From 2185d73d1d3d4b449e9e911971f00782ce5f3822 Mon Sep 17 00:00:00 2001
From: Matthew Thompson <matthew.thompson@nasa.gov>
Date: Mon, 5 Feb 2024 11:02:39 -0500
Subject: [PATCH 1/3] Initialize USE_WAVES to 0

---
 AGCM.rc.tmpl | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index c7e36e47..9ff59044 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -116,7 +116,7 @@ CLOSURE_CONGESTUS: 3
 @HIST_GOCARTCA.br::CA.brphilic default
 @HIST_GOCARTCA.oc::CA.ocphilic default
 @HIST_GOCARTNI::NO3an1 "NI::NO3an2,NI::NO3an3"
-@HIST_GOCARTPCHEM::OX default 
+@HIST_GOCARTPCHEM::OX default
 @HIST_GOCART::
 @HIST_GOCART###########################################################
 
@@ -905,6 +905,10 @@ USE_SATSIM_RADAR: @RADAR_SATSIM
 USE_SATSIM_LIDAR: @LIDAR_SATSIM
 USE_SATSIM_MISR:  @MISR_SATSIM
 
+# Flags to enable wave code
+# -------------------------
+USE_WAVES: 0
+
 @COUPLED INTERPOLATE_ATMLM: 0
 @COUPLED INTERPOLATE_ATMTAU: 1
 @COUPLED INTERPOLATE_OCEAN_ICE_CURRENTS: 0
@@ -929,7 +933,7 @@ USE_SATSIM_MISR:  @MISR_SATSIM
 @MOM5#DATA_SST_FILE: sst.data
 @MOM5#DATA_FRT_FILE: fraci.data
 
-@COUPLED 
+@COUPLED
 @COUPLED# Section for CICE
 @COUPLED# -----------------
 @CICE4USE_CICE_Thermo: 1

From a1f20948242edb71e16ba1a63bbfb051afb3d118 Mon Sep 17 00:00:00 2001
From: Matthew Thompson <matthew.thompson@nasa.gov>
Date: Tue, 6 Feb 2024 10:08:54 -0500
Subject: [PATCH 2/3] Add more USE_WAVES protections

---
 gcm_run.j | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gcm_run.j b/gcm_run.j
index 502ac093..8c6ef107 100755
--- a/gcm_run.j
+++ b/gcm_run.j
@@ -644,7 +644,7 @@ else
     end
 
     # WW3 restart file
-    if( $wavemodel == "WW3" ) then
+    if( $USE_WAVES != 0 && $wavemodel == "WW3" ) then
         set rst_ww3 = "restart.ww3"
         if(-e $EXPDIR/${rst_ww3} ) /bin/cp $EXPDIR/${rst_ww3} . &
     endif
@@ -679,7 +679,7 @@ if($numrs == 0) then
    wait
 @COUPLED    cp -r $EXPDIR/RESTART ${EXPDIR}/restarts/RESTART.${edate}
    # WW3 restart file
-   if( $wavemodel == "WW3" ) then
+   if( $USE_WAVES != 0 && $wavemodel == "WW3" ) then
        set rst_ww3 = "restart.ww3"
        if( -e ${rst_ww3} ) cp ${rst_ww3}  ${EXPDIR}/restarts/$EXPID.${rst_ww3}.${edate}.${GCMVER}.${BCTAG}_${BCRSLV}
    endif
@@ -1318,7 +1318,7 @@ end
 
 # WW3 restarts - assumes that there is at least one NEW restart file
 # ------------------------------------------------------------------
-if( $wavemodel == "WW3" ) then
+if( $USE_WAVES != 0 && $wavemodel == "WW3" ) then
 
     set ww3checkpoint  = `/bin/ls -1 restart[0-9][0-9][0-9].ww3 | sort -n | tail -n 1`
     set rst_ww3 = "restart.ww3"
@@ -1326,7 +1326,7 @@ if( $wavemodel == "WW3" ) then
     cp $rst_ww3 ${EXPDIR}/restarts/$EXPID.${rst_ww3}.${edate}.${GCMVER}.${BCTAG}_${BCRSLV}.bin
 
     # remove intermediate restarts
-    set ww3checkpoint  = `/bin/ls -1 restart[0-9][0-9][0-9].ww3 | sort -n | tail -n 1` 
+    set ww3checkpoint  = `/bin/ls -1 restart[0-9][0-9][0-9].ww3 | sort -n | tail -n 1`
     if ( $#ww3checkpoint != 0 ) /bin/rm  ./restart[0-9][0-9][0-9].ww3
 endif
 
@@ -1437,7 +1437,7 @@ else
      wait
      cp cap_restart $EXPDIR/cap_restart
 
-     if( $wavemodel == "WW3" ) then 
+     if( $USE_WAVES != 0 &&  $wavemodel == "WW3" ) then
         set rst_ww3 = "restart.ww3"
         /bin/rm -f $EXPDIR/$rst_ww3
         cp $rst_ww3 $EXPDIR/$rst_ww3 &

From e430fb103eb4adf525829c1b3a3a2d1954bf5153 Mon Sep 17 00:00:00 2001
From: Anton Darmenov <anton.s.darmenov@nasa.gov>
Date: Tue, 6 Feb 2024 11:02:51 -0500
Subject: [PATCH 3/3] Improve readability

This commit introduces a logical variable 'wavewatch'. Said flag
controls the handling of WAVEWATCH namelists and restarts in the
gcm_run.j script.
---
 gcm_run.j | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gcm_run.j b/gcm_run.j
index 8c6ef107..f7244a23 100755
--- a/gcm_run.j
+++ b/gcm_run.j
@@ -631,6 +631,7 @@ end
 # -----------------------
 set USE_WAVES = `grep '^\s*USE_WAVES:' AGCM.rc| cut -d: -f2`
 set wavemodel = `cat WGCM.rc | grep "wave_model:" | cut -d "#" -f1 | cut -d ":" -f 2 | sed 's/\s//g'`
+set wavewatch = `$USE_WAVES != 0 && $wavemodel == "WW3"`
 
 # Copy Restarts to Scratch Directory
 # ----------------------------------
@@ -644,7 +645,7 @@ else
     end
 
     # WW3 restart file
-    if( $USE_WAVES != 0 && $wavemodel == "WW3" ) then
+    if( $wavewatch ) then
         set rst_ww3 = "restart.ww3"
         if(-e $EXPDIR/${rst_ww3} ) /bin/cp $EXPDIR/${rst_ww3} . &
     endif
@@ -679,7 +680,7 @@ if($numrs == 0) then
    wait
 @COUPLED    cp -r $EXPDIR/RESTART ${EXPDIR}/restarts/RESTART.${edate}
    # WW3 restart file
-   if( $USE_WAVES != 0 && $wavemodel == "WW3" ) then
+   if( $wavewatch ) then
        set rst_ww3 = "restart.ww3"
        if( -e ${rst_ww3} ) cp ${rst_ww3}  ${EXPDIR}/restarts/$EXPID.${rst_ww3}.${edate}.${GCMVER}.${BCTAG}_${BCRSLV}
    endif
@@ -839,7 +840,7 @@ endif
 
 # Set WW3 start date and time
 # ---------------------------
-if ( $USE_WAVES != 0 && $wavemodel == "WW3" ) then
+if( $wavewatch ) then
     cp ww3_multi.nml ww3_multi.nml.orig
     awk '{$1=$1};1' < ww3_multi.nml.orig > ww3_multi.nml
 
@@ -1318,7 +1319,7 @@ end
 
 # WW3 restarts - assumes that there is at least one NEW restart file
 # ------------------------------------------------------------------
-if( $USE_WAVES != 0 && $wavemodel == "WW3" ) then
+if( $wavewatch ) then
 
     set ww3checkpoint  = `/bin/ls -1 restart[0-9][0-9][0-9].ww3 | sort -n | tail -n 1`
     set rst_ww3 = "restart.ww3"
@@ -1437,7 +1438,7 @@ else
      wait
      cp cap_restart $EXPDIR/cap_restart
 
-     if( $USE_WAVES != 0 &&  $wavemodel == "WW3" ) then
+     if( $wavewatch ) then
         set rst_ww3 = "restart.ww3"
         /bin/rm -f $EXPDIR/$rst_ww3
         cp $rst_ww3 $EXPDIR/$rst_ww3 &