v12: Remove support for mom5

AGCM.rc.tmpl

@@ -172,7 +172,6 @@ OGCM.JM_WORLD: @OGCM_JM
 OGCM.LM: @OGCM_LM
 @COUPLED OGCM.NX: @OGCM_NX
 @COUPLED OGCM.NY: @OGCM_NY
-@MOM5 OGCM.GRIDSPEC: MAPL_Tripolar.nc
 @MOM6 OGCM.GRIDSPEC: MAPL_Tripolar.nc
 @MIT  OGCM.GRIDSPEC: mit.ascii
 @MIT  OCEAN_DIR: mitocean_run
@@ -1007,15 +1006,15 @@ USE_WAVES: 0
 @COUPLED steady_state_ocean: 0
 @COUPLED OCEAN_PICE_SCALING: 0.0
 
-# For running MOM5 coupled model in dual ocean mode, uncomment three lines below,
+# For running MOM6 coupled model in dual ocean mode, uncomment three lines below,
 # make sure that regular replay is enabled, proper PRECIP_FILE is chosen,
 # sst.data and fraci.data are pointing to read forcing files on tripolar grid,
 # the run starts at 21z/03z/09z/15z,
 # HISTORY.rc collections have proper ref_time field
 # ---------------------------------------------------------------------------
-@MOM5#DUAL_OCEAN: 1
-@MOM5#DATA_SST_FILE: sst.data
-@MOM5#DATA_FRT_FILE: fraci.data
+@MOM6#DUAL_OCEAN: 1
+@MOM6#DATA_SST_FILE: sst.data
+@MOM6#DATA_FRT_FILE: fraci.data
 
 @COUPLED
 @COUPLED# Section for CICE

gcm_forecast.tmpl

@@ -420,7 +420,6 @@ done:
 setenv BCSDIR    @BCSDIR
 @DATAOCEANsetenv SSTDIR    @SSTDIR
 setenv BCRSLV    @ATMOStag_@OCEANtag
-@MOM5setenv SSTDIR  @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}/v1
 @MOM6setenv SSTDIR  @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}/v1
 
 #this is hard-wired for NAS for now - should make it more general
@@ -696,7 +695,6 @@ endif
 
 if (! -e tile.bin) then
 $GEOSBIN/binarytile.x tile.data tile.bin
-@MOM5 $GEOSBIN/binarytile.x tile_hist.data tile_hist.bin
 endif
 
 # If running in dual ocean mode, link sst and fraci data here

gcm_regress.j

@@ -262,12 +262,6 @@ COLLECTIONS: test_collection
 @DATAOCEAN                                    'T'   , 'DYN'  ,
 @DATAOCEAN                                    'U;V' , 'DYN'  ,
 @DATAOCEAN                                    'Q'   , 'MOIST', 'QV',
-@MOM5  test_collection.fields:           'UW'   ,'MOM'  , 'US',
-@MOM5                                    'VW'   ,'MOM'  , 'VS',
-@MOM5                                    'TW'   ,'MOM'  , 'TS',
-@MOM5                                    'SW'   ,'MOM'  , 'SS',
-@MOM5                                    'SLV'  ,'MOM'  ,
-@MOM5                                    'QFLUX','OCEAN' ,
 @MOM6  test_collection.fields:           'UW'   ,'MOM6'  , 'US',
 @MOM6                                    'VW'   ,'MOM6'  , 'VS',
 @MOM6                                    'TW'   ,'MOM6'  , 'TS',
@@ -801,7 +795,6 @@ if ( $RUN_LAYOUT == TRUE) then
    @COUPLED /bin/mv AGCM.rc AGCM.tmp
    @COUPLED cat AGCM.tmp | sed -e "s?$oldstring?$newstring?g" > AGCM.rc
 
-   @MOM5sed -r -i -e "/^ *layout/ s#= ([0-9]+),*([0-9]+)#= ${test_NY},${test_NX}#" input.nml
    @MOM6sed -r -i -e "s/#override LAYOUT = 3, 2/#override LAYOUT = ${test_NY}, ${test_NX}/g" MOM_override
 
    setenv YEAR `cat cap_restart | cut -c1-4`
@@ -924,7 +917,6 @@ if ( $RUN_OPENMP == TRUE) then
    @COUPLED /bin/mv AGCM.rc AGCM.tmp
    @COUPLED cat AGCM.tmp | sed -e "s?$oldstring?$newstring?g" > AGCM.rc
 
-   @MOM5sed -r -i -e "/^ *layout/ s#= ([0-9]+),*([0-9]+)#= ${OGCM_NX0},${OGCM_NY0}#" input.nml
    @MOM6sed -r -i -e "s/#override LAYOUT = 3, 2/#override LAYOUT = ${OGCM_NX0}, ${OGCM_NY0}/g" MOM_override
 
    setenv YEAR `cat cap_restart | cut -c1-4`

gcm_run.j

@@ -370,7 +370,6 @@ done:
 setenv BCSDIR    @BCSDIR
 @DATAOCEANsetenv SSTDIR    @SSTDIR
 setenv BCRSLV    @ATMOStag_@OCEANtag
-@MOM5setenv SSTDIR  @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}/v1
 @MOM6setenv SSTDIR  @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}/v1
 
 #this is hard-wired for NAS for now - should make it more general
@@ -804,8 +803,6 @@ endif
 @COUPLEDset HEARTBEAT_DT = `grep '^\s*HEARTBEAT_DT:' CAP.rc | cut -d: -f2 | awk '{print $1}'`
 
 @COUPLED sed -i -e "s/OGCM_RUN_DT: [0-9]\+\(\.[0-9]\+\)\?/OGCM_RUN_DT: $HEARTBEAT_DT/g" AGCM.rc
-@MOM5 sed -i -e "s/dt_cpld = [0-9]\+\(\.[0-9]\+\)\?,/dt_cpld = $HEARTBEAT_DT,/g" \
-@MOM5        -e "s/dt_atmos = [0-9]\+\(\.[0-9]\+\)\?,/dt_atmos = $HEARTBEAT_DT,/g" MOM_override
 @MOM6 sed -i -e "s/DT = [0-9]\+\(\.[0-9]\+\)\?/DT = $HEARTBEAT_DT/g" \
 @MOM6        -e "s/DT_THERM = [0-9]\+\(\.[0-9]\+\)\?/DT_THERM = $HEARTBEAT_DT/g" MOM_override
 @CICE6 sed -i -E "s/^([[:space:]]*dt[[:space:]]*=[[:space:]]*)[0-9]+(\.[0-9]+)?/\1${HEARTBEAT_DT}/" ice_in
@@ -1352,15 +1349,7 @@ end
 
 @COUPLED # MOM-Specific Output Files
 @COUPLED # -------------------------
-@MOM5 set dsets="ocean_month"
 @MOM6 set dsets="ocean_state prog_z sfc_ave forcing"
-@MOM5  foreach dset ( $dsets )
-@MOM5  set num = `/bin/ls -1 $dset.nc | wc -l`
-@MOM5  if($num != 0) then
-@MOM5     if(! -e $EXPDIR/MOM_Output) mkdir -p $EXPDIR/MOM_Output
-@MOM5     /bin/mv $SCRDIR/$dset.nc $EXPDIR/MOM_Output/$dset.${edate}.nc
-@MOM5  endif
-@MOM5  end
 @MOM6  foreach dset ( $dsets )
 @MOM6  set num = `/bin/ls -1 $dset.nc | wc -l`
 @MOM6  if($num != 0) then

gcm_run.j-new_rst_approach

@@ -383,7 +383,6 @@ done:
 setenv BCSDIR    @BCSDIR
 @DATAOCEANsetenv SSTDIR    @SSTDIR
 setenv BCRSLV    @ATMOStag_@OCEANtag
-@MOM5setenv SSTDIR  @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}/v1
 @MOM6setenv SSTDIR  @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}/v1
 
 #this is hard-wired for NAS for now - should make it more general
@@ -1278,15 +1277,7 @@ end
 
 @COUPLED # MOM-Specific Output Files
 @COUPLED # -------------------------
-@MOM5 set dsets="ocean_month"
 @MOM6 set dsets="ocean_state prog_z sfc_ave forcing"
-@MOM5  foreach dset ( $dsets )
-@MOM5  set num = `/bin/ls -1 $dset.nc | wc -l`
-@MOM5  if($num != 0) then
-@MOM5     if(! -e $EXPDIR/MOM_Output) mkdir -p $EXPDIR/MOM_Output
-@MOM5     /bin/mv $SCRDIR/$dset.nc $EXPDIR/MOM_Output/$dset.${edate}.nc
-@MOM5  endif
-@MOM5  end
 @MOM6  foreach dset ( $dsets )
 @MOM6  set num = `/bin/ls -1 $dset.nc | wc -l`
 @MOM6  if($num != 0) then

gcm_run_benchmark.j

@@ -313,8 +313,6 @@ setenv CHMDIR    @CHMDIR
 setenv DATELINE  DC
 setenv EMISSIONS @EMISSIONS
 
-@MOM5setenv ABCSDIR  @COUPLEDIR/atmosphere_bcs/@LSMBCS/MOM5/@ATMOStag_@OCEANtag
-@MOM5setenv OBCSDIR  @shared_COUPLED/ocean/MOM5/${OGCM_IM}x${OGCM_JM}
 @MOM6setenv ABCSDIR  @COUPLEDIR/atmosphere_bcs/@LSMBCS/MOM6/@ATMOStag_@OCEANtag
 @MOM6setenv OBCSDIR  @shared_COUPLED/ocean/MOM6/${OGCM_IM}x${OGCM_JM}
 @COUPLEDsetenv SSTDIR  @COUPLEDIR/SST/MERRA2/${OGCM_IM}x${OGCM_JM}
@@ -335,7 +333,6 @@ cat << _EOF_ > $FILE
 @COUPLED/bin/ln -sf $ABCSDIR/@[email protected]   runoff.bin
 @COUPLED/bin/ln -sf $OBCSDIR/MAPL_Tripolar.nc .
 @COUPLED/bin/ln -sf $OBCSDIR/vgrid${OGCM_LM}.ascii ./vgrid.ascii
-@MOM5#/bin/ln -s @COUPLEDIR/a@HIST_IMx@HIST_JM_o${OGCM_IM}x${OGCM_JM}/DC0@HIST_IMxPC0@[email protected] tile_hist.data
 @MOM6#/bin/ln -s @COUPLEDIR/MOM6/DC0@HIST_IMxPC0@HIST_JM_@OCEANtag/DC0@HIST_IMxPC0@[email protected] tile_hist.data
 
 # Precip correction
@@ -725,7 +722,6 @@ endif
 
 if (! -e tile.bin) then
 $GEOSBIN/binarytile.x tile.data tile.bin
-@MOM5 $GEOSBIN/binarytile.x tile_hist.data tile_hist.bin
 endif
 
 # If running in dual ocean mode, link sst and fraci data here
@@ -1080,7 +1076,6 @@ end
 
 @COUPLED # MOM-Specific Output Files
 @COUPLED # -------------------------
-@MOM5 set dsets="ocean_month"
 @MOM6 set dsets="ocean_state prog_z sfc_ave forcing"
 @COUPLED  foreach dset ( $dsets )
 @COUPLED  set num = `/bin/ls -1 $dset.nc | wc -l`

gcm_setup

@@ -546,7 +546,6 @@ if( $OGCM == TRUE ) then
     # -----------
     OCNMODEL:
     echo "Choose an ${C1}Ocean Model${CN}: (Default: ${C2}MOM6${CN})"
-    echo "   ${C2}MOM5${CN}"
     echo "   ${C2}MOM6${CN}"
     echo "   ${C2}MIT${CN}"
 
@@ -556,9 +555,9 @@ if( $OGCM == TRUE ) then
     else
        set OCNMODEL = `echo $OCNMODEL | tr "[:lower:]" "[:upper:]"`
 
-       if ( "$OCNMODEL" != "MOM5" & "$OCNMODEL" != "MOM6"  & "$OCNMODEL" != "MIT") then
+       if ( "$OCNMODEL" != "MOM6"  & "$OCNMODEL" != "MIT") then
           echo
-          echo "${C1}Ocean Model${CN} must be either MOM5, MOM6 or MIT!"
+          echo "${C1}Ocean Model${CN} must be either MOM6 or MIT!"
           goto OCNMODEL
        else
           echo
@@ -567,23 +566,11 @@ if( $OGCM == TRUE ) then
 
     # NOTE: We use a CMake variable here because the shared library
     # suffix is different on Linux and macOS. This is set by configure_file()
-    if ( "$OCNMODEL" == "MOM5" ) then
-       set OCEAN_NAME="MOM"
-       set OGRIDTYP  = "M5TP"
-       set OCEAN_PRELOAD = 'env @PRELOAD_COMMAND=$GEOSDIR/lib/libmom@CMAKE_SHARED_LIBRARY_SUFFIX@'
-       set MOM5=""
-       set MOM6 = "#DELETE"
-       set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM-MOM5.rc.tmpl"
-
-       set mom5_warning="######################################################\nYou (user) have chosen to set up a coupled model experiment with MOM5.\nBe aware that such a set up is _known_ to have problems. See following for more details.\nhttps://github.com/GEOS-ESM/MOM5/issues/19\nIf your intent is to help _fix_ above issue, your help is much appreciated. Thank you and good luck!\nOtherwise, until this above issue is _fixed_ you are on your own with above choice.\n######################################################"
-       echo "\033[31;5m"${mom5_warning}"\033[0m"
-       set MIT  = "#DELETE"
-    else if ( "$OCNMODEL" == "MOM6" ) then
+    if ( "$OCNMODEL" == "MOM6" ) then
        set OCEAN_NAME="MOM6"
        set OGRIDTYP  = "M6TP"
        set OCEAN_PRELOAD = 'env @PRELOAD_COMMAND=\$GEOSDIR/lib/libmom6@CMAKE_SHARED_LIBRARY_SUFFIX@'
        set MOM6=""
-       set MOM5 = "#DELETE"
        set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM.rc.tmpl"
        set MIT  = "#DELETE"
     else if ( "$OCNMODEL" == "MIT" ) then
@@ -592,7 +579,6 @@ if( $OGCM == TRUE ) then
        set OGRIDTYP  = "MITLLC"
        set MIT = ""
        set DEFAULT_HISTORY_TEMPLATE="HISTORY.AOGCM_MITgcm.rc.tmpl"
-       set MOM5 = "#DELETE"
        set MOM6 = "#DELETE"
     endif
 
@@ -608,25 +594,6 @@ if( $OGCM == TRUE ) then
         set OGCM_JM = 15
         set OGCM_IM = `expr $OGCM_JM \* 360`
 
-    else if ( $OCEAN_NAME == "MOM" ) then
-        set Resolution = `echo 360 200`
-        echo "Enter the Ocean Lat/Lon ${C1}Horizontal Resolution${CN}: ${C2}IM JM${CN} (Default:" $Resolution")"
-        set Resolution = `echo $<`
-        set num = $#Resolution
-        if( $num == 2 ) then
-           set OGCM_IM = $Resolution[1]
-           set OGCM_JM = $Resolution[2]
-        else
-           set Resolution = `echo 360 200`
-
-           if( $num == 0 ) then
-              set OGCM_IM = $Resolution[1]
-              set OGCM_JM = $Resolution[2]
-           else
-              goto CORSLV
-           endif
-        endif
-
     else if ( "$OCNMODEL" == "MOM6" ) then
        # For MOM6 we currently have only 3 allowed ocean resolutions based on the
        # atmospheric resolution. The allowed are:
@@ -910,7 +877,6 @@ else
     set OCEAN_PRELOAD = ""
     set OGCM_LM   =  34
     set COUPLED   = "#DELETE"
-    set MOM5      = "#DELETE"
     set MOM6      = "#DELETE"
     set CICE4     = "#DELETE"
     set CICE6     = "#DELETE"
@@ -2034,7 +2000,6 @@ s?@FORCEDAS?$FORCEDAS?g
 s?@FORCEGCM?$FORCEGCM?g
 s?@COUPLED?$COUPLED?g
 s?@CLDMICRO?$CLDMICRO?g
-s?@MOM5?$MOM5?g
 s?@MOM6?$MOM6?g
 s?@OCNMODEL?$OCNMODEL?g
 s?@CICE4?$CICE4?g
@@ -2198,11 +2163,7 @@ set FILES = `echo $FILES`
 set TMPOCEANDIR = `mktemp -d`
 
 if( $OGCM == TRUE & "$OCNMODEL" != "MIT" ) then
-   if ( $OCEAN_NAME == "MOM" ) then
-      /bin/cp ${ETCDIR}/MOM5/geos5/${OGCM_IM}x${OGCM_JM}/INPUT/input.nml ${TMPOCEANDIR}
-      /bin/cp ${ETCDIR}/MOM5/geos5/${OGCM_IM}x${OGCM_JM}/INPUT/*table ${TMPOCEANDIR}
-      set FILES = "$FILES field_table "
-   else if ( $OCEAN_NAME == "MOM6" ) then
+   if ( $OCEAN_NAME == "MOM6" ) then
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/MOM_input ${TMPOCEANDIR}
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/MOM_override ${TMPOCEANDIR}
       /bin/cp ${ETCDIR}/MOM6/mom6_app/${OGCM_IM}x${OGCM_JM}/input.nml ${TMPOCEANDIR}
@@ -2457,17 +2418,6 @@ if( $OGCM == TRUE ) then
 
       sed -i -e "s/DT = [0-9]*\.[0-9]*/DT = $OCEAN_DT/g" \
              -e "s/DT_THERM = [0-9]*\.[0-9]*/DT_THERM = $OCEAN_DT/g" $HOMDIR/MOM_override
-   else if ("$OCNMODEL" == "MOM5" ) then
-      # With MOM5 we need to change dt lines in input.nml to
-      # use $OCEAN_DT instead. NOTE: This sed assumes integer followed by comma
-
-      sed -i -e "s/dt_cpld = [0-9]*,/dt_cpld = $OCEAN_DT,/g" \
-             -e "s/dt_atmos = [0-9]*,/dt_atmos = $OCEAN_DT,/g" $HOMDIR/input.nml
-   endif
-
-   # We also need to change the dt in ice_in as well for CICE6
-   if ( $SEAICE_NAME == "CICE6" ) then
-      sed -i -E "s/^([[:space:]]*dt[[:space:]]*=[[:space:]]*)[0-9]+(\.[0-9]+)?/\1${OCEAN_DT}/" "$HOMDIR/ice_in"
    endif
 
 endif
@@ -2726,25 +2676,11 @@ if( $OGCM == TRUE ) then
 
 if ("$OCNMODEL" != "MIT" ) then
 
-# Some files are common to both MOM and MOM6
 cat >> $FILES_TO_PROCESS << EOF
 HOMDIR/input.nml
 HOMDIR/diag_table
 HOMDIR/__init__.py
 EXPDIR/plot/plotocn.j
-EOF
-endif
-
-# Some files are specific to MOM
-if ( "$OCNMODEL" == "MOM" ) then
-cat >> $FILES_TO_PROCESS << EOF
-HOMDIR/field_table
-EOF
-endif
-
-# Some files are specific to MOM6
-if ( "$OCNMODEL" == "MOM6" ) then
-cat >> $FILES_TO_PROCESS << EOF
 HOMDIR/MOM_override
 HOMDIR/MOM_input
 HOMDIR/data_table