August 25, 2000

General instructions for running the level model formulation:

1) Download the model, which includes levelcode.f, dimensions.h 
   and common_blocks.h, into the same directory and compile them. 

2) Download the program required to interpolate the layer model 
   output to level model output, l2l.f, into the same directory 
   and compile it.

You now have all of the executable programs required.

3) Download the forcing data file into the same directory. 
   Depending on your operating system, download either the 
   .Z files (Unix/Linux) or the .zip files (Win9x).
   There is a datafile for the diurnal and no diurnal forcing sets.
   
   Diurnal:    layercode_data.asc.Z      layercode_data.zip
   No diurnal: layercode_nod_data.asc.Z  layercode_nod_data.zip

   Uncompress the .Z file using the standard UNIX compression utility, or 
   unzip the .zip file using "winzip" or "pkzip" on your PC.

4) Run the executable of l2l.f to interpolate the datafile to level 
   coordinates. This will create a large binary file called levelcode.dat 
   which is required to run the biological level model.  

Now you should have the two things you need to run: the executable
biological level model (e.g., levelcode.exe) and a binary file 
containing the McCreary et al. model output interpolated to level 
coordinates (i.e., levelcode.dat).  When you run the model it will 
automatically pick up the binary forcing file and run over the time
period of the U.S. JGOFS Process Study and WHOI mooring site time
period (October, 1994 through October, 1995).

5) In addition to running with the required fields, it is also
   possible to use the initial values for N, P, Z and D that were 
   generated by the 3-D model at the begining of the run.  To do 
   this, download the intialization file initbio_layer.asc.
   and convert it to level coordinates using the program 
   l2l_init.f. In order to run the biological model using these initial 
   fields set icond = 1 in levelcode.f before it is compiled.  With icond = 1 
   the model will automatically pick up the file and initialize 
   with it. 

7) The model can also be run using the horizontal advection fields
   for the biological quantities generated by the McCreary et al. 
   3-D solution.  To do that, download the optional advective fields
   (bioadv_layer.asc or bioadv_nod.asc), uncompress, and 
   convert it to levels using l2l_adv.f.  In levelcode.f set opt = 1
   or opt = 2 before it is compiled.  With opt = 1 the model will
   automatically pick up the horizontal advection file and include 
   the effects of advection on the four state variables available 
   from the biological model in McCreary et al. (i.e., N, P, Z, 
   and D). [Note: since there is no advection field available for 
   DON or T the code uses the P gradient to calculate the effect of 
   advection on DON (i.e., it assumes that DON concentrations will
   covary with P concentrations) and assumes no horizontal gradient
   in T (i.e., no advective effects].  With opt = 2 the model 
   will include only the effects of horizontal advection of DIN.