The preprocessor sources files are in src and the makefile is in make.
Do ./clean; ./mk to create the executable.
Run the preprocessor by using one of the rn* scripts.
Typically, you'll just want to rebuilt everything -- use the ./rebuild_all script for that.
For testing, you can edit the rn_test script to do a single kap file.

The preprocessor is controlled by inlists.   
At the time of writing (Oct, 2013) we use the following inlists:

   inlist_OP_a05+Ne
   inlist_OP_a09
   inlist_OP_a09_Przybilla
   inlist_OP_gs98
   inlist_a05+Ne
   inlist_a09
   inlist_gn93
   inlist_gn93_CO
   inlist_gs98
   inlist_gs98_aFe_m2
   inlist_gs98_aFe_p2
   inlist_gs98_aFe_p3
   inlist_gs98_aFe_p4
   inlist_gs98_aFe_p4_CO
   inlist_gs98_aFe_p6
   inlist_gs98_aFe_p8
   inlist_lowT_Freedman11
   inlist_lowT_af94_gn93
   inlist_lowT_fa05_a09
   inlist_lowT_fa05_a09_aFe_p3
   inlist_lowT_fa05_ags04
   inlist_lowT_fa05_gn93
   inlist_lowT_fa05_gs98
   inlist_lowT_fa05_gs98_aFe_m2
   inlist_lowT_fa05_gs98_aFe_p2
   inlist_lowT_fa05_gs98_aFe_p4
   inlist_lowT_fa05_gs98_aFe_p6
   inlist_lowT_fa05_gs98_aFe_p8

The inlists give information about the location of the input data,
and the specifications for the output.  
For example, here's the contents of inlist_OP_a09:

      data_dir = 'kap_input_data/OP'
      OP_file = .true.
      type1_table = 'A09.OP17'
      logR_min = -8.00d0
      logR_max = 1.00d0
      logR_points = 37
      logT_file = 'logT_points_highT_8.0'
      output_dir = 'data/kap_data'
      table_prefix = 'OP_a09'
      header_info = 'fixed metal distribution -- based on Asplund, Grevesse, Sauval, and Scott (2009) solar abundances'
      table_version = 36

Each of these inlists appears in the rebuild_add script in a line like this:

   do_one inlist_OP_a09
   
The input data lives in a subdirectory of the kap/preprocessor/kap_input_data directory.
The 'data_dir' entry in the inlist gives the path, and the 'type1_table' entry gives the filename.
So the input data for OP_a09 is in the file kap_input_data/OP/A09.OP17.
The kap_input_data is distributed in the mesa download as a tar.bz2 file.
If you add to the kap_input_data files, rerun the build_kap_input_tar_bz2 script.

To add a new set of opacity tables, 
put the input data files in the right subdirectory in kap_input_data,
create a new inlist, and 
a line for the inlist to the rebuild_all script,
then run ./rebuild_all

At the end of rebuild_all, it will tell you to run ./build_4_export
Do that -- it will create kap_data.tar.bz2

At the end of build_4_export, it will tell you to do 
   cd .. ; ./build_data_and_export
   
Do that -- it will unpack and install the new mesa kap tables.

Now check the new data by making plots.
Edit the file mesa/kap/test/src/plot_kap.f to tell it which opacities to plot by setting kappa prefix strings.
Edit kap/test/src/test_kap_support to set the composition and logT, logRho bounds for the plot.
For composition, here's an example for doing Type1 opacities:
   xh = 0.30d0
   Z = 0.02d0
   XC = 0.0
   XN = 0.0
   XO = 0.0
   XNe = 0.0
   Zbase = -1

and here's an example for Type2 where you need to give zbase, xc, and xo.
   z =    2.67d-2
   zbase = 1d-5
   xh =    2.8d-2
   xc =    2d-3
   xo =    3.56d-3
   
Set the bounds for the plot like this:
   logT_max = 10.2d0
   logT_min = 1.7d0
   logRho_max = 11d0
   logRho_min = -11d0

And set the resolution like this:
   logT_points = 101
   logRho_points = 101

The do ./mk to rebuild the plotter and ./plotter to run it.
That will give terminal output like this
 kappa_file_prefix gs98
 kappa_lowT_prefix lowT_fa05_gs98
 write data for opacity plots to plot_data
           1
           2
           3
           4
           5
           6
and it will store files in the test/plot_data directory.

I make plots from that data using the tioga script kap/test/kap.rb
You can edit the "logK_with_contours" in that to set the range for the colormap.
        z_lower = -6.7
        z_upper = 9



