...

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

...

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

...

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

...

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          
!
eirene                                         <= IMAS database
10003                                              <= 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

...

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

Data types

...

The following data types are provided:

...

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

...

The module member routines are as follows:

...

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

...

    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

...

The module contains the following routines:

...

The function returns a type(triangular_grid)-structure, which is partly filled with information read from the GGD grid space having the identifier index equal to 1 (i.e., being the 'primary grid space'). The function takes as a parameter the AoS of all grid spaces.

Argument	Type	Intent	Description
eirene_grid	type(triangular_grid)	result	Partly filled grid structure
grid_ggd	type(ids_generic_grid_dynamic_space), dimension(:)	in	Space where the triangular grid is stored

subroutine arrange_material_properties (eirene_grid, subsets)

Get information about the MPs of grid edges from IDS and add it to the type(triangular_grid)-structure holding the grid description. This information is stored in GGD in the form of subsets uniting the edges with certain values of the MP.

Argument	Type	Intent	Description
eirene_grid	type(triangular_grid)	inout	Partly filled grid structure
subsets	type(ids_generic_grid_dynamic_grid_subset), dimension(:)	in	Space where the triangular grid is stored

subroutine put_eirene_grid_to_ids (eirene_grid, grid_ggd, nSpaces, eirene_space_index, grid_identifier, eirene_space_name, eirene_space_description)

Place a grid into a given  grid_ggd  structure by allocating the space AOS with a given number of grid spaces, putting a triangular grid given as a  type(triangular_grid)-structure into a desired element of the  space  AOS, and organizing the necessary grid subsets. This subroution cannot be used for putting a grid into the 'equilibrium' IDS (because the type of the structure used for storing the GGD grid in this IDS is peculiar). To put the grid into the 'equilibrium' IDS, use the function put_eirene_grid_to_equilibrium.

Argument	Type	Intent	Description
eirene_grid	type(triangular_grid)	in	The grid to be saved
grid_ggd	type(ids_generic_grid_aos3_root)	pointer	Pointer to the  grid_ggd  AOS element to hold the grid
nSpaces	integer	in	The dimension of  space  AOS to be allocated
eirene_space_index	integer	in	Index of the triangular grid space in  space  AOS
grid_identifier	type(ids_identifier_dynamic_aos3)	in	Grid identifier to be put to IDS
eirene_space_name	character(len=*)	in	Name assigned to the triangular grid space
eirene_space_description	character(len=*)	in	Verbose description of the triangular grid space

subroutine put_eirene_grid_to_equilibrium (eirene_grid, grid_ggd, nSpaces, eirene_space_index, grid_identifier, eirene_space_name, eirene_space_description)

Place a grid into a given  grid_ggd  structure by allocating the space AOS with a given number of grid spaces, putting a triangular grid given as a  type(triangular_grid)-structure into a desired element of the  space  AOS, and organizing the necessary grid subsets. This subroution can be used only for putting a grid into the 'equilibrium' IDS (because the type of the structure used for storing the GGD grid in this IDS is peculiar). To put the grid into another IDS, use the function put_eirene_grid_to_ids.

Argument	Type	Intent	Description
eirene_grid	type(triangular_grid)	in	The grid to be saved
grid_ggd	type(ids_generic_grid_dynamic)	pointer	Pointer to the  grid_ggd  AOS element to hold the grid
nSpaces	integer	in	The dimension of  space  AOS to be allocated
eirene_space_index	integer	in	Index of the triangular grid space in  space  AOS
grid_identifier	type(ids_identifier_dynamic_aos3)	in	Grid identifier to be put to IDS
eirene_space_name	character(len=*)	in	Name assigned to the triangular grid space
eirene_space_description	character(len=*)	in	Verbose description of the triangular grid space

function arrange_grid_spaces (grid, nSpaces, eirene_space_index, eirene_space_name, eirene_space_description) result (spaces)

Place a grid into a given  grid_ggd  structure by allocating the space AOS with a given number of grid spaces, putting a triangular grid given as a  type(triangular_grid)-structure into a desired element of the  space  AOS, and organizing the necessary grid subsets. This subroution can be used only for putting a grid into the 'equilibrium' IDS (because the type of the structure used for storing the GGD grid in this IDS is peculiar). To put the grid into another IDS, use the function put_eirene_grid_to_ids.

Argument	Type	Intent	Description
spaces	type(ids_generic_grid_dynamic_space), dimension(:), pointer	result	Pointer to the allocated and filled 'space' AoS
grid	type(triangular_grid)	in	The grid to be saved
nSpaces	integer	in	The dimension of  space  AOS to be allocated
eirene_space_index	integer	in	Index of the triangular grid space in  space  AOS
eirene_space_name	character(len=*)	in	Name assigned to the triangular grid space
eirene_space_description	character(len=*)	in	Verbose description of the triangular grid space

function arrange_triangular_grid_space (grid, space_name, space_description) result (space)

...

Create a GGD space and put the objects (nodes, edges, and cells) of an EIRENE triangular grid there. The information about grid objects is taken from a  type(triangular_grid)-structure.

Argument	Type	Intent	Description
subsets	type(ids_generic_grid_dynamic_grid_subset), pointer, dimension(:)	result	IDS space structure holding the grid
eirene_space	type(ids_generic_grid_dynamic_space)	in	the GGD grid space to which the subsets are attached
eirene_space_index	integer	in	the index of this space in the 'space' AoS
grid	type(triangular_grid)	in	The grid to be saved

subroutine  arrange_standard_2d_subset(subset, space, space_index, dimensionality, subset_id)

...

Arrange a subset for edges with a certain value of MP. The subset gets the name 'MPnnnn', where nnnn is the MP value.

Argument	Type	Intent	Description
subset	type(ids_generic_grid_dynamic_grid_subset)	pointer	Pointer to the  grid_subset  AOS element to hold the subset
space	type(ids_generic_grid_dynamic_space)	in	The  space  AOS element holding the triangular grid space
space_index	integer	in	Index of the triangular grid space in the  space  AOS
grid	type(triangular_grid)	in	The grid being saved
mat_property	integer	in	MP value
subset_id	integer	in	Integer identifier of the subset

subroutine  arrange_subset_for_averages (subset, subset_id)

...

Argument	Type	Intent	Description
subset	type(ids_generic_grid_dynamic_grid_subset)	pointer	Pointer to the  grid_subset  AOS element to hold the subset
subset_id	integer	in	Integer identifier of the subset

EIRENE input wrappers

Only a part of input quantities is now processed. The storage of velocities will become possible after IMAS 3.38 is implemented.

Structure of EIRENE input files

In addition to the files containing the grid, the EIRENE input includes file holding spatial distributions of physical quantities (magnetic field components, temperatures and densities of plasma species etc.). The values of the quantities are given at the cells (triangles) constituting the grid. The easiest way to describe the format of the input files is to present a sample code reading it:

        READ (IFILE,'(A72)') Text_header1 
        READ (IFILE,'(A72)') Text_header2
        READ (IFILE,'(A72)') Text_header3
        READ (IFILE,'(A24)') Text_header4
        READ (IFILE,'(A24)') Text_header5
        READ (IFILE,'(A72)') Text_header6
        READ (IFILE,'(A72)') Text_header7
        READ (IFILE,*) NR,NP,NT,NB,NTT
        DO IRAD=1,NTT,5
            READ (IFILE,*) (PROF(IR),IR=IRAD,IRAD+4)
        END DO

Here NR=NTRI+1, NTRI is the number of grid triangles, NP=1, NT=1, NB=1, NTT = total number of cells including the additional cells outside of the triangle grid, see below. The additional array element with the index NR usually contains the average over all cells. Further extra elements with indices NR+1, ..., NTT correspond to extra cells outside the implemented triangular mesh (i.e., cells in pump ducts). These elements are not processed now. 

The text headers are comments describing the file content, system units etc. It is agreed with the EIRENE team that (a) when reading a data file, the wrapper will consider all lines starting with '*' or '!' as a header line and will not store in IMAS the header texts; (b) when writing a fata file, the wrapper will generate new reasonable headers anew. The headers are not implemented yet.

 Module eirene_data_io

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

 Data types provided

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 provided

The module contains the following routines:

• deallocate_data_set
  Dallocate the components of a type(eirene_data) variable.
• read_quantity_from_file
  Read an EIRENE input file holding a distribution of a physical quantity.
• write_quantity_to_file
  Write an EIRENE input file holding a distribution of a physical quantity.

subroutine deallocate_data_set (quantity)

Arrange a special subset for storing 2d averages.  The subset gets the name 'average'.

...

Argument

...

Type

...

Intent

...

Description

...

quantity

...

type(eirene_data)

...

inout

...

Structure to be deallocated

subroutine read_quantity_from_file (file_name, quantity, report, io_unit)

Arrange a special subset for storing 2d averages.  The subset gets the name 'average'.

...

Argument

...

Type

...

Intent

...

Description

...

quantity

...

type(eirene_data)

...

out

...

Structure to be filled with data from the file

...

subroutine write_quantity_to_file (file_name, quantity, report, io_unit)

Arrange a special subset for storing 2d averages.  The subset gets the name 'average'.

...

Argument

...

Type

...

Intent

...

Description

...

quantity

...

type(eirene_data)

...

in

...

Structure holding data to be saved

...

Module imas_data_io

The module contains???

Module edge_profiles_io

?????

Module equilibrium_io

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

Module global_parameters

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

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:

...

Two wrapper programs are provided. The first program, save_input.exe, accepts the EIRENE input (files with a grid description and files with spatial distributions of physical quantities) prepared by some programs and saves their content in a desired IMAS database. The second program, provide_input.exe, recreate these input files, so that they can be used by EIRENE. Both programs are controlled by certain text files ('command files') described in Section 4.

Only a part of input quantities is now processed. According to information received from the EIRENE team, the storage of the following tallies (physical quantities) is of first priority: electron temperature; temperature, density, and velocity components (in cylindrical coordinates) of several sorts of ions; total magnetic field; components of the magnetic field unit vector in cylindrical coordinates.

The storage of the magnetic field, temperatures, and densities is already implemented in the wrappers. However, there is a restriction: the wrappers are able to deal with single-atom ions only.

The storage of velocities will become possible after IMAS 3.38 is implemented.

Structure of EIRENE input files

In addition to the files containing the grid, the EIRENE input includes file holding spatial distributions of physical quantities (magnetic field components, temperatures and densities of plasma species etc.). The values of the quantities are given at the cells (triangles) constituting the grid. The easiest way to describe the format of the input files is to present a sample code reading it:

        READ (IFILE,'(A72)') Text_header1 
        READ (IFILE,'(A72)') Text_header2
        READ (IFILE,'(A72)') Text_header3
        READ (IFILE,'(A24)') Text_header4
        READ (IFILE,'(A24)') Text_header5
        READ (IFILE,'(A72)') Text_header6
        READ (IFILE,'(A72)') Text_header7
        READ (IFILE,*) NR,NP,NT,NB,NTT
        DO IRAD=1,NTT,5
            READ (IFILE,*) (PROF(IR),IR=IRAD,IRAD+4)
        END DO

Here NR=NTRI+1, NTRI is the number of grid triangles, NP=1, NT=1, NB=1, NTT = total number of cells including the additional cells outside of the triangle grid, see below. The additional array element with the index NR usually contains the average over all cells. Further extra elements with indices NR+1, ..., NTT correspond to extra cells outside the implemented triangular mesh (i.e., cells in pump ducts). These elements are not processed now. 

The text headers are comments describing the file content, system units etc. It is agreed with the EIRENE team that (a) when reading a data file, the wrapper will consider all lines starting with '*' or '!' as a header line and will not store in IMAS the header texts; (b) when writing a fata file, the wrapper will generate new reasonable headers anew. The headers are not implemented yet.

 Module eirene_data_io

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

 Data types

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

The module contains the following routines:

• deallocate_data_set
  Dallocate the components of a type(eirene_data) variable.
• read_quantity_from_file
  Read an EIRENE input file holding a distribution of a physical quantity.
• write_quantity_to_file
  Write an EIRENE input file holding a distribution of a physical quantity.

subroutine deallocate_data_set (quantity)

Deallocate all components of the structure.

subroutine read_quantity_from_file (file_name, quantity, report, io_unit)

Read a physical quantity from a file with the format of EIRENE input tallies.

subroutine write_quantity_to_file (file_name, quantity, report, io_unit)

Write a physical quantity to a file with the format of EIRENE input tallies.

Module imas_data_io

The module contains methods used for 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 (the subset identifier name 'pol3'); the 'average' component, with the subset having the name 'average'. 

It is a difficult choice to decide whether the methods should look for the subsets in the 'subset' AoS by their identifier names or by their dictionary indices (the idea to assign fixed places in the AoS to the subsets seems very bad because it can result in numerous bugs and confusions if it happens that the AoS requires changes). Now the subsets are found by their names. The main reason for this choice is that we have many subsets that have no standard dictionary indices (subsets of edges with given MPs, subset for averages). It is possible to introducing custom indices for them, but it seems a way to great confusion.

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

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

• 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'.

subroutine put_quantity_to_ids (quantity, grid_subset, grid_index, quantity_aos, code_to_imas_unit_ratio)

Put a quantity to a given IDS slot (sub-AoS of the ggd AoS intended for the storage of a single physical quantity). The AoS is allocated with the size of 2 in order to save values attached to two grid subsets: the subset of all triangles and the subset organized to store the averages. These subsets are found by their identifier names, which are given by the module constants main_subset_label and average_subset_label, respectively.

function get_quantity_from_ids (grid_ggd_aos, quantity_aos, code_to_imas_unit_ratio) result (quantity)

Get a quantity from a given IDS slot (sub-AoS of the ggd AoS intended for the storage of a single physical quantity). The subroutine scans the slot, investigating the identifier names of the grid subsets to which the slot array elements are attached (the 'grid_index' and the 'subset_index' components of the element are used to reach this subset). The subroutine obtains the value arrays attached to two grid subsets: the subset of all triangles and the subset organized to store the averages. These subsets are found by their identifier names, which are given by the module constants main_subset_label and average_subset_label, respectively. The obtained arrays are put into the components 'main_data' and 'average' of the function result. Not suitable for the 'equilibrium' IDS (use get_quantity_from_equilibrium for this IDS).

function get_quantity_from_equilibrium (grid_ggd_aos, quantity_aos, code_to_imas_unit_ratio) result (quantity)

Get a quantity from a given IDS slot (sub-AoS of the ggd AoS intended for the storage of a single physical quantity) of the 'equilibrium' IDS. The subroutine scans the slot, investigating the identifier names of the grid subsets to which the slot array elements are attached (the 'grid_index' and the 'subset_index' components of the element are used to reach this subset). The subroutine obtains the value arrays attached to two grid subsets: the subset of all triangles and the subset organized to store the averages. These subsets are found by their identifier names, which are given by the module constants main_subset_label and average_subset_label, respectively. The obtained arrays are put into the components 'main_data' and 'average' of the function result. Use get_quantity_from_ids for IDS other than 'equilibrium'.

subroutine put_quantity_for_single_subset (quantity, ids_slot, code_to_imas_unit_ratio, grid_subset, grid_index, subset_label)

Write a quantity given as array to a given IDS slot, attaching it to a grid subset with a given name. The array size must coincide with the size of the grid subset.

subroutine get_quantity_for_single_subset (ids_slot, subset_label, code_to_imas_unit_ratio, grid_ggd_aos, quantity, grid_index, subset_index)

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).

subroutine get_quantity_for_single_subset_in_equilibrium (ids_slot, subset_label, code_to_imas_unit_ratio, grid_ggd_aos, quantity, grid_index, subset_index)

Get from a given IDS slot a quantity given as an array attached to the grid subset with a given name (suitable onlyfor the 'equilibrium' IDS).

Module edge_profiles_io

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

Data types

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

This structure holds the collection of names of data files that store characteristics for one ion sort.

type ion_data_set
    type(eirene_data) :: n, T  !, vx, vy, vz ! To be added
end type ion_data_set

This structure holds the collection of data for one ion sort.

type ion_parameters
    character(len=ids_string_length) :: label
    real(ids_real) :: mass, Z_ion, Z_element
    type(ion_file_set) :: files
    type(ion_data_set) :: data
end type ion_parameters

This structure holds all parameters characterizing an ion sort.

Methods

• 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

subroutine deallocate_edge_profiles_data (all_data)

Deallocate all components of the structure.

function initiate_ion_list_for_input_saving (io_unit) result (ion_list)

Read that part of the command file of the input wrapper which concerns ions.

function initiate_edge_profiles_data_for_input_saving (io_unit) result (edge_profiles_data)

Read the part of the command file that controls saving the EIRENE data to the edge_profiles IDS.

subroutine collect_data_for_edge_profiles_input (edge_profiles_data)

Read the EIRENE input data intended for the edge_profiles IDS from files. At the entry, the 'edge_profiles_data' structure is filled only partly (from the command file). The subroutine fills the remaining part, reading the information from data files.

Uses the subroutine read_quantity_from_file (module eirene_data_io).

subroutine save_input_to_edge_profiles (idx, imas_controls, grid_controls, edge_profiles_data, eirene_grid)

Put EIRENE input to the edge_profiles IDS. The input consists of (1) a triangular grid; (2) a set of quantities (characteristics of several plasma species) defined on this grid; (3) properties of these species. The first item is provided in 'eirene_grid'; the last two, in 'edge_profiles_data'.

Uses the subroutines: put_quantity_to_ids (module imas_data_io), put_eirene_grid_to_ids (module triangular_grid_ids_io), put_ions_to_edge_profiles (this module).

subroutine organize_ion_storage (ion_list, ggd)

Primary organization of the structure array for storing the ion data (allocation of AoS and putting basic ion properties there).

Restrictions to be overcome: only single atoms (no molecules); one charge state per ion sort.

subroutine put_ions_to_edge_profiles (ion_list, ggd, grid_subset, grid_index)

Put quantities associated with ions to the edge_profiles IDS.

Restrictions to be overcome: only single atoms (no molecules); one charge state per ion sort.

subroutine fetch_input_from_edge_profiles (idx, grid_controls, fetch_grid, edge_profiles_data, eirene_grid)

Get all physical quantities from the edge_profiles IDS, putting them to a type(edge_profiles_data_set) structure. If required, get the triangular grid.

Uses the subroutines: get_triangular_grid_from_ids (module triangular_grid_ids_io), get_quantities_from_edge_profiles (this module).

function get_quantities_from_edge_profiles (ggd, grid_ggd_aos) result (edge_profiles_data)

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

function get_ions_from_edge_profiles (grid_ggd_aos, ggd_ions) result (ion_list)

Get quantities associated with ions from the edge_profiles IDS.

Restrictions: only single-atom ions (no molecules); one charge state per ion sort.

subroutine write_input_data_from_edge_profiles_ids (edge_profiles_data, file_suffix)

Write the data extracted from the edge_profiles IDS to files in the format of EIRENE input tallies.

The names of the generated files look like <ion_label>_<quantity_label>_<file_suffix>. For example, if the file suffix is "input.dat", and the ion label is "D+", the ion temperature will be written to the file "D+_n_input.dat".

Module equilibrium_io

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

 Data types

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

This type is a collection of magnetic field components.

type equilibrium_file_set
    character(len=32) :: bx, by, bz, Btotal
end type equilibrium_file_set

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

 Methods

• 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
  
  

subroutine deallocate_equilibrium_data (all_data)

Deallocate all components of the structure.

function initiate_equilibrium_data_for_input (io_unit) result (equilibrium_files)

Read the part of the command file that controls saving the EIRENE data to the equilibrium IDS.

function collect_data_for_equilibrium_input (equilibrium_files) result (equilibrium_data)

Read the EIRENE input data intended for the equilibrium IDS from files. 

Uses the subroutine read_quantity_from_file (module eirene_data_io).

subroutine transform_equilibrium_for_ids (equilibrium_data)

Transform the magnetic field data to the form suitable for the equilibrium IDS. On entry, only a part of the 'equilibrium_data' structure is filled. The subroutine fills the rest.

The input files 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).

subroutine save_input_to_equilibrium (idx, imas_controls, grid_controls, equilibrium_data, eirene_grid)

Put EIRENE input to the equilibrium IDS. The input consists of (1) a triangular grid; (2) a set of quantities (characteristics of several plasma species) defined on this grid. The first item is provided in 'eirene_grid'; the second one, in 'equilibrium_data'. 

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).

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

Get all physical quantities from the equilibrium IDS, putting them to a type(equilibrium_data_set) structure. If required, get the triangular grid.

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).

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.

subroutine transform_equilibrium_for_eirene (equilibrium_data)

Transform the magnetic field data obtained from the equilibrium IDS into form suitable for EIRENE. On entry, only a part of the 'equilibrium_data' structure is filled. The subroutine fills the rest.

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).

subroutine write_input_data_from_equilibrium_ids (equilibrium_data, equilibrium_files)

Write the data extracted from the edge_profiles IDS to files in the format of EIRENE input tallies.

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

Module global_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

...

.

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 worth whileworthwhile)