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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 provided
      2. Methods provided 
   4. Module  triangular_grid_ids_io
      1. Data types provided
      2. Methods provided
6. EIRENE input wrapper
   1. Structure of EIRENE input files
   2. Module eirene_data_io
      1. Data types provided
      2. Methods provided 
   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.
! 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.
!

! 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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The module depends on the IMAS module  ids_types   (uses the constant  IDS_real  – the kind of real variables in IMAS).

Data types

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The following data types are provided:

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The type  edge_structure  is intended for information about an edge. The integer child array  vertex   holds indices of the edge vertices in  triangular_grid%vertex  . The leaf  material_property   holds the MP of the edge. The child array  adjacent   holds the indices of the neighbouring triangles in  triangular_grid%triangle .

Methods

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The module member routines are as follows:

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At present, only one grid space is arranged: a two-dimensional poloidal grid space holding a triangular grid. However, the routines of this modules are organized in a way that should facilitate adding additional spaces (most probably, a 1D toroidal space) if required. When the poloidal grid is recovered from an IDS, it is taken from the space having the identifier index equal to 1 (see the function get_grid_objects).

 Data types

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    type grid_control_panel
        type(ids_identifier_dynamic_aos3) :: grid_identifier
        character(len=ids_string_length) :: poloidal_space_name, poloidal_space_description
        character(len=ids_string_length) :: node_file, triangle_file, neighbor_file
        integer :: grid_index = 1             ! Use grid_ggd in time slice 1
        integer :: ggd_index = 1              ! Use ggd in time slice 1
        ! The following fields are not used when getting the grid from IDS
        integer :: grid_dictionary_index
        !! Allocation of IMAS grid space for EIRENE triangular grid
        integer :: nSpaces = 1                ! Total number of GGD spaces;
                                                          ! may change if toroidal coordinate is added
        integer :: eirene_space_index = 1     ! May change if toroidal coordinate is added
        integer :: Ngrid_slices = 1                 ! Number of grid_ggd slices to be allocated
        integer :: Nggd_slices = 1                 ! Number of ggd slices to be allocated
    end type grid_control_panel

The structure type grid_control_panel is intended for holding the control parameters taken from a command file. These parameters determine how the EIRENE triangular grid is saved in / recovered from an IMAS IDS.

 Methods

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The module contains the following routines:

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This module provides tools for dealing with files containing EIRENE input data (see the file format in Section 6.1).

 Data types

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type eirene_data
    real(ids_real), allocatable :: main_part(:)
    real(ids_real) :: average
    real(ids_real), allocatable :: extra_data(:) ! To be implemented yet
    logical :: extra_data_present                   ! Shows if extra_data is filled
end type eirene_data

This structure item 'main_part' is intended for storage of array elements 1, ..., NTRI, which correspond to grid triangles (see Section 6.1). The item 'average' is to contain average (element NTRI+1). The item 'extra_data' is intended for storing the extra elements NTRI+2, ..., NTT if they are available, with the item 'extra_data_present' showing if the extra elements are present.

 Methods

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The module contains the following routines:

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Storage of 'extra_data' is yet to be done (after adding the corresponding extra part to the grid).

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Constants

 ! Name of the subset to which the values at all triangles are attached
character(len=ids_string_length), parameter :: main_subset_label = 'pol3' 
 ! Name of the subset to which the average value is attached
character(len=ids_string_length), parameter :: average_subset_label = 'average'

The constants are the identifier names by which the subsets are found by the methods of this module when writing an EIRENE tally (given as a type(eirene_data)-structure) to IMAS IDS and, vice versa, reading it from IDS. The 'main_part' component is associated with the grid subset of all triangles (named 'pol3'); the 'average' component, with the subset having the name 'average'. 

 Methods

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• put_quantity_to_ids
  Put a type(eirene_data)-structure to IDS.
• get_quantity_from_ids
  Get a type(eirene_data)-structure from an IDS (not suitable for the 'equilibrium' IDS).
• get_quantity_from_equilibrium
  Get a type(eirene_data)-structure from the 'equilibrium' IDS.
• put_quantity_for_single_subset
  Write a quantity given as array to a given IDS slot, attaching it to a grid subset with a given name.
• get_quantity_for_single_subset
  Get from a given IDS slot a quantity given as an array attached to the grid subset with a given name (not suitable for the 'equilibrium' IDS).
• get_quantity_for_single_subset_in_equilibrium
  Get from a given IDS slot a quantity given as an array attached to the grid subset with a given name; suitable only for 'equilibrium'.

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The module provides tools for information exchange with the 'edge_profiles' IDS.

Data types

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type ion_file_set
    character(len=32) :: n, T !, vx, vy, vz ! To be added
end type ion_file_set

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This structure holds all parameters characterizing an ion sort.

Methods

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• deallocate_edge_profiles_data
  Deallocate all components of a type(edge_profiles_data_set)-stucture.
• initiate_ion_list_for_input_saving
  Read that part of the command file controls the input wrapper which concerns ions.
• initiate_edge_profiles_data_for_input_saving
  Read the part of the command file that controls saving the EIRENE data to the edge_profiles IDS.
• collect_data_for_edge_profiles_input
  Read the EIRENE input data intended for the edge_profiles IDS from files.
• save_input_to_edge_profiles
  Put EIRENE input to the edge_profiles IDS.
• organize_ion_storage
  Primary organization of the structure array for storing the ion data.
• put_ions_to_edge_profiles
  Put quantities associated with ions to the edge_profiles IDS.
• fetch_input_from_edge_profiles
  Get data from the edge_profiles IDS
• get_quantities_from_edge_profiles
  Get all physical quantities from the edge_profiles IDS
• get_ions_from_edge_profiles
  Get quantities associated with ions from the edge_profiles IDS
• write_input_data_from_edge_profiles_ids
  Write the data extracted from the edge_profiles IDS to files in the format of EIRENE input tallies

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The module provides tools for information exchange with the 'edge_profiles' IDS.

 Data types

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type equilibrium_data_set
     type(eirene_data) :: bx, by, bz, Btotal  ! Components used by EIRENE
     type(eirene_data) :: BR, Bvert, Btor      ! Components stored in IMAS
end type equilibrium_data_set

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This type holds names of the files holding the magnetic field components.

 Methods

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• deallocate_equilibrium_data
  Deallocate all components of the structure.
• initiate_equilibrium_data_for_input
  Read the part of the command file that controls saving the EIRENE data to the equilibrium IDS.
• collect_data_for_equilibrium_input
  Read the EIRENE input data intended for the equilibrium IDS from files,
• transform_equilibrium_for_ids
  Transform the magnetic field data to the form suitable for the equilibrium IDS.
• save_input_to_equilibrium
  Put EIRENE input to the equilibrium IDS.
• fetch_input_from_equilibrium
  Get all physical quantities from the equilibrium IDS.
• get_quantities_from_equilibrium
  Get all physical quantities from the equilibrium IDS.
• transform_equilibrium_for_eirene
  
  
• write_input_data_from_equilibrium_ids
  
  

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Uses the subroutines: put_quantity_to_ids (module imas_data_io), put_eirene_grid_to_equilibrium (module triangular_grid_ids_io), transform_equilibrium_for_ids (this module).

Argument	Type	Intent	Description
idx	integer	in	index of the I/O unit attached to the IMAS database
imas_controls	type(imas_control_panel)	in	parameters of the IMAS database and basic information to be put to IDS
grid_controls	type(grid_control_panel)	in	parameters controlling the grid saving
equilibrium_data	type(equilibrium_data_set)	inout	structure holding the distributions of physical quantities
eirene_grid	type(triangular_grid)	in	structure keeping the EIRENE triangular grid

subroutine fetch_input_from_equilibrium (idx, grid_controls, fetch_grid, equilibrium_data, eirene_grid)

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Uses the subroutines: get_triangular_grid_from_equilibrium (module triangular_grid_ids_io), get_quantities_from_equilibrium (this module), transform_equilibrium_for_eirene (this module).

Argument	Type	Intent	Description
idx	integer	in	index of the I/O unit attached to the IMAS database
grid_controls	type(grid_control_panel)	in	parameters controlling the grid saving/recovering
fetch_grid	logical	in	switches on reading the grid
equilibrium_data	type(equilibrium_data_set)	out	the structure holding the data found in the equilibrium IDS (except for the grid)
eirene_grid	type(triangular_grid)	inout	structure containing the grid; if fetch_input=.true., it is filled with data read from the IDS; otherwise, it remains unchanged.

function get_quantities_from_equilibrium (ggd, grid_ggd_aos) result (equilibrium_data)

Get all physical quantities from the equilibrium IDS, putting them to a type(equilibrium_data_set) structure.

Argument	Type	Intent	Description
equilibrium_data	type(equilibrium_data_set)	result	the structure holding the obtained data
ggd	type(ids_equilibrium_ggd)	in	ggd AoS element where the quantities are written
grid_ggd_aos	type(ids_generic_grid_dynamic), dimension(:)	in	AoS containing the GGD grids

subroutine transform_equilibrium_for_eirene (equilibrium_data)

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The input files must contain b_x, b_y, b_z (b is the mag. field unit vector), and B_total. The equilibrium IDS accepts B_R, B_Z, B_phi. Here x=R, y=Z (vertical), z=phi (toroidal).

Argument	Type	Intent	Description
equilibrium_data	type(equilibrium_data_set)	inout	structure that holds all magnetic field data

subroutine write_input_data_from_equilibrium_ids (equilibrium_data, equilibrium_files)

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The names of the generated files are taken from the 'equilibrium_files' structure.

Argument	Type	Intent	Description
equilibrium_data	type(equilibrium_data_set)	in	the structure holding the obtained data
equilibrium_files	type(equilibrium_file_set)	in	the structure containing the file names

Module global_

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

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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objects

The module contains global constants and service routines used in other modules.

Constants

    real(IDS_real), parameter :: density_unit_ratio = 1.e6_IDS_real, &
                               & velocity_unit_ratio = 1.e-2_IDS_real, &
                               & temperature_unit_ratio = 1._IDS_real, &
                               & Bfield_unit_ratio = 1._IDS_real
    real(IDS_real), parameter :: length_unit_ratio = 1.e-2_IDS_real

Each of these constants is the ratio of an EIRENE unit to the corresponding IMAS unit (for example, 1 cm / 1 m = 10^(-2) for length).

Methods

• 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.

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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