--- MITgcm_contrib/osse/README	2004/06/08 17:37:45	1.4
+++ MITgcm_contrib/osse/README	2004/08/22 18:47:41	1.6
@@ -32,42 +32,63 @@
 
 CONTENTS
 
+EnKF: empty
+
+build: handy place to compile MITgcm
+
 code: modifications to MITgcm to run in cyclindrical coordinates.  At
 the time of this writing, it requires checkpoint48 to compile and run.
 
-input: initialization and input files for MITgcm
+codemod: modification to MITgcm to run with checkpoint 54.  Not quite
+ready for prime time.
 
-filter: source and data files to run the data assimilation and Kalman
-filter.
+da: location for ensemble members and initialization and input files 
 
-utils: assorted Matlab m-files 
+input: initialization and input files for running MITgcm
 
-EnKF: empty
+filter: source and data files to run the data assimilation and Kalman
+filter.
 
 run: empty
 
+utils: assorted Matlab m-files 
+
 
-COMPILING AND RUNNING THE MODEL
+COMPILING AND TESTING THE MODEL
 
 The following series of commands creates the MITgcm executable.  
 
 From the MITgcm root:
 
-cd verification/osse
-mkdir build   # directory name is arbitrary  
-cd build
+cd verification/osse/build  
 ../../../tools/genmake -mods=../code  # creates makefile
 make depend       # contructs Fortran code from model codebase
 make              # makes executable mitgcmuv
 
 Try a test run, while redirecting the standard output to a file.  The
 input directory contains files that should be present in the working
-directory when you run mitgcmuv.  It is recommended that you copy the
-input contents to a different directory for running -- mitgcmuv does
-not change them, but they can be lost in the multitudes of output
-files.
+directory when you run mitgcmuv.  Assuming that you compiled the 
+MITgcm executable in the build/ directory, you would run 
+``../build/mitgcmuv >& output.txt''  It is recommended that you copy the
+contents of the directory input/ to a different directory for running 
+-- mitgcmuv does not change them, but they can be lost in the multitudes 
+of output files.
 
 The data assimilation code is made by typing ``make'' in the filter
-directory.
+directory, which creates an executable named ``osse''.  
+
+Before running osse, the initial ensemble needs to be set up by
+running the mkens script in verification/osse/da.  mkens creates the
+directories, symbolically links files necessary to run the model, and
+copies in the initial ensemble files.  osse should be run from the
+directory verification/osse/da/inits since it expects the ensemble
+members to be one directory above.  It also expects to have in its
+working directory the file iobsloc-003.txt, which contains the
+locations of the observations.  This file is located in
+verification/osse/da/inits.
+
+
+
+