From 4290d43c32601bde66d0177c7bb8a59ba37f1a00 Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Mon, 15 Feb 2021 14:41:57 +0100
Subject: [PATCH 1/3] Switch to new config_init_vertical_grid_type option

Any test cases that use the Haney-number constrained coordinate
need to use the new namelist option:
config_init_vertical_grid_type = 'haney-number'
---
 ocean/global_ocean/template_init_with_land_ice.xml              | 2 +-
 ocean/isomip/template_init.xml                                  | 2 +-
 ocean/isomip_plus/template_init.xml                             | 2 +-
 ocean/sub_ice_shelf_2D/5km/Haney_number_init/config_init1.xml   | 2 +-
 ocean/sub_ice_shelf_2D/5km/Haney_number_init/config_init2.xml   | 2 +-
 .../5km/Haney_number_iterative_init/config_init1.xml            | 2 +-
 .../5km/Haney_number_iterative_init/config_init2.xml            | 2 +-
 ocean/sub_ice_shelf_2D/5km/restart_test/config_init1.xml        | 2 +-
 ocean/sub_ice_shelf_2D/5km/restart_test/config_init2.xml        | 2 +-
 ocean/sub_ice_shelf_2D/5km/with_frazil/config_init1.xml         | 2 +-
 ocean/sub_ice_shelf_2D/5km/with_frazil/config_init2.xml         | 2 +-
 11 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/ocean/global_ocean/template_init_with_land_ice.xml b/ocean/global_ocean/template_init_with_land_ice.xml
index 1609359789..0362734744 100644
--- a/ocean/global_ocean/template_init_with_land_ice.xml
+++ b/ocean/global_ocean/template_init_with_land_ice.xml
@@ -3,7 +3,7 @@
 	<namelist>
 		<option name="config_use_debugTracers">.true.</option>
 		<option name="config_land_ice_flux_mode">'standalone'</option>
-		<option name="config_use_rx1_constraint">.true.</option>
+		<option name="config_init_vertical_grid_type">'haney-number'</option>
 		<option name="config_rx1_max">5.0</option>
 		<option name="config_global_ocean_topography_file">'topography.nc'</option>
 		<option name="config_global_ocean_topography_nlat_dimname">'lat'</option>
diff --git a/ocean/isomip/template_init.xml b/ocean/isomip/template_init.xml
index 915640a972..944abaddec 100644
--- a/ocean/isomip/template_init.xml
+++ b/ocean/isomip/template_init.xml
@@ -5,7 +5,7 @@
 		<option name="config_ocean_run_mode">'init'</option>
 		<option name="config_land_ice_flux_mode">'standalone'</option>
 		<option name="config_eos_type">'jm'</option>
-		<option name="config_use_rx1_constraint">.true.</option>
+		<option name="config_init_vertical_grid_type">'haney-number'</option>
 		<option name="config_rx1_max">5.0</option>
 	</namelist>
 
diff --git a/ocean/isomip_plus/template_init.xml b/ocean/isomip_plus/template_init.xml
index 6ee4dc37e2..f12165dcdf 100644
--- a/ocean/isomip_plus/template_init.xml
+++ b/ocean/isomip_plus/template_init.xml
@@ -11,7 +11,7 @@
 		<option name="config_eos_linear_Tref">-1.0</option>
 		<option name="config_eos_linear_Sref">34.2</option>
 		<option name="config_eos_linear_densityref">1027.51</option>
-		<option name="config_use_rx1_constraint">.true.</option>
+		<option name="config_init_vertical_grid_type">'haney-number'</option>
 		<option name="config_rx1_max">5.0</option>
 		<option name="config_isomip_plus_min_column_thickness">10.0</option>
 		<option name="config_isomip_plus_topography_file">'input_geometry_processed.nc'</option>
diff --git a/ocean/sub_ice_shelf_2D/5km/Haney_number_init/config_init1.xml b/ocean/sub_ice_shelf_2D/5km/Haney_number_init/config_init1.xml
index 6682fac7af..a9c46ef989 100644
--- a/ocean/sub_ice_shelf_2D/5km/Haney_number_init/config_init1.xml
+++ b/ocean/sub_ice_shelf_2D/5km/Haney_number_init/config_init1.xml
@@ -12,7 +12,7 @@
 	<namelist name="namelist.ocean" mode="init">
 		<template file="template_init.xml" path_base="script_resolution_dir"/>
 		<option name="config_write_cull_cell_mask">.true.</option>
-		<option name="config_use_rx1_constraint">.true.</option>
+		<option name="config_init_vertical_grid_type">'haney-number'</option>
 		<option name="config_rx1_max">5.0</option>
 	</namelist>
 
diff --git a/ocean/sub_ice_shelf_2D/5km/Haney_number_init/config_init2.xml b/ocean/sub_ice_shelf_2D/5km/Haney_number_init/config_init2.xml
index b273564360..847afb7133 100644
--- a/ocean/sub_ice_shelf_2D/5km/Haney_number_init/config_init2.xml
+++ b/ocean/sub_ice_shelf_2D/5km/Haney_number_init/config_init2.xml
@@ -8,7 +8,7 @@
 	<namelist name="namelist.ocean" mode="init">
 		<template file="template_init.xml" path_base="script_resolution_dir"/>
 		<option name="config_write_cull_cell_mask">.false.</option>
-		<option name="config_use_rx1_constraint">.true.</option>
+		<option name="config_init_vertical_grid_type">'haney-number'</option>
 		<option name="config_rx1_max">5.0</option>
 	</namelist>
 
diff --git a/ocean/sub_ice_shelf_2D/5km/Haney_number_iterative_init/config_init1.xml b/ocean/sub_ice_shelf_2D/5km/Haney_number_iterative_init/config_init1.xml
index 6682fac7af..a9c46ef989 100644
--- a/ocean/sub_ice_shelf_2D/5km/Haney_number_iterative_init/config_init1.xml
+++ b/ocean/sub_ice_shelf_2D/5km/Haney_number_iterative_init/config_init1.xml
@@ -12,7 +12,7 @@
 	<namelist name="namelist.ocean" mode="init">
 		<template file="template_init.xml" path_base="script_resolution_dir"/>
 		<option name="config_write_cull_cell_mask">.true.</option>
-		<option name="config_use_rx1_constraint">.true.</option>
+		<option name="config_init_vertical_grid_type">'haney-number'</option>
 		<option name="config_rx1_max">5.0</option>
 	</namelist>
 
diff --git a/ocean/sub_ice_shelf_2D/5km/Haney_number_iterative_init/config_init2.xml b/ocean/sub_ice_shelf_2D/5km/Haney_number_iterative_init/config_init2.xml
index b273564360..847afb7133 100644
--- a/ocean/sub_ice_shelf_2D/5km/Haney_number_iterative_init/config_init2.xml
+++ b/ocean/sub_ice_shelf_2D/5km/Haney_number_iterative_init/config_init2.xml
@@ -8,7 +8,7 @@
 	<namelist name="namelist.ocean" mode="init">
 		<template file="template_init.xml" path_base="script_resolution_dir"/>
 		<option name="config_write_cull_cell_mask">.false.</option>
-		<option name="config_use_rx1_constraint">.true.</option>
+		<option name="config_init_vertical_grid_type">'haney-number'</option>
 		<option name="config_rx1_max">5.0</option>
 	</namelist>
 
diff --git a/ocean/sub_ice_shelf_2D/5km/restart_test/config_init1.xml b/ocean/sub_ice_shelf_2D/5km/restart_test/config_init1.xml
index 6682fac7af..a9c46ef989 100644
--- a/ocean/sub_ice_shelf_2D/5km/restart_test/config_init1.xml
+++ b/ocean/sub_ice_shelf_2D/5km/restart_test/config_init1.xml
@@ -12,7 +12,7 @@
 	<namelist name="namelist.ocean" mode="init">
 		<template file="template_init.xml" path_base="script_resolution_dir"/>
 		<option name="config_write_cull_cell_mask">.true.</option>
-		<option name="config_use_rx1_constraint">.true.</option>
+		<option name="config_init_vertical_grid_type">'haney-number'</option>
 		<option name="config_rx1_max">5.0</option>
 	</namelist>
 
diff --git a/ocean/sub_ice_shelf_2D/5km/restart_test/config_init2.xml b/ocean/sub_ice_shelf_2D/5km/restart_test/config_init2.xml
index 3ab3f4efbc..09bb4b6b1f 100644
--- a/ocean/sub_ice_shelf_2D/5km/restart_test/config_init2.xml
+++ b/ocean/sub_ice_shelf_2D/5km/restart_test/config_init2.xml
@@ -9,7 +9,7 @@
 		<template file="template_init.xml" path_base="script_resolution_dir"/>
                 <option name="config_sub_ice_shelf_2D_temperature">-3.0</option>
 		<option name="config_write_cull_cell_mask">.false.</option>
-		<option name="config_use_rx1_constraint">.true.</option>
+		<option name="config_init_vertical_grid_type">'haney-number'</option>
 		<option name="config_rx1_max">5.0</option>
 	</namelist>
 
diff --git a/ocean/sub_ice_shelf_2D/5km/with_frazil/config_init1.xml b/ocean/sub_ice_shelf_2D/5km/with_frazil/config_init1.xml
index 6682fac7af..a9c46ef989 100644
--- a/ocean/sub_ice_shelf_2D/5km/with_frazil/config_init1.xml
+++ b/ocean/sub_ice_shelf_2D/5km/with_frazil/config_init1.xml
@@ -12,7 +12,7 @@
 	<namelist name="namelist.ocean" mode="init">
 		<template file="template_init.xml" path_base="script_resolution_dir"/>
 		<option name="config_write_cull_cell_mask">.true.</option>
-		<option name="config_use_rx1_constraint">.true.</option>
+		<option name="config_init_vertical_grid_type">'haney-number'</option>
 		<option name="config_rx1_max">5.0</option>
 	</namelist>
 
diff --git a/ocean/sub_ice_shelf_2D/5km/with_frazil/config_init2.xml b/ocean/sub_ice_shelf_2D/5km/with_frazil/config_init2.xml
index 1002677a45..9d8e15d0b6 100644
--- a/ocean/sub_ice_shelf_2D/5km/with_frazil/config_init2.xml
+++ b/ocean/sub_ice_shelf_2D/5km/with_frazil/config_init2.xml
@@ -10,7 +10,7 @@
 		<option name="config_sub_ice_shelf_2D_vert_levels">100</option>
 		<option name="config_sub_ice_shelf_2D_temperature">-3.0</option>
 		<option name="config_write_cull_cell_mask">.false.</option>
-		<option name="config_use_rx1_constraint">.true.</option>
+		<option name="config_init_vertical_grid_type">'haney-number'</option>
 		<option name="config_rx1_max">5.0</option>
 	</namelist>
 

From 15a9f6e59b82d2ef13a962a88eaad06fe707e87f Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Mon, 15 Feb 2021 15:07:12 +0100
Subject: [PATCH 2/3] rename pbcs --> pcs in namelist options

These namelist options can also be used for top cells.
---
 ocean/drying_slope/init_idealized_transect.xml | 2 +-
 ocean/global_ocean/template_initial_state.xml  | 4 ++--
 ocean/scripts/LIGHTparticles/user_nl_mpaso     | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/ocean/drying_slope/init_idealized_transect.xml b/ocean/drying_slope/init_idealized_transect.xml
index adf984b00c..54ec3602b7 100644
--- a/ocean/drying_slope/init_idealized_transect.xml
+++ b/ocean/drying_slope/init_idealized_transect.xml
@@ -14,7 +14,7 @@
 		<option name="config_tidal_boundary_left_value">0.0</option>
 		<option name="config_tidal_boundary_right_value">8.0e3</option>
 		<option name="config_tidal_forcing_monochromatic_baseline">3.0</option>
-		<option name="config_alter_ICs_for_pbcs">.true.</option>
+		<option name="config_alter_ICs_for_pcs">.true.</option>
 		<option name="config_thickness_flux_type">'centered'</option>
 	</namelist>
 </template>
diff --git a/ocean/global_ocean/template_initial_state.xml b/ocean/global_ocean/template_initial_state.xml
index cd18f08198..956bc7052b 100644
--- a/ocean/global_ocean/template_initial_state.xml
+++ b/ocean/global_ocean/template_initial_state.xml
@@ -10,8 +10,8 @@
 		<option name="config_expand_sphere">.true.</option>
 		<option name="config_realistic_coriolis_parameter">.true.</option>
 
-		<option name="config_alter_ICs_for_pbcs">.true.</option>
-		<option name="config_pbc_alteration_type">'partial_cell'</option>
+		<option name="config_alter_ICs_for_pcs">.true.</option>
+		<option name="config_pc_alteration_type">'partial_cell'</option>
 
 		<option name="config_use_activeTracers_surface_restoring">.true.</option>
 		<option name="config_use_bulk_wind_stress">.true.</option>
diff --git a/ocean/scripts/LIGHTparticles/user_nl_mpaso b/ocean/scripts/LIGHTparticles/user_nl_mpaso
index 3a5992dc35..275246cf5b 100644
--- a/ocean/scripts/LIGHTparticles/user_nl_mpaso
+++ b/ocean/scripts/LIGHTparticles/user_nl_mpaso
@@ -5,7 +5,7 @@
 ! *** EXCEPT FOR ***
 ! 1. DO NOT CHANGE config_start_time, config_run_duration, config_stop_time,
 !    config_do_restart, config_Restart_timestamp_filename, config_calendar_type,
-!    config_set_restingThickness_to_IC, config_alter_ICs_for_pbcs
+!    config_set_restingThickness_to_IC, config_alter_ICs_for_pcs
 ! 2. To preview the namelists, invoke $CASEROOT preview-namelists and look at
 !    $CASEROOT/CaseDocs/mpaso_in
 !

From fffbad48395fd4d01654568f297edd4e323c4d1b Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Thu, 25 Mar 2021 17:16:23 +0100
Subject: [PATCH 3/3] Update ocean/develop submodule

The latest ocean/develop is needed in order for these COMPASS
changes to work properly.
---
 MPAS-Model/ocean/develop | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/MPAS-Model/ocean/develop b/MPAS-Model/ocean/develop
index 233da699cf..29a819a00d 160000
--- a/MPAS-Model/ocean/develop
+++ b/MPAS-Model/ocean/develop
@@ -1 +1 @@
-Subproject commit 233da699cf7bd9f6e40812d8594a95f1c69de984
+Subproject commit 29a819a00d008fec9eb3e359c4a9d866266e5b87