From dd22b3937b3a048e9d8749a981b988954486d4af Mon Sep 17 00:00:00 2001
From: Luke Van Roekel <luke.vanroekel@gmail.com>
Date: Thu, 1 Sep 2022 23:00:46 -0500
Subject: [PATCH 1/9] Enables submesoscale eddy parameterization

---
 .../mpas-ocean/bld/namelist_files/namelist_defaults_mpaso.xml   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/mpas-ocean/bld/namelist_files/namelist_defaults_mpaso.xml b/components/mpas-ocean/bld/namelist_files/namelist_defaults_mpaso.xml
index cd15a29e84a6..b67e6a910726 100644
--- a/components/mpas-ocean/bld/namelist_files/namelist_defaults_mpaso.xml
+++ b/components/mpas-ocean/bld/namelist_files/namelist_defaults_mpaso.xml
@@ -147,7 +147,7 @@
 <config_Redi_horizontal_ramp_max ocn_grid="WCAtl12to45E2r4">40e3</config_Redi_horizontal_ramp_max>
 
 <!-- submesoscale_eddy_parameterization -->
-<config_submesoscale_enable>.false.</config_submesoscale_enable>
+<config_submesoscale_enable>.true.</config_submesoscale_enable>
 <config_submesoscale_tau>172800</config_submesoscale_tau>
 <config_submesoscale_Ce>0.06</config_submesoscale_Ce>
 <config_submesoscale_Lfmin>1000.0</config_submesoscale_Lfmin>

From 58ab0684fc42680da9df5aa0d915453a347ebad7 Mon Sep 17 00:00:00 2001
From: Luke Van Roekel <luke.vanroekel@gmail.com>
Date: Fri, 9 Sep 2022 22:46:21 -0500
Subject: [PATCH 2/9] Adds MLE velocity to default output

---
 components/mpas-ocean/cime_config/buildnml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/components/mpas-ocean/cime_config/buildnml b/components/mpas-ocean/cime_config/buildnml
index c6b328ff730b..acc7948c2a7b 100755
--- a/components/mpas-ocean/cime_config/buildnml
+++ b/components/mpas-ocean/cime_config/buildnml
@@ -1118,6 +1118,8 @@ def buildnml(case, caseroot, compname):
         lines.append('    <var name="vertVelocityTop"/>')
         lines.append('    <var name="zMid"/>')
         lines.append('    <var name="atmosphericPressure"/>')
+		lines.append('    <var name="normalMLEvelocity"/>')
+		lines.append('    <var name="vertMLEVelocityTop"/>')
         if not ocn_grid.startswith("oRRS1"):
             lines.append('    <var name="normalGMBolusVelocity"/>')
             lines.append('    <var name="vertGMBolusVelocityTop"/>')

From 6f010a59d998fada3d1c9b0b48a5fdac833f27d9 Mon Sep 17 00:00:00 2001
From: Luke Van Roekel <luke.vanroekel@gmail.com>
Date: Fri, 9 Sep 2022 23:12:48 -0500
Subject: [PATCH 3/9] adds MLE velocity to mpas stand alone

---
 components/mpas-ocean/cime_config/buildnml                    | 4 ++--
 .../Registry_time_series_stats_monthly_mean.xml               | 2 ++
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/components/mpas-ocean/cime_config/buildnml b/components/mpas-ocean/cime_config/buildnml
index acc7948c2a7b..7f403d5e8392 100755
--- a/components/mpas-ocean/cime_config/buildnml
+++ b/components/mpas-ocean/cime_config/buildnml
@@ -1118,8 +1118,8 @@ def buildnml(case, caseroot, compname):
         lines.append('    <var name="vertVelocityTop"/>')
         lines.append('    <var name="zMid"/>')
         lines.append('    <var name="atmosphericPressure"/>')
-		lines.append('    <var name="normalMLEvelocity"/>')
-		lines.append('    <var name="vertMLEVelocityTop"/>')
+        lines.append('    <var name="normalMLEvelocity"/>')
+        lines.append('    <var name="vertMLEVelocityTop"/>')
         if not ocn_grid.startswith("oRRS1"):
             lines.append('    <var name="normalGMBolusVelocity"/>')
             lines.append('    <var name="vertGMBolusVelocityTop"/>')
diff --git a/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_monthly_mean.xml b/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_monthly_mean.xml
index 11942da077af..7ca3df931f1d 100644
--- a/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_monthly_mean.xml
+++ b/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_monthly_mean.xml
@@ -134,6 +134,8 @@
 			<var name="atmosphericPressure"/>
 			<var name="normalGMBolusVelocity"/>
 			<var name="vertGMBolusVelocityTop"/>
+			<var name="normalMLEvelocity"/>
+			<var name="vertMLEVelocityTop"/>
 			<var name="GMBolusVelocityZonal"/>
 			<var name="GMBolusVelocityMeridional"/>
 			<var name="cGMphaseSpeed"/>

From 8b60b73bd857f9f56c12e1ad7a4cdb6910929fab Mon Sep 17 00:00:00 2001
From: Luke Van Roekel <luke.vanroekel@gmail.com>
Date: Fri, 23 Sep 2022 12:32:56 -0500
Subject: [PATCH 4/9] Fixes unit issue in submesoscale code

---
 components/mpas-ocean/src/shared/mpas_ocn_submesoscale_eddies.F | 1 +
 1 file changed, 1 insertion(+)

diff --git a/components/mpas-ocean/src/shared/mpas_ocn_submesoscale_eddies.F b/components/mpas-ocean/src/shared/mpas_ocn_submesoscale_eddies.F
index 99bab62abb5e..24653cbaed72 100644
--- a/components/mpas-ocean/src/shared/mpas_ocn_submesoscale_eddies.F
+++ b/components/mpas-ocean/src/shared/mpas_ocn_submesoscale_eddies.F
@@ -135,6 +135,7 @@ subroutine ocn_submesoscale_compute_velocity()
         end do
         bvfML = bvfML / (1.0E-20_RKIND + hML)
         gradBuoyML = gradBuoyML / (1.0E-20_RKIND + hML)
+        gradBuoyML = gravity*gradBuoyML/rho_sw !convert from density unit to buoyancy
 
         !compute depths and shape function
 

From 9503ea80188b1b1dc7ee153642d387cc2f9a4468 Mon Sep 17 00:00:00 2001
From: Luke Van Roekel <luke.vanroekel@gmail.com>
Date: Fri, 23 Sep 2022 13:35:59 -0500
Subject: [PATCH 5/9] Changes name of gradBuoyEddy

The computation is for the gradient of density but the array was called
gradBuoyEddy.  This commit switches it to gradDensityEddy for clarity
---
 components/mpas-ocean/src/Registry.xml               |  4 ++--
 .../src/shared/mpas_ocn_diagnostics_variables.F      | 12 ++++++------
 .../shared/mpas_ocn_eddy_parameterization_helpers.F  |  2 +-
 components/mpas-ocean/src/shared/mpas_ocn_gm.F       |  6 +++---
 .../src/shared/mpas_ocn_submesoscale_eddies.F        |  4 ++--
 5 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/components/mpas-ocean/src/Registry.xml b/components/mpas-ocean/src/Registry.xml
index a8ae9695b45e..3b5e0568795e 100644
--- a/components/mpas-ocean/src/Registry.xml
+++ b/components/mpas-ocean/src/Registry.xml
@@ -2875,8 +2875,8 @@
 			description="count of times redi limiter is invoked on a timestep"
 			packages="gm"
 		/>
-		<var name="gradBuoyEddy" type="real" dimensions="nVertLevelsP1 nEdges Time" units="s^-2"
-			description="horizontal gradient of buoyancy at cell edge and interfaces in vertical.  this is used for the GM parameterization and the submesoscale eddy parameterization"
+		<var name="gradDensityEddy" type="real" dimensions="nVertLevelsP1 nEdges Time" units="kg m^-4"
+			description="horizontal gradient of density at cell edge and interfaces in vertical.  this is used for the GM parameterization and the submesoscale eddy parameterization"
 			 packages="gm;submeso"
 		/>
 		<var name="mleVelocityZonal" type="real" dimensions="nVertLevels nCells Time" units="m s^-1"
diff --git a/components/mpas-ocean/src/shared/mpas_ocn_diagnostics_variables.F b/components/mpas-ocean/src/shared/mpas_ocn_diagnostics_variables.F
index 3850155fb4a3..2ecae166ff34 100644
--- a/components/mpas-ocean/src/shared/mpas_ocn_diagnostics_variables.F
+++ b/components/mpas-ocean/src/shared/mpas_ocn_diagnostics_variables.F
@@ -122,7 +122,7 @@ module ocn_diagnostics_variables
    real(kind=RKIND), dimension(:,:), pointer :: RediKappaScaling
    real(kind=RKIND), dimension(:,:), pointer :: RediKappaSfcTaper
    real(kind=RKIND), dimension(:,:), pointer :: k33
-   real(kind=RKIND), dimension(:,:), pointer :: gradBuoyEddy
+   real(kind=RKIND), dimension(:,:), pointer :: gradDensityEddy
    real(kind=RKIND), dimension(:), pointer   :: gmBolusKappa
    real(kind=RKIND), dimension(:), pointer   :: cGMphaseSpeed
    real(kind=RKIND), dimension(:,:,:), pointer :: slopeTriadUp, slopeTriadDown
@@ -271,8 +271,8 @@ subroutine ocn_diagnostics_variables_init(domain, jenkinsOn, hollandJenkinsOn, e
       end if
 
       if (config_use_GM .or. config_submesoscale_enable) then
-         call mpas_pool_get_array(diagnosticsPool, 'gradBuoyEddy', &
-                   gradBuoyEddy)
+         call mpas_pool_get_array(diagnosticsPool, 'gradDensityEddy', &
+                   gradDensityEddy)
       end if
 
       if ( config_compute_active_tracer_budgets ) then
@@ -781,7 +781,7 @@ subroutine ocn_diagnostics_variables_init(domain, jenkinsOn, hollandJenkinsOn, e
          !$acc                   )
       end if
       if (config_use_GM.or.config_submesoscale_enable) then
-         !$acc enter data create(gradBuoyEddy)
+         !$acc enter data create(gradDensityEddy)
       end if
       if ( config_compute_active_tracer_budgets ) then
          !$acc enter data create(                                         &
@@ -1029,7 +1029,7 @@ subroutine ocn_diagnostics_variables_destroy(err) !{{{
          !$acc                   )
       end if
       if (config_use_GM.or.config_submesoscale_enable) then
-         !$acc exit data delete(gradBuoyEddy)
+         !$acc exit data delete(gradDensityEddy)
       end if
       if ( config_compute_active_tracer_budgets ) then
          !$acc exit data delete(                                          &
@@ -1230,7 +1230,7 @@ subroutine ocn_diagnostics_variables_destroy(err) !{{{
                  RossbyRadius)
       end if
       if (config_use_GM.or.config_submesoscale_enable) then
-         nullify(gradBuoyEddy)
+         nullify(gradDensityEddy)
       end if
       if ( config_compute_active_tracer_budgets ) then
          nullify(activeTracerHorMixTendency,              &
diff --git a/components/mpas-ocean/src/shared/mpas_ocn_eddy_parameterization_helpers.F b/components/mpas-ocean/src/shared/mpas_ocn_eddy_parameterization_helpers.F
index 236da8d38849..8ac494147374 100644
--- a/components/mpas-ocean/src/shared/mpas_ocn_eddy_parameterization_helpers.F
+++ b/components/mpas-ocean/src/shared/mpas_ocn_eddy_parameterization_helpers.F
@@ -166,7 +166,7 @@ subroutine ocn_eddy_compute_buoyancy_gradient()
      do iEdge = 1, nEdges
         if (maxLevelEdgeTop(iEdge) .GE. minLevelEdgeBot(iEdge)) then
            do k = minLevelEdgeBot(iEdge), maxLevelEdgeTop(iEdge)+1
-              gradBuoyEddy(k,iEdge) = (gradDensityTopOfEdge(k,iEdge) - dDensityDzTopOfEdge(k,iEdge) &
+              gradDensityEddy(k,iEdge) = (gradDensityTopOfEdge(k,iEdge) - dDensityDzTopOfEdge(k,iEdge) &
                                              * gradZMidTopOfEdge(k,iEdge))
            end do
         end if
diff --git a/components/mpas-ocean/src/shared/mpas_ocn_gm.F b/components/mpas-ocean/src/shared/mpas_ocn_gm.F
index 336a160e3b9f..13bb0279de84 100644
--- a/components/mpas-ocean/src/shared/mpas_ocn_gm.F
+++ b/components/mpas-ocean/src/shared/mpas_ocn_gm.F
@@ -716,7 +716,7 @@ subroutine ocn_GM_compute_Bolus_velocity(statePool, &
                tridiagC(k - 1) = 2.0_RKIND*cGMphaseSpeed(iEdge)**2/layerThickEdgeMean(k, iEdge) &
                                  /(layerThickEdgeMean(k - 1, iEdge) + layerThickEdgeMean(k, iEdge))
                rightHandSide(k - 1) = gmBolusKappa(iEdge)*gmKappaScaling(k,iEdge)*gravity/rho_sw* &
-                                            gradBuoyEddy(k,iEdge) 
+                                            gradDensityEddy(k,iEdge) 
 
                ! Second to next to the last rows
                do k = minLevelEdgeBot(iEdge) + 2, maxLevelEdgeTop(iEdge) - 1
@@ -729,7 +729,7 @@ subroutine ocn_GM_compute_Bolus_velocity(statePool, &
                   tridiagC(k - 1) = 2.0_RKIND*cGMphaseSpeed(iEdge)**2/layerThickEdgeMean(k, iEdge) &
                                     /(layerThickEdgeMean(k - 1, iEdge) + layerThickEdgeMean(k, iEdge))
                   rightHandSide(k - 1) = gmBolusKappa(iEdge)*gmKappaScaling(k,iEdge)*gravity/rho_sw* &
-                                             gradBuoyEddy(k,iEdge)
+                                             gradDensityEddy(k,iEdge)
                end do
 
                ! Last row
@@ -741,7 +741,7 @@ subroutine ocn_GM_compute_Bolus_velocity(statePool, &
                tridiagB(k - 1) = -2.0_RKIND*cGMphaseSpeed(iEdge)**2/(layerThickEdgeMean(k - 1, iEdge) &
                                                                      *layerThickEdgeMean(k, iEdge)) - BruntVaisalaFreqTopEdge
                rightHandSide(k - 1) = gmBolusKappa(iEdge)*gmKappaScaling(k,iEdge)*gravity/rho_sw* &
-                                            gradBuoyEddy(k,iEdge)
+                                            gradDensityEddy(k,iEdge)
                ! Total number of rows
                N = maxLevelEdgeTop(iEdge) - minLevelEdgeBot(iEdge)
 
diff --git a/components/mpas-ocean/src/shared/mpas_ocn_submesoscale_eddies.F b/components/mpas-ocean/src/shared/mpas_ocn_submesoscale_eddies.F
index 24653cbaed72..882b1c63dc35 100644
--- a/components/mpas-ocean/src/shared/mpas_ocn_submesoscale_eddies.F
+++ b/components/mpas-ocean/src/shared/mpas_ocn_submesoscale_eddies.F
@@ -96,7 +96,7 @@ subroutine ocn_submesoscale_compute_velocity()
      !This is thickness weighted to allow for non uniform grid spacing, 
      !and centered on layer interfaces. The mixed layer goes from the 
      !ocean top layer to mid-depth of layer(indMLDedge)
-     !NOTE, gradBuoyEddy and BFV are defined at the top cell interface 
+     !NOTE, gradDensityEddy and BFV are defined at the top cell interface 
      !and not valid for minLevelCell, so properties for the top layer 
      !rely on the values at (minLevelCell+1).
      !$omp parallel
@@ -118,7 +118,7 @@ subroutine ocn_submesoscale_compute_velocity()
         hML = 0.5_RKIND*layerThickEdgeMean(minLevelEdgeBot(iEdge),iEdge)
         bvfML = bvfML + hML*bvfAv
         if (minLevelEdgeTop(iEdge) .ge. 1) then
-           gradBuoyML = hML*gradBuoyEddy(minLevelEdgeTop(iEdge)+1,iEdge)
+           gradBuoyML = hML*gradDensityEddy(minLevelEdgeTop(iEdge)+1,iEdge)
            bvfML = hML*bvfAv
         else
            cycle

From 7c27a6223133bfeaf11402c74b689d01aeee523a Mon Sep 17 00:00:00 2001
From: Luke Van Roekel <luke.vanroekel@gmail.com>
Date: Sat, 24 Sep 2022 23:01:18 -0500
Subject: [PATCH 6/9] fixes one more gradBuoyEddy

---
 components/mpas-ocean/src/shared/mpas_ocn_submesoscale_eddies.F | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/mpas-ocean/src/shared/mpas_ocn_submesoscale_eddies.F b/components/mpas-ocean/src/shared/mpas_ocn_submesoscale_eddies.F
index 882b1c63dc35..1236336d8b44 100644
--- a/components/mpas-ocean/src/shared/mpas_ocn_submesoscale_eddies.F
+++ b/components/mpas-ocean/src/shared/mpas_ocn_submesoscale_eddies.F
@@ -131,7 +131,7 @@ subroutine ocn_submesoscale_compute_velocity()
                               max(BruntVaisalaFreqTop(k,cell2),1.0E-20_RKIND)))
            bvfML = bvfML + hAv*bvfAv
            hML = hML + hAv
-           gradBuoyML = gradBuoyML + hAv*gradBuoyEddy(k,iEdge)
+           gradBuoyML = gradBuoyML + hAv*gradDensityEddy(k,iEdge)
         end do
         bvfML = bvfML / (1.0E-20_RKIND + hML)
         gradBuoyML = gradBuoyML / (1.0E-20_RKIND + hML)

From f2e7dea3cf75f37d48267a87a2e170668419b126 Mon Sep 17 00:00:00 2001
From: Luke Van Roekel <luke.vanroekel@gmail.com>
Date: Mon, 26 Sep 2022 23:18:51 -0500
Subject: [PATCH 7/9] Fixes registry variables

---
 components/mpas-ocean/cime_config/buildnml                      | 2 +-
 .../Registry_time_series_stats_monthly_mean.xml                 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/components/mpas-ocean/cime_config/buildnml b/components/mpas-ocean/cime_config/buildnml
index 7f403d5e8392..33553b239939 100755
--- a/components/mpas-ocean/cime_config/buildnml
+++ b/components/mpas-ocean/cime_config/buildnml
@@ -1119,7 +1119,7 @@ def buildnml(case, caseroot, compname):
         lines.append('    <var name="zMid"/>')
         lines.append('    <var name="atmosphericPressure"/>')
         lines.append('    <var name="normalMLEvelocity"/>')
-        lines.append('    <var name="vertMLEVelocityTop"/>')
+        lines.append('    <var name="vertMLEBolusVelocityTop"/>')
         if not ocn_grid.startswith("oRRS1"):
             lines.append('    <var name="normalGMBolusVelocity"/>')
             lines.append('    <var name="vertGMBolusVelocityTop"/>')
diff --git a/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_monthly_mean.xml b/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_monthly_mean.xml
index 7ca3df931f1d..247dac423e6d 100644
--- a/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_monthly_mean.xml
+++ b/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_monthly_mean.xml
@@ -135,7 +135,7 @@
 			<var name="normalGMBolusVelocity"/>
 			<var name="vertGMBolusVelocityTop"/>
 			<var name="normalMLEvelocity"/>
-			<var name="vertMLEVelocityTop"/>
+			<var name="vertMLEBolusVelocityTop"/>
 			<var name="GMBolusVelocityZonal"/>
 			<var name="GMBolusVelocityMeridional"/>
 			<var name="cGMphaseSpeed"/>

From ddd41fd20e7a87f271a64d96bf0016d14aa3cb36 Mon Sep 17 00:00:00 2001
From: Luke Van Roekel <luke.vanroekel@gmail.com>
Date: Wed, 28 Sep 2022 14:04:18 -0500
Subject: [PATCH 8/9] changes submesoscale efficiency default strength

---
 .../mpas-ocean/bld/namelist_files/namelist_defaults_mpaso.xml   | 2 +-
 components/mpas-ocean/cime_config/buildnml                      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/components/mpas-ocean/bld/namelist_files/namelist_defaults_mpaso.xml b/components/mpas-ocean/bld/namelist_files/namelist_defaults_mpaso.xml
index b67e6a910726..0e410e7a1f74 100644
--- a/components/mpas-ocean/bld/namelist_files/namelist_defaults_mpaso.xml
+++ b/components/mpas-ocean/bld/namelist_files/namelist_defaults_mpaso.xml
@@ -149,7 +149,7 @@
 <!-- submesoscale_eddy_parameterization -->
 <config_submesoscale_enable>.true.</config_submesoscale_enable>
 <config_submesoscale_tau>172800</config_submesoscale_tau>
-<config_submesoscale_Ce>0.06</config_submesoscale_Ce>
+<config_submesoscale_Ce>0.08</config_submesoscale_Ce>
 <config_submesoscale_Lfmin>1000.0</config_submesoscale_Lfmin>
 <config_submesoscale_ds_max>100000.0</config_submesoscale_ds_max>
 
diff --git a/components/mpas-ocean/cime_config/buildnml b/components/mpas-ocean/cime_config/buildnml
index 33553b239939..b6a74dd07565 100755
--- a/components/mpas-ocean/cime_config/buildnml
+++ b/components/mpas-ocean/cime_config/buildnml
@@ -1118,7 +1118,7 @@ def buildnml(case, caseroot, compname):
         lines.append('    <var name="vertVelocityTop"/>')
         lines.append('    <var name="zMid"/>')
         lines.append('    <var name="atmosphericPressure"/>')
-        lines.append('    <var name="normalMLEvelocity"/>')
+        lines.append('    <var name="normalMLEBolusvelocity"/>')
         lines.append('    <var name="vertMLEBolusVelocityTop"/>')
         if not ocn_grid.startswith("oRRS1"):
             lines.append('    <var name="normalGMBolusVelocity"/>')

From 856b062f971642c003fb24b210c16944c32940d6 Mon Sep 17 00:00:00 2001
From: Jon Wolfe <jonbob@lanl.gov>
Date: Thu, 29 Sep 2022 17:33:47 -0500
Subject: [PATCH 9/9] Change stream field from normalMLEBolusvelocity to
 normalMLEvelocity

---
 components/mpas-ocean/cime_config/buildnml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/mpas-ocean/cime_config/buildnml b/components/mpas-ocean/cime_config/buildnml
index b6a74dd07565..33553b239939 100755
--- a/components/mpas-ocean/cime_config/buildnml
+++ b/components/mpas-ocean/cime_config/buildnml
@@ -1118,7 +1118,7 @@ def buildnml(case, caseroot, compname):
         lines.append('    <var name="vertVelocityTop"/>')
         lines.append('    <var name="zMid"/>')
         lines.append('    <var name="atmosphericPressure"/>')
-        lines.append('    <var name="normalMLEBolusvelocity"/>')
+        lines.append('    <var name="normalMLEvelocity"/>')
         lines.append('    <var name="vertMLEBolusVelocityTop"/>')
         if not ocn_grid.startswith("oRRS1"):
             lines.append('    <var name="normalGMBolusVelocity"/>')