine.
    type(ids_ids_properties) :: ids_properties
    type(ids_code) :: code                 !! Code properties
    character(len=16) :: generic_suffix    !! The last part of the file name if the
                                           !! is generated automatically
end type imas_control_panel

This type is designed to hold the control parameters taken from the command file.

 Methods

• get_imas_controls_for_input_saving
• get_imas_controls_for_input_fetching

function get_imas_controls_for_input_saving (io_unit) result (imas_controls)

Prepare control parameters for saving the EIRENE input to IMAS. Most control parameters are taken from a command file.

function get_imas_controls_for_input_fetching (io_unit) result (imas_controls)

repare control parameters for getting the EIRENE input from IMAS. Most control parameters are taken from a command file.

Main files  save_input_main.f90   and  provide_input_main .f90 

The wrapper program contained in the file  save_input_main .f90  performs the following actions:

• Reads the command file 'save_input.par', putting its content to the structures 'imas_controls', 'grid_controls', 'equilibrium_files', and 'edge_profiles_data'.
• Reads information about the grid from files and establishes grid edges, using the  read_eirene_grid  function (module  triangular_grid_module).
• Inputs distributions of input tallies from data files, invoking the functions 'collect_data_for_edge_profiles_input' and 'collect_data_for_equilibrium_input'.
• Creates an IMAS database entry, invoking the IMAS library subroutine 'imas_create_env'.
• Puts the information (the grid and the tallies) into 2 IMAS IDS's, using the subroutines  'save_input_to_edge_profiles' and 'save_input_to_equilibrium'. 
• Closes the database, invoking the IMAS library subroutine 'imas_close'.
• Deallocates the structures holding the data.

The program contained in the file  provide_input_main .f90  performs the following actions:

• Reads the command file 'provide_input.par', putting its content to the structures 'imas_controls', 'grid_controls', and 'equilibrium_files'.
• Opens the IMAS database, invoking the IMAS library subroutine  imas_open_env  .
• Inputs the data (the grid and the tallies) from 2 IMAS IDS's, using the subroutines  'fetch_input_from_edge_profiles' and 'fetch_input_from_equilibrium'.
• Writes these data to EIRENE-format files, invoking the subroutines 'write_eirene_grid', 'write_input_data_from_edge_profiles_ids', and 'write_input_data_from_equilibrium_ids'.
• Closes the database, invoking the IMAS library subroutine 'imas_close'.
• Deallocates the structures holding the data.

 Known issues

The statements that are to deallocate the IDS's in the program memory when they are not needed anymore are now commented out (they are in the modules 'edge_profiles_io' and 'equilibrium_io'). The reason is that the IMAS library subroutine 'ids_deallocate' hangs the program 'save_input.exe' if it is called for both IDS's ('edge_profiles' and 'equilibrium'). This issue is yet to be resolved

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Things to be done

• Code parameters
• Headers of data files
• Generalize to multi-atom ions
• Resolve the issue with non-deallocated structures
• Implement ion velocities (after IMAS 3.38 appears)
• Extend the list of input quantities
• IMASification of the EIRENE output
• Try to adjust the processing of exceptions to GSL practices (if worthwhile)

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