Processing all directories
--------------------------

Given the standard layout of the NEMOv4 src directories, the following script can be used to
produce all the submod.list files::

  #!/bin/bash
  # Start in src directory
  #
  # set modmap_dir to the location of the NEMOmodmap scripts
  #
       export modmap_dir=/home/acc/NEMOmodmap
  #
  # Create module/subroutine/function list for OCE top-directory
  #
       cd OCE
       $modmap_dir/mksubmodlist
       mv newsubmod.list OCE_submod.list
  #
  # Repeat for all OCE subdirectories
  #
       for f in ASM  DIA  FLO  LDF BDY  DIU  ICB C1D  DOM  IOM CRS  DYN  LBC OBS SBC TRA ZDF STO TRD USR
       do 
        cd $f
        $modmap_dir/mksubmodlist
        mv newsubmod.list ../${f}_submod.list
        cd ../
       done
  #
  # Similarly for TOP
  #
       cd ../TOP
       $modmap_dir/mksubmodlist
       mv newsubmod.list TOP_submod.list
  #
  # and TOP subdirectories
  #
       for f in AGE C14 CFC PISCES MY_TRC 
       do 
        cd $f
        $modmap_dir/mksubmodlist
        mv newsubmod.list ../${f}_submod.list
        cd ../
       done
  #
  # .. but PISCES has subdirectories of its own
  #
       cd PISCES
       for f in SED P2Z P4Z
       do 
        cd $f
        $modmap_dir/mksubmodlist
        mv newsubmod.list ../${f}_submod.list
        cd ../
       done
  #
  # Rename these to reference their parent directory
  #
       mv P2Z_submod.list ../PISCES_P2Z_submod.list
       mv P4Z_submod.list ../PISCES_P4Z_submod.list
       mv SED_submod.list ../PISCES_SED_submod.list
       cd ../
  #
  # Also list ICE routunes
  #
       cd ../ICE
       $modmap_dir/mksubmodlist
       mv newsubmod.list ../ICE_submod.list
       cd ../
  #
  # and Finally the remaining bits
  #
       for f in NST OFF  SAO  SAS
       do
        cd $f
        $modmap_dir/mksubmodlist
        mv newsubmod.list ../${f}_submod.list 
        cd ../
       done
  #
  # Which should provide this lot:
  # cd ../
  # find ./ -name '*submod*'
  #
  # ./src/TOP
  # ./src/TOP/AGE_submod.list         ./src/TOP/C14_submod.list         ./src/TOP/CFC_submod.list
  # ./src/TOP/MY_TRC_submod.list      ./src/TOP/PISCES_submod.list      ./src/TOP/TRP_submod.list
  # ./src/TOP/PISCES_P2Z_submod.list  ./src/TOP/PISCES_P4Z_submod.list  ./src/TOP/PISCES_SED_submod.list
  # 
  # ./src/OCE
  # ./src/OCE/ASM_submod.list         ./src/OCE/LDF_submod.list         ./src/OCE/DIU_submod.list
  # ./src/OCE/ICB_submod.list         ./src/OCE/DOM_submod.list         ./src/OCE/IOM_submod.list
  # ./src/OCE/CRS_submod.list         ./src/OCE/DYN_submod.list         ./src/OCE/TRD_submod.list
  # ./src/OCE/OBS_submod.list         ./src/OCE/SBC_submod.list         ./src/OCE/TRA_submod.list
  # ./src/OCE/ZDF_submod.list         ./src/OCE/OCE_submod.list         ./src/OCE/BDY_submod.list
  # ./src/OCE/C1D_submod.list         ./src/OCE/DIA_submod.list         ./src/OCE/FLO_submod.list
  # ./src/OCE/LBC_submod.list         ./src/OCE/STO_submod.list         ./src/OCE/USR_submod.list
  # 
  # ./src/ICE_submod.list
  # 
  # ./src/OFF_submod.list             ./src/SAO_submod.list
  # ./src/SAS_submod.list             ./src/NST_submod.list