atlas12_ada :

The Ada version of the famous Atlas12 code by R. Kurucz  (object oriented and parallelised)

Contents of the step by step user's guide to atlas12_ada

Step 1 : Downloading and installing the compiler
Step 2 : Splitting (chopping) the code
Step 3 : Compiling the code
Step 4 : The data files
Step 5 : Contents of the input files
Step 6 : Calculating stellar atmospheres with atlas12_ada

 A step by step user's guide to atlas12_ada   (version 2024-01-21)

• Step 1 : Downloading the compiler
  
  

  The latest free 32-bit or 64-bit GNAT compiler may be obtained from the AdaCore site
  or any of the numerous Linux distributions.
  
  
  

• Step 2 : Splitting (chopping)  the code
  
  

  The file  atlas12_ada_2024_01_21.ada   contains a number of packages, procedure and functions.
  GNAT users have to split (gnatchop) this file, because GNAT requires different compilation units to be
  in different files.
  
  The following command will split the file:     gnatchop  -w  atlas12_ada_2024_01_21.ada
  
  Note:  The  -w option overwrites existing source files.
  
  
  

• Step 3 : Compiling the code
  
  

  You then have to create the executable  atlas12_ada   by issuing the following command:
  
       gnatmake  -O3  -gnatfvp  atlas12_ada
  
  Note:  In order to be able to execute atlas12_ada, make sure that your system provides
  unlimited stacksize.
  
  With the tcsh shell for example set "limit stacksize unlimited"
  
  
  

• Step 4 : The data files
  
  

  Download at least the following files from R. Kurucz's homepage
  
  http://kurucz.harvard.edu/programs/atlas12/
  
  

  lowlines.dat highlines.dat diatomicsiwl.bin    (rename as diatomics.dat) b_nlte_lines.dat gf_all_nlte.dat molecules.dat

  
  
  

• Step 5 : Contents of the input files
  
  

  The input data and auxiliary files required have to be specified in  atlas12_super.inp
  
  What you have to specify in the input file atlas12_super.inp

  
  

  1. No. of processors or cores
     
  2. No. of wavelength points   (recommended 500000, minimum 300000)
  3. Atmospheric model file (Kurucz format)
  4. File with commands used by atlas12_ada to establish line data
  5. File with commands used by atlas12_ada to execute iterations
  6. Output file name
     
  7. Element file with the abundances to be used by atlas12_ada
  8. 2 lines containing just "./" (may be changed in later versions)
     
  9. No. of stratification files (= no. of '+'s in the element file)    --    must be >= 1
     
  10. For each element in question, one file with (stratified) abundances
      (for all layers from top to bottom of the atmosphere)
      

  
  
  
• Step 6 : Calculating stellar atmospheres with atlas12_ada
  
  

  The command   ./atlas12_ada s   starts execution of the code and establishes the necessary
  spectral line data base in the file "selected_lines.little.bin"
  
  The command   ./atlas12_ada r   starts execution of the code, uses the file "selected_lines.little.bin",
  and carries out the iterations for the establishment of the desired stellar atmosphere.
  
  The Cossam atmospheric input file and the Kurucz atmosphere file are created as  [output_file_name].fil.[version]
  and [output_file_name].mod.[version] respectively. There is also a file [output_file_name].ros.[version].
  

  
  

  An example for names and contents of these 3 files : 
  
     t10000_400_99.mod.4012348637
     t10000_400_99.fil.4012348637
     t10000_400_99.ros.4012348637

  
  The code establishes a sub-directory containing various log-files and output-files.
  
  

  401234863_dir atlas12.mod.4012348637 atlas12.fil.4012348637 atlas12.ros.4012348637 atlas12.err.4012348637 atlas12_super.inp.r.012348637 atlas12.inp.r.4012348637 atlas12.abund.r.4012348637 strat.abund.26.4012348637

  sub-directory    Kurucz atmosphere file  atmospheric input file for Cossam    various log-files    the numerical extensions reflect the  date of creation

  
  Using the command   ./atlas12_ada r > atlas_02.res &    allows archivation of the
  extensive output and detailed control of the quality of the converged model.
  

  
  

• Contents of the file atlas12_super.inp
  
  

  Data start at line 4, col 35    : ! === Comment : --------------------------------: ATLAS12 No. of processors               : 12 No. of wavelength points        : 500000 Kurucz model file               : t10000_400_99.mod start file                      : t10000.s exec file                       : t10000.r output file                     : t10000_400_99 Element file                    : grev_sau.abund.orig --------------------------------: ERROR LIMITS Fm_max  F1_max Fmed_max F2_max  : 0.025  0.010  0.010  0.010 Dm_max  D1_max Dmed_max D2_max  : 0.500  0.080  0.050  0.060 --------------------------------: ./ ./ 1 strat_init.26.homog

  atmosphere with which to start (Kurucz format)  file with commands used by atlas12_ada to establish line data  file with commands used by atlas12_ada to enter iterations    element file with the abundances to be used by atlas12_ada  convergence criteria  convergence criteria    leave unchanged (may be used in later versions)  leave unchanged (may be used in later versions)  no. of stratification files (= no. of '+'s in element file)  file with (stratified) Fe abundances for all layers

  
  
  
• Contents of the initial start file t10000.s
  
  

  CORRECTION OFF MOLECULES OFF ABUNDANCE STRATIFIED READ PUNCH READ LINES VTURB  0.0 ITERATIONS 1 PRINT 3 PUNCH 0 BEGIN END EOF

  take abundances from element file

  
  
  
• Contents of the initial exec file t10000.r
  
  

  MOLECULES OFF ABUNDANCE STRATIFIED READ PUNCH OPACITY ON LINES   CONVECTION OFF TITLE [0.0] VTURB=0 NOVER NEW ODF    SCALEMODEL  1  99 TAULIMITS   -5.0  2.0 ITERATIONS 45 VTURB 0.0 BEGIN END EOF

  take abundances from element file   has to be 1 and number of atmospheric depth points   final upper/lower limit in log (tau5000)   maximum number of iterations   microturbulence   with TAULIMITS  0.0 0.0  the limits are freely adjusted

  
  
  
• The element file
  
  The abundances in the element file are logarithmic (with the abundance of hydrogen = 12.00).
   

  1  H   12.00    1.008 2   : -  2  He  10.93    4.00  3   : -  3  Li   1.10    6.94  4   : -  4  Be   1.40    9.02  4   : -  5  B    2.55   10.82  4   : -  6  C    8.52   12.01  6   : -  7  N    7.92   14.01  6   : -  8  O    8.83   16.00  6   : -  9  F    4.56   19.00  6   : - 10  Ne   8.08   20.18  6   : - 11  Na   6.33   23.00  6   : - 12  Mg   7.58   24.32  6   : - 13  Al   6.47   26.97  6   : - 14  Si   7.55   28.06  6   : - 8.10 15  P    5.45   30.98  6   : - 16  S    7.33   32.07  6   : - 17  Cl   5.50   35.46  5   : - 18  Ar   6.40   39.94  5   : - 19  K    5.12   39.10  5   : - 20  Ca   6.36   40.08  5   : - 21  Sc   3.17   45.10  5   : - 22  Ti   5.02   47.90  5   : - 23  V    4.00   50.95  5   : - 24  Cr   5.67   52.01  5   : - 6.25 25  Mn   5.39   54.93  5   : - 26  Fe   7.50   55.85  5   : + 27  Co   4.92   58.94  5   : - 28  Ni   6.25   58.69  5   : - 7.00 29  Cu   4.21   63.54  3   : - ...

  All elements are listed with:       atomic number, element symbol, solar abundance,         atomic weight, no. of ionisation stages considered   There must be no blanks following the '-'       except when vertically constant non-standard abundances       are specified as (in this example) for Mg       There must be no blanks after the numbers   Elements for which (stratified) abundances are given are marked by a '+'   There must be no blanks following the '+'    For each element with '+' there has to be a file named  strat_init.xx        e.g. strat_init.26 for Fe   a further extension can be added to this file name, e.g. strat_init.26.homog   each file has to contain the abundances for all depth points   There has to be at least 1 '+' and its associated stratification file

  
  
  
• The atmospheric model file (Kurucz format)
  
    A Kurucz atmospheric model file with T_eff = 10000 K, log_g = 4.00, solar abundances, and 99 depth points look as follows
  
  

  TEFF  10000.0   GRAVITY   4.00   LTE TITLE  [0.0] VTURB=0  NOVER NEW ODF                                                   OPACITY IFOP 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 0 0 0 0  CONVECTION OFF  1.00  TURBULENCE OFF  0.00  0.00  0.00  0.00  ABUNDANCE SCALE     1.00000   ABUNDANCE CHANGE   1 0.92042 2 0.07834  ABUNDANCE CHANGE    3 -10.94  4 -10.64  5  -9.49  6  -3.52  7  -4.12  8  -3.21  ABUNDANCE CHANGE    9  -7.48 10  -3.96 11  -5.71 12  -4.46 13  -5.57 14  -4.49  ABUNDANCE CHANGE   15  -6.59 16  -4.71 17  -6.54 18  -5.64 19  -6.92 20  -5.68  ABUNDANCE CHANGE   21  -8.87 22  -7.02 23  -8.04 24  -6.37 25  -6.65 26  -4.54  ABUNDANCE CHANGE   27  -7.12 28  -5.79 29  -7.83 30  -7.44 31  -9.16 32  -8.63  ABUNDANCE CHANGE   33  -9.75 34  -8.71 35  -9.48 36  -8.76 37  -9.44 38  -9.07  ABUNDANCE CHANGE   39  -9.80 40  -9.44 41 -10.62 42 -10.12 43 -12.03 44 -10.20  ABUNDANCE CHANGE   45 -10.92 46 -10.35 47 -11.10 48 -10.27 49 -10.38 50 -10.04  ABUNDANCE CHANGE   51 -11.04 52  -9.85 53 -10.53 54  -9.77 55 -10.97 56  -9.91  ABUNDANCE CHANGE   57 -10.87 58 -10.46 59 -11.33 60 -10.54 61 -12.03 62 -11.03  ABUNDANCE CHANGE   63 -11.53 64 -10.92 65 -11.76 66 -10.90 67 -11.78 68 -11.11  ABUNDANCE CHANGE   69 -12.03 70 -10.96 71 -11.98 72 -11.16 73 -12.03 74 -10.93  ABUNDANCE CHANGE   75 -11.81 76 -10.59 77 -10.69 78 -10.24 79 -11.03 80 -10.91  ABUNDANCE CHANGE   81 -11.14 82 -10.09 83 -11.39 84 -12.03 85 -12.03 86 -12.03  ABUNDANCE CHANGE   87 -12.03 88 -12.03 89 -12.03 90 -11.98 91 -12.03 92 -12.03  ABUNDANCE CHANGE   93 -12.04 94 -12.04 95 -12.04 96 -12.04 97 -12.04 98 -12.04  ABUNDANCE CHANGE   99 -12.04 READ   DECK6   99 Rho_x, T, P_gas, N_e, abs_ross, ACCRAD, v_turb  2.29217593E-04   7036.8 2.288E+00 5.417E+11 2.065E-01 1.964E+01 0.000E+00 0.000E+00 0.000E+00  2.62762764E-04   7060.4 2.623E+00 6.077E+11 2.106E-01 1.997E+01 0.000E+00 0.000E+00 0.000E+00  3.00530902E-04   7083.1 3.000E+00 6.798E+11 2.146E-01 2.011E+01 0.000E+00 0.000E+00 0.000E+00  ....  2.07107611E+00  21331.2 2.020E+04 3.410E+15 1.203E+01 2.268E+02 0.000E+00 0.000E+00 0.000E+00  2.39591986E+00  22049.9 2.338E+04 3.821E+15 1.204E+01 2.267E+02 0.000E+00 0.000E+00 0.000E+00  2.76790177E+00  22796.0 2.701E+04 4.273E+15 1.208E+01 2.261E+02 0.000E+00 0.000E+00 0.000E+00 PRADK    1.3437E+01

  everything is in Kurucz's format       but beware of Fortran style   floating point numbers :   in Ada it's  10000.0           not   10000.  last line is the one with PRADK

  
  

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