Dump variables to dat files

There are two ways to add variables to the dat files:

Extra variables

This method adds extra variables in the dat file (which is also used for restart) and it is used in many tests: ard/analytic_test_1d, demo/Advect_ParticleSampling_2D, hd/Gresho_Chan_2D, ... To see all the tests which use this method, in the tests folder run:

find . -name 'mod_usr.t' -exec grep -H "var_set_extravar" {} \;

This method consists in:

1. Assign an index in the variable list w in usr_init subroutine (in mod_usr.t) using var_set_extravar
2. Implement one of the user methods which are called every timestep: usr_process_grid, usr_modify_output,... and set there the extra variables (and properly assign the pointer to the implemented subroutine in usr_init).

New dat files

With this method an extra dat file is generated with new variables. (see amrvacio/mod_convert.t).

1. Set convert_type to "dat_generic_mpi":

    &filelist
          ...
          convert_type = "dat_generic_mpi"
          ...
    /
   

2. Add a convert method in usr_init subroutine (use mod_convert):

    call add_convert_method2(dump_vars, 4, "jx jy jz sxr", "_aux_") 
   

   or

       call add_convert_method(dump_vars, 4, (/" jx", " jy", " jz", "sxr"/), "_aux_")
   

   The first way is preferred as because Fortran requires the strrings in an array to have the same length and extra spaces might be necessary for this. The last argument _aux_ is the suffix added to base_filename in order to generate the name of the new dat file.
3. Implement dump_vars function:

    function dump_vars(ixI^L, ixO^L, w, x, nwc) result(wnew)
      use mod_global_parameters
      use mod_thermal_emission
      integer, intent(in)             :: ixI^L,ixO^L, nwc
      double precision, intent(in)    :: w(ixO^S, 1:nw)
      double precision, intent(in)    :: x(ixO^S,1:ndim)
      double precision    :: wnew(ixO^S, 1:nwc)
      double precision :: current(ixI^S,7-2*ndir:3)
      integer :: idirmin,idir
      double precision    :: tmp(ixI^S)
      call get_current(w,ixI^L,ixO^L,idirmin,current)
      wnew(ixO^S,1) =  current(ixO^S,1)
      wnew(ixO^S,2) =  current(ixO^S,2)
      wnew(ixO^S,3) =  current(ixO^S,3)
      call get_SXR(ixI^L,ixO^L,w,x,te_fl_c,tmp,9,12)
      wnew(ixO^S,4) =  tmp(ixO^S)
    end function dump_vars
   

   Examples of use in the main code

1. For the mhd model for dumping full variables by setting in the parameter file:

    &mhd_list
      mhd_dump_full_vars=.true.
    /  
   

   A new file is created with hardcoded suffix new.
2. For the two-fluid model for:
   1. dumping full variables by setting in the parameter file:

       &twofl_list
         twofl_dump_full_vars=.true.
       /  
      

      A new file is created with hardcoded suffix new.
   2. dumping the collisional terms by setting in the parameter file:

       &twofl_list
         twofl_dump_coll_terms=.true.
       /  
      

      A new file is created with hardcoded suffix _coll.