Made initialisation files more modular

file_guide.txt

@@ -36,12 +36,11 @@ romscice_ini.py: Builds a ROMS initialisation file using ECCO2 data for
                  temperature and salinity; starts with a motionless ocean and
 		 zero sea surface height. Depends on calc_z.py.
 		 To run: First edit user parameters (file paths and grid
-		         parameters) partway through the file (after the
-			 function interp_ecco2roms). Then make sure that you
-			 have scipy version 0.14 or higher (on raijin, this
-			 means switching to python/2.7.6; instructions at the
-			 top of the file). Then open python/ipython and type
-			 "run romscice_ini.py".
+		         parameters) near the bottom of the file. Then make
+			 sure that you have scipy version 0.14 or higher (on
+			 raijin, this means switching to python/2.7.6;
+			 instructions at the top of the file). Then open
+			 python/ipython and type "run romscice_ini.py".
 
 woa_netcdf.py: Converts World Ocean Atlas temperature and salinity data from
                text file (FESOM input format) to NetCDF.
@@ -55,12 +54,12 @@ romscice_ini_woa.py: Builds a ROMS initialisation file using World Ocean Atlas
 		     and uses WOA data assumed to be converted from FESOM input
 		     using woa_netcdf.py
 		     To run: First edit user parameters (file paths and grid
-		             parameters) partway through the file (after the
-			     function interp_woa2roms). Then make sure that you
-			     have scipy version 0.14 or higher (on raijin, this
-			     means switching to python/2.7.6; instructions at
-			     the top of the file). Then open python/ipython and
-			     type "run romscice_ini_woa.py".
+		             parameters) near the bottom of the file (after the
+			     Then make sure that you have scipy version 0.14 or
+			     higher (on raijin, this  means switching to
+			     python/2.7.6; instructions at the top of the file).
+			     Then open python/ipython and type "run
+			     romscice_ini_woa.py".
 
 convert_ecco.job: A batch job which converts 1 year of ECCO2 data into
                   northern lateral bounday conditions for ROMS. Depends on
@@ -154,8 +153,8 @@ romscice_ini_iceshelf.py: Given a ROMS initial condition file from ECCO2 data
 			  it's more realistic than filling the cavities with
 			  constant salinity, and certainly more stable).
 			  To run: Edit the user parameters (paths to 3 files)
-			          near the top of the script, then open python
-				  or ipython and type "run
+			          near the bottom of the script, then open
+				  python or ipython and type "run
 				  romscice_ini_iceshelf.py".