From 9de03179ec927a148b44e89c5b44ad91e6308b10 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Thu, 20 Nov 2025 10:31:05 -0600
Subject: [PATCH 01/47] Organize init steps by forcing, sharing as applicable

---
 polaris/tasks/ocean/single_column/__init__.py | 115 +++++++++++++++++-
 .../ocean/single_column/cvmix/__init__.py     |  22 ++--
 .../ocean/single_column/ekman/__init__.py     |   8 +-
 .../ocean/single_column/ideal_age/__init__.py |  14 +--
 .../ocean/single_column/inertial/__init__.py  |  16 +--
 polaris/tasks/ocean/single_column/init.py     |  13 +-
 .../ocean/single_column/single_column.cfg     |   2 +
 7 files changed, 145 insertions(+), 45 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/__init__.py b/polaris/tasks/ocean/single_column/__init__.py
index 9999db60f4..580416d55f 100644
--- a/polaris/tasks/ocean/single_column/__init__.py
+++ b/polaris/tasks/ocean/single_column/__init__.py
@@ -1,7 +1,9 @@
+from polaris.config import PolarisConfigParser as PolarisConfigParser
 from polaris.tasks.ocean.single_column.cvmix import CVMix as CVMix
 from polaris.tasks.ocean.single_column.ekman import Ekman as Ekman
 from polaris.tasks.ocean.single_column.ideal_age import IdealAge as IdealAge
 from polaris.tasks.ocean.single_column.inertial import Inertial as Inertial
+from polaris.tasks.ocean.single_column.init import Init
 
 
 def add_single_column_tasks(component):
@@ -11,7 +13,112 @@ def add_single_column_tasks(component):
     component : polaris.tasks.ocean.Ocean
         the ocean component that the tasks will be added to
     """
-    component.add_task(Ekman(component=component))
-    component.add_task(CVMix(component=component))
-    component.add_task(IdealAge(component=component))
-    component.add_task(Inertial(component=component))
+    group_name = 'single_column'
+
+    forcing = ['wind', 'evap']
+    name = 'cvmix'
+    filepath = f'{component.name}/{group_name}/{name}/{name}.cfg'
+    config = PolarisConfigParser(filepath=filepath)
+    config.add_from_package(
+        'polaris.tasks.ocean.single_column', f'{group_name}.cfg'
+    )
+    for forcing_name in forcing:
+        config.add_from_package(
+            'polaris.tasks.ocean.single_column', f'{forcing_name}.cfg'
+        )
+    config.add_from_package(
+        'polaris.tasks.ocean.single_column', 'stable_stratification.cfg'
+    )
+    init_step = component.get_or_create_shared_step(
+        step_cls=Init,
+        subdir=f'{group_name}/{"_".join(forcing)}/init_stable',
+        config=config,
+        config_filename=f'{name}.cfg',
+    )
+    for enable_vadv in [True, False]:
+        component.add_task(
+            CVMix(
+                component=component,
+                config=config,
+                init=init_step,
+                indir=f'{group_name}',
+                enable_vadv=enable_vadv,
+            )
+        )
+
+    forcing_name = 'wind'
+    name = 'ekman'
+    filepath = f'{component.name}/{group_name}/{name}/{name}.cfg'
+    config = PolarisConfigParser(filepath=filepath)
+    config.add_from_package(
+        'polaris.tasks.ocean.single_column', f'{group_name}.cfg'
+    )
+    config.add_from_package(
+        'polaris.tasks.ocean.single_column', f'{forcing_name}.cfg'
+    )
+    init_step = component.get_or_create_shared_step(
+        step_cls=Init,
+        subdir=f'{group_name}/{forcing_name}/init',
+        config=config,
+        config_filename=f'{name}.cfg',
+    )
+    component.add_task(
+        Ekman(
+            component=component,
+            config=config,
+            init=init_step,
+            indir=f'{group_name}',
+        )
+    )
+
+    name = 'ideal_age'
+    filepath = f'{component.name}/{group_name}/{name}/{name}.cfg'
+    config = PolarisConfigParser(filepath=filepath)
+    config.add_from_package(
+        'polaris.tasks.ocean.single_column', f'{group_name}.cfg'
+    )
+    config.add_from_package(
+        'polaris.tasks.ocean.single_column', f'{forcing_name}.cfg'
+    )
+    config.add_from_package(
+        'polaris.tasks.ocean.single_column', 'stable_stratification.cfg'
+    )
+    init_step = component.get_or_create_shared_step(
+        step_cls=Init,
+        subdir=f'{group_name}/{forcing_name}/init_stable',
+        config=config,
+        config_filename=f'{name}.cfg',
+    )
+    component.add_task(
+        IdealAge(
+            component=component,
+            init=init_step,
+            config=config,
+            indir=f'{group_name}',
+        )
+    )
+
+    forcing_name = 'no_forcing'
+    name = 'inertial'
+    filepath = f'{component.name}/{group_name}/{name}/{name}.cfg'
+    config = PolarisConfigParser(filepath=filepath)
+    config.add_from_package(
+        'polaris.tasks.ocean.single_column', f'{group_name}.cfg'
+    )
+    config.add_from_package(
+        'polaris.tasks.ocean.single_column', 'stable_stratification.cfg'
+    )
+    init_step = component.get_or_create_shared_step(
+        step_cls=Init,
+        subdir=f'{group_name}/{forcing_name}/init_stable',
+        config=config,
+        config_filename=f'{name}.cfg',
+    )
+    component.add_task(
+        Inertial(
+            component=component,
+            init=init_step,
+            config=config,
+            indir=f'{group_name}',
+        )
+    )
diff --git a/polaris/tasks/ocean/single_column/cvmix/__init__.py b/polaris/tasks/ocean/single_column/cvmix/__init__.py
index 38349a7113..5198406ffd 100644
--- a/polaris/tasks/ocean/single_column/cvmix/__init__.py
+++ b/polaris/tasks/ocean/single_column/cvmix/__init__.py
@@ -2,7 +2,6 @@
 
 from polaris import Task
 from polaris.tasks.ocean.single_column.forward import Forward
-from polaris.tasks.ocean.single_column.init import Init
 from polaris.tasks.ocean.single_column.viz import Viz
 
 
@@ -12,7 +11,7 @@ class CVMix(Task):
     then performs a short forward run testing vertical mixing on 1 core.
     """
 
-    def __init__(self, component):
+    def __init__(self, component, config, init, indir, enable_vadv=True):
         """
         Create the test case
         Parameters
@@ -21,15 +20,17 @@ def __init__(self, component):
             The ocean component that this task belongs to
         """
         name = 'cvmix'
-        subdir = os.path.join('single_column', name)
+        if not enable_vadv:
+            subdir = os.path.join(indir, f'{name}_no_vadv')
+        else:
+            subdir = os.path.join(indir, name)
         super().__init__(component=component, name=name, subdir=subdir)
+        config_filename = 'cvmix.cfg'
+        self.set_shared_config(config, link=config_filename)
         self.config.add_from_package(
-            'polaris.tasks.ocean.single_column', 'single_column.cfg'
+            'polaris.tasks.ocean.single_column.cvmix', config_filename
         )
-        self.config.add_from_package(
-            'polaris.tasks.ocean.single_column.cvmix', 'cvmix.cfg'
-        )
-        self.add_step(Init(component=component, indir=self.subdir))
+        self.add_step(init, symlink='init')
 
         validate_vars = [
             'temperature',
@@ -40,16 +41,17 @@ def __init__(self, component):
         self.add_step(
             Forward(
                 component=component,
-                indir=self.subdir,
+                indir=subdir,
                 ntasks=1,
                 min_tasks=1,
                 openmp_threads=1,
                 validate_vars=validate_vars,
                 task_name=name,
+                # enable_vadv=enable_vadv,
             )
         )
 
         self.add_step(
-            Viz(component=component, indir=self.subdir),
+            Viz(component=component, indir=subdir),
             run_by_default=False,
         )
diff --git a/polaris/tasks/ocean/single_column/ekman/__init__.py b/polaris/tasks/ocean/single_column/ekman/__init__.py
index 822642265f..17fbf32ad8 100644
--- a/polaris/tasks/ocean/single_column/ekman/__init__.py
+++ b/polaris/tasks/ocean/single_column/ekman/__init__.py
@@ -3,7 +3,6 @@
 from polaris import Task
 from polaris.tasks.ocean.single_column.ekman.analysis import Analysis
 from polaris.tasks.ocean.single_column.forward import Forward
-from polaris.tasks.ocean.single_column.init import Init
 from polaris.tasks.ocean.single_column.viz import Viz
 
 
@@ -13,7 +12,7 @@ class Ekman(Task):
     then performs a short forward run spinning up an ekman layer on 1 core.
     """
 
-    def __init__(self, component):
+    def __init__(self, component, config, init, indir):
         """
         Create the test case
         Parameters
@@ -22,17 +21,18 @@ def __init__(self, component):
             The ocean component that this task belongs to
         """
         name = 'ekman'
-        subdir = os.path.join('single_column', name)
+        subdir = os.path.join(indir, name)
         super().__init__(component=component, name=name, subdir=subdir)
 
         self.config.add_from_package(
             'polaris.tasks.ocean.single_column', 'single_column.cfg'
         )
+        self.set_shared_config(config, link='ekman.cfg')
         self.config.add_from_package(
             'polaris.tasks.ocean.single_column.ekman', 'ekman.cfg'
         )
 
-        self.add_step(Init(component=component, indir=self.subdir))
+        self.add_step(init, symlink='init')
 
         validate_vars = [
             'temperature',
diff --git a/polaris/tasks/ocean/single_column/ideal_age/__init__.py b/polaris/tasks/ocean/single_column/ideal_age/__init__.py
index 614eff6da1..6c14f4dd2c 100644
--- a/polaris/tasks/ocean/single_column/ideal_age/__init__.py
+++ b/polaris/tasks/ocean/single_column/ideal_age/__init__.py
@@ -2,7 +2,6 @@
 
 from polaris import Task as Task
 from polaris.tasks.ocean.single_column.forward import Forward as Forward
-from polaris.tasks.ocean.single_column.init import Init as Init
 from polaris.tasks.ocean.single_column.viz import Viz as Viz
 
 
@@ -13,7 +12,7 @@ class IdealAge(Task):
     on 1 core.
     """
 
-    def __init__(self, component, ideal_age=True):
+    def __init__(self, component, config, init, indir, ideal_age=True):
         """
         Create the test case
         Parameters
@@ -22,15 +21,14 @@ def __init__(self, component, ideal_age=True):
             The ocean component that this task belongs to
         """
         name = 'ideal_age'
-        subdir = os.path.join('single_column', name)
+        subdir = os.path.join(indir, name)
         super().__init__(component=component, name=name, subdir=subdir)
+        config_filename = 'ideal_age.cfg'
+        self.set_shared_config(config, link=config_filename)
         self.config.add_from_package(
-            'polaris.tasks.ocean.single_column', 'single_column.cfg'
-        )
-
-        self.add_step(
-            Init(component=component, indir=self.subdir, ideal_age=ideal_age)
+            'polaris.tasks.ocean.single_column.ideal_age', config_filename
         )
+        self.add_step(init, symlink='init')
 
         validate_vars = ['temperature', 'salinity', 'iAge']
         step = Forward(
diff --git a/polaris/tasks/ocean/single_column/inertial/__init__.py b/polaris/tasks/ocean/single_column/inertial/__init__.py
index fb7bd85ac0..36c0f9f8c4 100644
--- a/polaris/tasks/ocean/single_column/inertial/__init__.py
+++ b/polaris/tasks/ocean/single_column/inertial/__init__.py
@@ -3,7 +3,6 @@
 from polaris import Task
 from polaris.tasks.ocean.single_column.forward import Forward
 from polaris.tasks.ocean.single_column.inertial.analysis import Analysis
-from polaris.tasks.ocean.single_column.init import Init
 from polaris.tasks.ocean.single_column.viz import Viz
 
 
@@ -13,7 +12,7 @@ class Inertial(Task):
     then performs a short forward run testing inertial oscillations on 1 core.
     """
 
-    def __init__(self, component):
+    def __init__(self, component, config, init, indir):
         """
         Create the test case
         Parameters
@@ -22,17 +21,14 @@ def __init__(self, component):
             The ocean component that this task belongs to
         """
         name = 'inertial'
-        subdir = os.path.join('single_column', name)
+        subdir = os.path.join(indir, name)
         super().__init__(component=component, name=name, subdir=subdir)
-
-        self.config.add_from_package(
-            'polaris.tasks.ocean.single_column', 'single_column.cfg'
-        )
+        config_filename = 'inertial.cfg'
+        self.set_shared_config(config, link=config_filename)
         self.config.add_from_package(
-            'polaris.tasks.ocean.single_column.inertial', 'inertial.cfg'
+            'polaris.tasks.ocean.single_column.inertial', config_filename
         )
-
-        self.add_step(Init(component=component, indir=self.subdir))
+        self.add_step(init, symlink='init')
 
         validate_vars = [
             'temperature',
diff --git a/polaris/tasks/ocean/single_column/init.py b/polaris/tasks/ocean/single_column/init.py
index 4d59e7ac7f..c3c249e4b3 100644
--- a/polaris/tasks/ocean/single_column/init.py
+++ b/polaris/tasks/ocean/single_column/init.py
@@ -14,7 +14,7 @@ class Init(Step):
     test cases
     """
 
-    def __init__(self, component, indir, ideal_age=False):
+    def __init__(self, component, subdir):
         """
         Create the step
 
@@ -26,12 +26,8 @@ def __init__(self, component, indir, ideal_age=False):
         indir : str
             The subdirectory that the task belongs to, that this step will
             go into a subdirectory of
-
-        ideal_age : bool, optional
-            Whether the initial condition should include the ideal age tracer
         """
-        super().__init__(component=component, name='init', indir=indir)
-        self.ideal_age = ideal_age
+        super().__init__(component=component, name='init', subdir=subdir)
         for file in [
             'base_mesh.nc',
             'culled_mesh.nc',
@@ -48,7 +44,6 @@ def run(self):
         logger = self.logger
         config = self.config
         section = config['single_column']
-        ideal_age = self.ideal_age
         resolution = section.getfloat('resolution')
         nx = section.getint('nx')
         ny = section.getint('ny')
@@ -140,8 +135,8 @@ def run(self):
         normal_velocity = normal_velocity.transpose('nEdges', 'nVertLevels')
         normal_velocity = normal_velocity.expand_dims(dim='Time', axis=0)
 
-        if ideal_age:
-            ds['idealAgeTracers'] = xr.zeros_like(x_cell)
+        # We include this variable in initial conditions even when unused
+        ds['idealAgeTracers'] = xr.zeros_like(x_cell)
 
         ds['temperature'] = temperature
         ds['salinity'] = salinity
diff --git a/polaris/tasks/ocean/single_column/single_column.cfg b/polaris/tasks/ocean/single_column/single_column.cfg
index 930d527db3..5eca8e7576 100644
--- a/polaris/tasks/ocean/single_column/single_column.cfg
+++ b/polaris/tasks/ocean/single_column/single_column.cfg
@@ -71,6 +71,8 @@ meridional_velocity = 0.0
 # config options for forcing single column testcases
 [single_column_forcing]
 
+apply_wind_stress = False
+
 # Piston velocity to control rate of restoring toward temperature_surface_restoring_value
 temperature_piston_velocity = 4.0e-6
 

From 9e8d99e6f6f3b4163fe93ab0c9b4fdf44d412d15 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Mon, 15 Dec 2025 15:10:58 -0600
Subject: [PATCH 02/47] Reorg cfg options for shared init step

---
 .../tasks/ocean/single_column/cvmix/cvmix.cfg | 36 +------
 .../tasks/ocean/single_column/ekman/ekman.cfg | 93 -------------------
 polaris/tasks/ocean/single_column/evap.cfg    | 18 ++++
 .../single_column/ideal_age/ideal_age.cfg     | 35 +------
 .../ocean/single_column/single_column.cfg     | 10 +-
 .../single_column/stable_stratification.cfg   | 12 +++
 polaris/tasks/ocean/single_column/wind.cfg    |  4 +
 7 files changed, 43 insertions(+), 165 deletions(-)
 create mode 100644 polaris/tasks/ocean/single_column/evap.cfg
 create mode 100644 polaris/tasks/ocean/single_column/stable_stratification.cfg
 create mode 100644 polaris/tasks/ocean/single_column/wind.cfg

diff --git a/polaris/tasks/ocean/single_column/cvmix/cvmix.cfg b/polaris/tasks/ocean/single_column/cvmix/cvmix.cfg
index 0252aced50..7394d9c777 100644
--- a/polaris/tasks/ocean/single_column/cvmix/cvmix.cfg
+++ b/polaris/tasks/ocean/single_column/cvmix/cvmix.cfg
@@ -1,33 +1,3 @@
-# config options for single column testcases
-[single_column]
-
-# Temperature gradient below the mixed layer
-temperature_gradient_interior = 0.01
-
-# Depth of the temperature mixed layer
-mixed_layer_depth_temperature =  25.0
-
-# The salinity below the mixed layer
-salinity_difference_across_mixed_layer = 1.0
-
-# config options for forcing single column testcases
-[single_column_forcing]
-
-# Net latent heat flux applied when bulk forcing is used. Positive values indicate a net
-# input of heat to ocean
-latent_heat_flux = -50.0
-
-# Net sensible heat flux applied when bulk forcing is used. Positive values indicate a
-# net input of heat to ocean
-sensible_heat_flux = -25.0
-
-# Net solar shortwave heat flux applied when bulk forcing is used. Positive values
-# indicate a net input of heat to ocean
-shortwave_heat_flux = 200.0
-
-# Net surface evaporation when bulk forcing is used. Positive values indicate a net
-# input of water to ocean
-evaporation_flux = 6.5E-4
-
-# Zonal surface wind stress over the domain
-wind_stress_zonal = 0.1
+# stable_stratification.cfg
+# evap.cfg
+# wind.cfg
diff --git a/polaris/tasks/ocean/single_column/ekman/ekman.cfg b/polaris/tasks/ocean/single_column/ekman/ekman.cfg
index 29aabf77f2..8720d2bb08 100644
--- a/polaris/tasks/ocean/single_column/ekman/ekman.cfg
+++ b/polaris/tasks/ocean/single_column/ekman/ekman.cfg
@@ -3,99 +3,6 @@
 # Bottom depth
 bottom_depth = 100.
 
-# config options for single column testcases
-[single_column]
-
-# Surface temperature
-surface_temperature = 20.0
-
-# Temperature gradient in the mixed layer in degC/m
-temperature_gradient_mixed_layer = 0.0
-
-# The temperature below the mixed layer
-temperature_difference_across_mixed_layer = 0.0
-
-# Temperature gradient below the mixed layer
-temperature_gradient_interior = 0.0
-
-# Depth of the temperature mixed layer
-mixed_layer_depth_temperature =  0.0
-
-# Surface salinity
-surface_salinity = 35.0
-
-# Salinity gradient in the mixed layer in PSU/m
-salinity_gradient_mixed_layer = 0.0
-
-# The salinity below the mixed layer
-salinity_difference_across_mixed_layer = 0.0
-
-# Salinity gradient below the mixed layer
-salinity_gradient_interior = 0.0
-
-# Depth of the salinity mixed layer
-mixed_layer_depth_salinity = 0.0
-
-# coriolis parameter
-coriolis_parameter = 1.0e-4
-
-# config options for forcing single column testcases
-[single_column_forcing]
-
-# Piston velocity to control rate of restoring toward temperature_surface_restoring_value
-temperature_piston_velocity = 0.0
-
-# Piston velocity to control rate of restoring toward salinity_surface_restoring_value
-salinity_piston_velocity = 0.0
-
-# Rate at which temperature is restored toward the initial condition
-temperature_interior_restoring_rate = 0.0
-
-# Rate at which salinity is restored toward the initial condition
-salinity_interior_restoring_rate = 0.0
-
-# Net latent heat flux applied when bulk forcing is used. Positive values indicate a net
-# input of heat to ocean
-latent_heat_flux = 0.0
-
-# Net sensible heat flux applied when bulk forcing is used. Positive values indicate a
-# net input of heat to ocean
-sensible_heat_flux = 0.0
-
-# Net solar shortwave heat flux applied when bulk forcing is used. Positive values
-# indicate a net input of heat to ocean
-shortwave_heat_flux = 0.0
-
-# Net surface evaporation when bulk forcing is used. Positive values indicate a net
-# input of water to ocean
-evaporation_flux = 0.0
-
-# Net surface rain flux when bulk forcing is used. Positive values indicate a net input
-# of water to ocean
-rain_flux = 0.0
-
-# Net surface river runoff flux when bulk forcing is used. Positive values indicate a net
-#flux of water to ocean
-river_runoff_flux = 0.0
-
-# Net surface subglacial runoff flux when bulk forcing is used. Positive values indicate a net
-#flux of water to ocean
-subglacial_runoff_flux = 0.0
-
-# Net surface ice runoff flux when bulk forcing is used. Positive values indicate a net
-#flux of water to ocean
-ice_runoff_flux = 0.0
-
-# Net iceberg freshwater flux when bulk forcing is used. Positive values indicate a net
-#flux of water to ocean
-iceberg_flux = 0.0
-
-# Zonal surface wind stress over the domain
-wind_stress_zonal = 0.1
-
-# Meridional surface wind stress over the domain
-wind_stress_meridional = 0.0
-
 [single_column_ekman]
 
 # Constant vertical eddy diffusivity
diff --git a/polaris/tasks/ocean/single_column/evap.cfg b/polaris/tasks/ocean/single_column/evap.cfg
new file mode 100644
index 0000000000..688bae9293
--- /dev/null
+++ b/polaris/tasks/ocean/single_column/evap.cfg
@@ -0,0 +1,18 @@
+# config options for forcing single column testcases
+[single_column_forcing]
+
+# Net latent heat flux applied when bulk forcing is used. Positive values indicate a net
+# input of heat to ocean
+latent_heat_flux = -50.0
+
+# Net sensible heat flux applied when bulk forcing is used. Positive values indicate a
+# net input of heat to ocean
+sensible_heat_flux = -25.0
+
+# Net solar shortwave heat flux applied when bulk forcing is used. Positive values
+# indicate a net input of heat to ocean
+shortwave_heat_flux = 200.0
+
+# Net surface evaporation when bulk forcing is used. Positive values indicate a net
+# input of water to ocean
+evaporation_flux = 6.5E-4
diff --git a/polaris/tasks/ocean/single_column/ideal_age/ideal_age.cfg b/polaris/tasks/ocean/single_column/ideal_age/ideal_age.cfg
index 0252aced50..54db266069 100644
--- a/polaris/tasks/ocean/single_column/ideal_age/ideal_age.cfg
+++ b/polaris/tasks/ocean/single_column/ideal_age/ideal_age.cfg
@@ -1,33 +1,2 @@
-# config options for single column testcases
-[single_column]
-
-# Temperature gradient below the mixed layer
-temperature_gradient_interior = 0.01
-
-# Depth of the temperature mixed layer
-mixed_layer_depth_temperature =  25.0
-
-# The salinity below the mixed layer
-salinity_difference_across_mixed_layer = 1.0
-
-# config options for forcing single column testcases
-[single_column_forcing]
-
-# Net latent heat flux applied when bulk forcing is used. Positive values indicate a net
-# input of heat to ocean
-latent_heat_flux = -50.0
-
-# Net sensible heat flux applied when bulk forcing is used. Positive values indicate a
-# net input of heat to ocean
-sensible_heat_flux = -25.0
-
-# Net solar shortwave heat flux applied when bulk forcing is used. Positive values
-# indicate a net input of heat to ocean
-shortwave_heat_flux = 200.0
-
-# Net surface evaporation when bulk forcing is used. Positive values indicate a net
-# input of water to ocean
-evaporation_flux = 6.5E-4
-
-# Zonal surface wind stress over the domain
-wind_stress_zonal = 0.1
+# stable_stratification.cfg
+# wind.cfg
diff --git a/polaris/tasks/ocean/single_column/single_column.cfg b/polaris/tasks/ocean/single_column/single_column.cfg
index 5eca8e7576..d034b42fb6 100644
--- a/polaris/tasks/ocean/single_column/single_column.cfg
+++ b/polaris/tasks/ocean/single_column/single_column.cfg
@@ -71,13 +71,11 @@ meridional_velocity = 0.0
 # config options for forcing single column testcases
 [single_column_forcing]
 
-apply_wind_stress = False
-
 # Piston velocity to control rate of restoring toward temperature_surface_restoring_value
-temperature_piston_velocity = 4.0e-6
+temperature_piston_velocity = 0.0
 
 # Piston velocity to control rate of restoring toward salinity_surface_restoring_value
-salinity_piston_velocity = 4.0e-6
+salinity_piston_velocity = 0.0
 
 # Temperature to restore towards when surface restoring is turned on
 temperature_surface_restoring_value = ${single_column:surface_temperature}
@@ -86,10 +84,10 @@ temperature_surface_restoring_value = ${single_column:surface_temperature}
 salinity_surface_restoring_value = ${single_column:surface_salinity}
 
 # Rate at which temperature is restored toward the initial condition
-temperature_interior_restoring_rate = 1.0e-6
+temperature_interior_restoring_rate = 0.0
 
 # Rate at which salinity is restored toward the initial condition
-salinity_interior_restoring_rate = 1.0e-6
+salinity_interior_restoring_rate = 0.0
 
 # Net latent heat flux applied when bulk forcing is used. Positive values indicate a net
 # input of heat to ocean
diff --git a/polaris/tasks/ocean/single_column/stable_stratification.cfg b/polaris/tasks/ocean/single_column/stable_stratification.cfg
new file mode 100644
index 0000000000..9f749bd918
--- /dev/null
+++ b/polaris/tasks/ocean/single_column/stable_stratification.cfg
@@ -0,0 +1,12 @@
+
+# config options for single column testcases
+[single_column]
+
+# Temperature gradient below the mixed layer
+temperature_gradient_interior = 0.01
+
+# Depth of the temperature mixed layer
+mixed_layer_depth_temperature =  25.0
+
+# The salinity below the mixed layer
+salinity_difference_across_mixed_layer = 1.0
diff --git a/polaris/tasks/ocean/single_column/wind.cfg b/polaris/tasks/ocean/single_column/wind.cfg
new file mode 100644
index 0000000000..9daa95b973
--- /dev/null
+++ b/polaris/tasks/ocean/single_column/wind.cfg
@@ -0,0 +1,4 @@
+[single_column_forcing]
+
+# Zonal surface wind stress over the domain
+wind_stress_zonal = 0.1

From b49b9fb1e7005ffeb2b3ee7a3a09a7445a569d1c Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Thu, 20 Nov 2025 10:32:48 -0600
Subject: [PATCH 03/47] Add option to turn vadv off for single column tests

---
 polaris/tasks/ocean/single_column/cvmix/__init__.py |  2 +-
 polaris/tasks/ocean/single_column/forward.py        | 12 ++++++++++++
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/polaris/tasks/ocean/single_column/cvmix/__init__.py b/polaris/tasks/ocean/single_column/cvmix/__init__.py
index 5198406ffd..43411a55e5 100644
--- a/polaris/tasks/ocean/single_column/cvmix/__init__.py
+++ b/polaris/tasks/ocean/single_column/cvmix/__init__.py
@@ -47,7 +47,7 @@ def __init__(self, component, config, init, indir, enable_vadv=True):
                 openmp_threads=1,
                 validate_vars=validate_vars,
                 task_name=name,
-                # enable_vadv=enable_vadv,
+                enable_vadv=enable_vadv,
             )
         )
 
diff --git a/polaris/tasks/ocean/single_column/forward.py b/polaris/tasks/ocean/single_column/forward.py
index ed9c992aea..1cb40ecea7 100644
--- a/polaris/tasks/ocean/single_column/forward.py
+++ b/polaris/tasks/ocean/single_column/forward.py
@@ -24,6 +24,7 @@ def __init__(
         openmp_threads=1,
         validate_vars=None,
         task_name='',
+        enable_vadv=True,
     ):
         """
         Create a new test case
@@ -93,6 +94,8 @@ def __init__(
 
         self.task_name = task_name
 
+        self.enable_vadv = enable_vadv
+
     def dynamic_model_config(self, at_setup):
         if self.task_name == 'ekman':
             nu = self.config.getfloat(
@@ -102,3 +105,12 @@ def dynamic_model_config(self, at_setup):
                 options={'config_cvmix_background_viscosity': nu},
                 config_model='mpas-ocean',
             )
+        if not self.enable_vadv:
+            self.add_model_config_options(
+                options={
+                    'config_vert_coord_movement': 'impermeable_interfaces',
+                    'config_disable_vel_vadv': True,
+                    'config_disable_tr_adv': True,
+                },
+                config_model='mpas-ocean',
+            )

From 2d4f51988b6db017fdc939f64037d8544ce6b6c7 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Mon, 15 Dec 2025 13:21:19 -0600
Subject: [PATCH 04/47] Namelist changes in accordance with omega pr#310

---
 polaris/ocean/model/mpaso_to_omega.yaml | 21 +++++++++++++++++++++
 polaris/suites/ocean/mpaso_pr.txt       |  1 +
 2 files changed, 22 insertions(+)

diff --git a/polaris/ocean/model/mpaso_to_omega.yaml b/polaris/ocean/model/mpaso_to_omega.yaml
index 15b5882835..359c02af47 100644
--- a/polaris/ocean/model/mpaso_to_omega.yaml
+++ b/polaris/ocean/model/mpaso_to_omega.yaml
@@ -114,3 +114,24 @@ config:
     config_eos_linear_alpha: DRhoDT
     config_eos_linear_beta: DRhoDS
     config_eos_linear_densityref: RhoT0S0
+
+- section:
+    cvmix: [VertMix, Background]
+  options:
+    config_cvmix_background_diffusion: Diffusivity
+    config_cvmix_background_viscosity: Viscosity
+
+- section:
+    cvmix: [VertMix, Convective]
+  options:
+    config_use_cvmix_convection: Enable
+    config_cvmix_convective_diffusion: Diffusivity
+    config_cvmix_convective_triggerBVF: TriggerBVF
+
+- section:
+    cvmix: [VertMix, Shear]
+  options:
+    config_use_cvmix_shear: Enable
+    config_cvmix_shear_PP_nu_zero: NuZero
+    config_cvmix_shear_PP_alpha: Alpha
+    config_cvmix_shear_PP_exp: Exponent
diff --git a/polaris/suites/ocean/mpaso_pr.txt b/polaris/suites/ocean/mpaso_pr.txt
index 0520e8903c..f7821c9504 100644
--- a/polaris/suites/ocean/mpaso_pr.txt
+++ b/polaris/suites/ocean/mpaso_pr.txt
@@ -11,6 +11,7 @@ ocean/planar/internal_wave/vlr/default
 # ocean/planar/merry_go_round/default
 ocean/planar/overflow/default
 ocean/single_column/cvmix
+ocean/single_column/cvmix_no_vadv
 ocean/single_column/ekman
 ocean/single_column/ideal_age
 ocean/single_column/inertial

From 681105b983325d487988fbdc9c0d3c28cb82c463 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Mon, 15 Dec 2025 15:59:45 -0600
Subject: [PATCH 05/47] Include restoring parameters in cfg and turn restoring
 on for individual single column tests, not the group

---
 polaris/tasks/ocean/single_column/cvmix/forward.yaml     | 4 ++++
 polaris/tasks/ocean/single_column/forward.yaml           | 4 ----
 polaris/tasks/ocean/single_column/ideal_age/forward.yaml | 4 ++++
 polaris/tasks/ocean/single_column/single_column.cfg      | 8 ++++----
 4 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/cvmix/forward.yaml b/polaris/tasks/ocean/single_column/cvmix/forward.yaml
index f2a7bd5282..51336d619d 100644
--- a/polaris/tasks/ocean/single_column/cvmix/forward.yaml
+++ b/polaris/tasks/ocean/single_column/cvmix/forward.yaml
@@ -6,6 +6,10 @@ mpas-ocean:
     config_mom_del4: 2.0e14
   frazil_ice:
     config_use_frazil_ice_formation: true
+  tracer_forcing_activeTracers:
+    config_use_activeTracers_surface_bulk_forcing: true
+    config_use_activeTracers_surface_restoring: true
+    config_use_activeTracers_interior_restoring: true
   cvmix:
     config_use_cvmix_convection: true
     config_use_cvmix_shear: true
diff --git a/polaris/tasks/ocean/single_column/forward.yaml b/polaris/tasks/ocean/single_column/forward.yaml
index bdaab85fb9..8d349a8394 100644
--- a/polaris/tasks/ocean/single_column/forward.yaml
+++ b/polaris/tasks/ocean/single_column/forward.yaml
@@ -9,10 +9,6 @@ mpas-ocean:
     config_btr_dt: 0000_00:00:30
   forcing:
     config_use_bulk_wind_stress: true
-  tracer_forcing_activeTracers:
-    config_use_activeTracers_surface_bulk_forcing: true
-    config_use_activeTracers_surface_restoring: true
-    config_use_activeTracers_interior_restoring: true
   streams:
     mesh:
       filename_template: initial_state.nc
diff --git a/polaris/tasks/ocean/single_column/ideal_age/forward.yaml b/polaris/tasks/ocean/single_column/ideal_age/forward.yaml
index 487efcc5a1..62e8dbcdf5 100644
--- a/polaris/tasks/ocean/single_column/ideal_age/forward.yaml
+++ b/polaris/tasks/ocean/single_column/ideal_age/forward.yaml
@@ -1,6 +1,10 @@
 mpas-ocean:
   time_management:
     config_run_duration: 0010_00:00:00
+  tracer_forcing_activeTracers:
+    config_use_activeTracers_surface_bulk_forcing: true
+    config_use_activeTracers_surface_restoring: true
+    config_use_activeTracers_interior_restoring: true
   tracer_forcing_idealAgeTracers:
     config_use_idealAgeTracers: true
     config_use_idealAgeTracers_idealAge_forcing: true
diff --git a/polaris/tasks/ocean/single_column/single_column.cfg b/polaris/tasks/ocean/single_column/single_column.cfg
index d034b42fb6..930d527db3 100644
--- a/polaris/tasks/ocean/single_column/single_column.cfg
+++ b/polaris/tasks/ocean/single_column/single_column.cfg
@@ -72,10 +72,10 @@ meridional_velocity = 0.0
 [single_column_forcing]
 
 # Piston velocity to control rate of restoring toward temperature_surface_restoring_value
-temperature_piston_velocity = 0.0
+temperature_piston_velocity = 4.0e-6
 
 # Piston velocity to control rate of restoring toward salinity_surface_restoring_value
-salinity_piston_velocity = 0.0
+salinity_piston_velocity = 4.0e-6
 
 # Temperature to restore towards when surface restoring is turned on
 temperature_surface_restoring_value = ${single_column:surface_temperature}
@@ -84,10 +84,10 @@ temperature_surface_restoring_value = ${single_column:surface_temperature}
 salinity_surface_restoring_value = ${single_column:surface_salinity}
 
 # Rate at which temperature is restored toward the initial condition
-temperature_interior_restoring_rate = 0.0
+temperature_interior_restoring_rate = 1.0e-6
 
 # Rate at which salinity is restored toward the initial condition
-salinity_interior_restoring_rate = 0.0
+salinity_interior_restoring_rate = 1.0e-6
 
 # Net latent heat flux applied when bulk forcing is used. Positive values indicate a net
 # input of heat to ocean

From 6d3b409dca2f7bea1059bb3a51e71b9ff0fc1c9c Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Tue, 16 Dec 2025 18:07:04 -0600
Subject: [PATCH 06/47] Update single_column docs

---
 docs/users_guide/ocean/tasks/single_column.md | 67 ++++++++++---------
 1 file changed, 37 insertions(+), 30 deletions(-)

diff --git a/docs/users_guide/ocean/tasks/single_column.md b/docs/users_guide/ocean/tasks/single_column.md
index 9d656dacd3..9f6b2939f6 100644
--- a/docs/users_guide/ocean/tasks/single_column.md
+++ b/docs/users_guide/ocean/tasks/single_column.md
@@ -14,7 +14,7 @@ the vertical dynamics of the ocean model only. The test cases are:
 
 ## suppported models
 
-These tasks support only MPAS-Ocean.
+These tasks support MPAS-Ocean and Omega.
 
 ## mesh
 
@@ -58,30 +58,8 @@ min_pc_fraction = 0.1
 
 ## initial conditions
 
-The temperature and salinity profiles are defined using the following equations:
-
-$$
-\Phi(z) = \begin{cases}
-    \Phi_0 &\text{ if } z = z[0]\\
-    \Phi_0 + {d\Phi/dz}_{ML} z &
-    \text{ if } z > z_{MLD}\\
-    (\Phi_0 + {\Delta\Phi}_{ML}) + {d\Phi/dz}_{int} (z - z_{MLD}) &
-    \text{ if } z \le z_{MLD}
-\end{cases}
-$$
-
-where $\Phi_0 = $`surface_X`, ${d\Phi/dz}_{ML} = $`X_gradient_mixed_layer`,
-$z_{MLD} = -$`mixed_layer_depth_X`, ${\Delta\Phi}_{ML} = $
-`X_difference_across_mixed_layer`, and ${d\Phi/dz}_{int} = $
-`X_gradient_interior`. `X` in the config options above is either `temperature`
-or `salinity`.
-
-The initial velocity is vertically uniform and given by
-`single_column:zonal_velocity` and `single_column:meridional_velocity`, which
-are 0 by default (at rest).
-
-The Coriolis parameter is spatially constant and set equal to
-`coriolis_parameter`.
+The initial conditions are either stably stratified or uniform. See each task
+below.
 
 ### forcing
 
@@ -245,8 +223,35 @@ See {ref}`ocean-single-column`.
 
 See {ref}`ocean-single-column`.
 
+(ocean-single-column-stable)=
+
 ### initial conditions
 
+The temperature and salinity profiles are defined using the following equations:
+
+$$
+\Phi(z) = \begin{cases}
+    \Phi_0 &\text{ if } z = z[0]\\
+    \Phi_0 + {d\Phi/dz}_{ML} z &
+    \text{ if } z > z_{MLD}\\
+    (\Phi_0 + {\Delta\Phi}_{ML}) + {d\Phi/dz}_{int} (z - z_{MLD}) &
+    \text{ if } z \le z_{MLD}
+\end{cases}
+$$
+
+where $\Phi_0 = $`surface_X`, ${d\Phi/dz}_{ML} = $`X_gradient_mixed_layer`,
+$z_{MLD} = -$`mixed_layer_depth_X`, ${\Delta\Phi}_{ML} = $
+`X_difference_across_mixed_layer`, and ${d\Phi/dz}_{int} = $
+`X_gradient_interior`. `X` in the config options above is either `temperature`
+or `salinity`.
+
+The initial velocity is vertically uniform and given by
+`single_column:zonal_velocity` and `single_column:meridional_velocity`, which
+are 0 by default (at rest).
+
+The Coriolis parameter is spatially constant and set equal to
+`coriolis_parameter`.
+
 These config options overwrite those in {ref}`ocean-single-column`:
 
 ```cfg
@@ -263,7 +268,7 @@ mixed_layer_depth_temperature =  25.0
 salinity_difference_across_mixed_layer = 1.0
 ```
 
-The rest of the config options are given in {ref}`ocean-single-column`.
+(ocean-single-column-wind-evap)=
 
 ### forcing
 
@@ -301,8 +306,7 @@ days.
 
 ### config options
 
-See {ref}`ocean-single-column`. Currently, config options are only given in the
-shared framework.
+See {ref}`ocean-single-column-wind-evap` and {ref}`ocean-single-column-stable`.
 
 ### cores
 
@@ -345,7 +349,8 @@ The rest of the vertical grid features follow {ref}`ocean-single-column`.
 ### initial conditions
 
 The temperature and salinity are constant and the flow is at rest.
-See {ref}`ocean-single-column`.
+
+(ocean-single-column-wind)=
 
 ### forcing
 
@@ -378,7 +383,8 @@ viscosity:
 vertical_viscosity = 1.e-3
 ```
 
-All other config options derive from {ref}`ocean-single-column`.
+All other config options derive from {ref}`ocean-single-column` and
+{ref}`ocean-single-column-wind`.
 
 ### cores
 
@@ -412,6 +418,7 @@ See {ref}`ocean-single-column`.
 ### initial conditions
 
 `idealAgeTracers` is initialized as zero seconds throughout the water column.
+See {ref}`ocean-single-column-stable`.
 
 ### forcing
 

From 27afbb406e4187bfefa5869fc52f54497366aeaa Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Tue, 16 Dec 2025 18:49:33 -0600
Subject: [PATCH 07/47] Add no_vadv as a forward step

---
 polaris/tasks/ocean/single_column/__init__.py | 16 ++++----
 .../ocean/single_column/cvmix/__init__.py     | 39 +++++++++----------
 polaris/tasks/ocean/single_column/viz.py      | 16 +++++++-
 3 files changed, 41 insertions(+), 30 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/__init__.py b/polaris/tasks/ocean/single_column/__init__.py
index 580416d55f..518eb0dab7 100644
--- a/polaris/tasks/ocean/single_column/__init__.py
+++ b/polaris/tasks/ocean/single_column/__init__.py
@@ -35,16 +35,14 @@ def add_single_column_tasks(component):
         config=config,
         config_filename=f'{name}.cfg',
     )
-    for enable_vadv in [True, False]:
-        component.add_task(
-            CVMix(
-                component=component,
-                config=config,
-                init=init_step,
-                indir=f'{group_name}',
-                enable_vadv=enable_vadv,
-            )
+    component.add_task(
+        CVMix(
+            component=component,
+            config=config,
+            init=init_step,
+            indir=f'{group_name}',
         )
+    )
 
     forcing_name = 'wind'
     name = 'ekman'
diff --git a/polaris/tasks/ocean/single_column/cvmix/__init__.py b/polaris/tasks/ocean/single_column/cvmix/__init__.py
index 43411a55e5..d5d48de246 100644
--- a/polaris/tasks/ocean/single_column/cvmix/__init__.py
+++ b/polaris/tasks/ocean/single_column/cvmix/__init__.py
@@ -1,5 +1,3 @@
-import os
-
 from polaris import Task
 from polaris.tasks.ocean.single_column.forward import Forward
 from polaris.tasks.ocean.single_column.viz import Viz
@@ -11,7 +9,7 @@ class CVMix(Task):
     then performs a short forward run testing vertical mixing on 1 core.
     """
 
-    def __init__(self, component, config, init, indir, enable_vadv=True):
+    def __init__(self, component, config, init, indir):
         """
         Create the test case
         Parameters
@@ -20,11 +18,7 @@ def __init__(self, component, config, init, indir, enable_vadv=True):
             The ocean component that this task belongs to
         """
         name = 'cvmix'
-        if not enable_vadv:
-            subdir = os.path.join(indir, f'{name}_no_vadv')
-        else:
-            subdir = os.path.join(indir, name)
-        super().__init__(component=component, name=name, subdir=subdir)
+        super().__init__(component=component, name=name, indir=indir)
         config_filename = 'cvmix.cfg'
         self.set_shared_config(config, link=config_filename)
         self.config.add_from_package(
@@ -38,20 +32,25 @@ def __init__(self, component, config, init, indir, enable_vadv=True):
             'layerThickness',
             'normalVelocity',
         ]
-        self.add_step(
-            Forward(
-                component=component,
-                indir=subdir,
-                ntasks=1,
-                min_tasks=1,
-                openmp_threads=1,
-                validate_vars=validate_vars,
-                task_name=name,
-                enable_vadv=enable_vadv,
+        for enable_vadv in [True, False]:
+            self.add_step(
+                Forward(
+                    component=component,
+                    indir=self.subdir,
+                    ntasks=1,
+                    min_tasks=1,
+                    openmp_threads=1,
+                    validate_vars=validate_vars,
+                    task_name=name,
+                    enable_vadv=enable_vadv,
+                )
             )
-        )
 
         self.add_step(
-            Viz(component=component, indir=subdir),
+            Viz(
+                component=component,
+                indir=self.subdir,
+                comparison_path=f'{self.subdir}/forward_no_vadv',
+            ),
             run_by_default=False,
         )
diff --git a/polaris/tasks/ocean/single_column/viz.py b/polaris/tasks/ocean/single_column/viz.py
index 9d02337290..5fcf165026 100644
--- a/polaris/tasks/ocean/single_column/viz.py
+++ b/polaris/tasks/ocean/single_column/viz.py
@@ -11,7 +11,9 @@ class Viz(Step):
     A step for plotting the results of a single-column test
     """
 
-    def __init__(self, component, indir, ideal_age=False):
+    def __init__(
+        self, component, indir, ideal_age=False, comparison_path=None
+    ):
         """
         Create the step
 
@@ -29,12 +31,17 @@ def __init__(self, component, indir, ideal_age=False):
         """
         super().__init__(component=component, name='viz', indir=indir)
         self.ideal_age = ideal_age
+        self.comparison_path = comparison_path
         self.add_input_file(
             filename='initial_state.nc', target='../init/initial_state.nc'
         )
         self.add_input_file(
             filename='output.nc', target='../forward/output.nc'
         )
+        if comparison_path is not None:
+            self.add_input_file(
+                filename='comparison.nc', target=f'{comparison_path}/output.nc'
+            )
 
     def run(self):
         """
@@ -43,6 +50,8 @@ def run(self):
         use_mplstyle()
         ideal_age = self.ideal_age
         ds = xr.load_dataset('output.nc')
+        if self.comparison_path is not None:
+            ds_comp = xr.load_dataset('comparison.nc')
         t_days = ds.daysSinceStartOfSim.values
         t = t_days.astype('timedelta64[ns]')
         t = t / np.timedelta64(1, 'D')
@@ -64,10 +73,15 @@ def run(self):
             var = ds[field_name].mean(dim='nCells')
             var_init = var.isel(Time=0)
             var_final = var.isel(Time=t_index)
+            if self.comparison_path is not None:
+                var_comp = ds_comp[field_name].mean(dim='nCells')
+                var_comp = var_comp.isel(Time=t_index)
             plt.figure(figsize=(3, 5))
             ax = plt.subplot(111)
             ax.plot(var_init, z_mid_init, '--k', label='initial')
             ax.plot(var_final, z_mid_final, '-k', label='final')
+            if self.comparison_path is not None:
+                ax.plot(var_comp, z_mid_final, '-r', label='comparison')
             ax.set_xlabel(f'{field_name} ({field_units})')
             ax.set_ylabel('z (m)')
             ax.legend()

From 24342f286c5894d78768edd50d348f755fd35f48 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Tue, 16 Dec 2025 18:51:09 -0600
Subject: [PATCH 08/47] Add omega support

---
 .../ocean/single_column/cvmix/forward.yaml    | 17 +++++---
 .../ocean/single_column/ekman/forward.yaml    | 17 +++++---
 polaris/tasks/ocean/single_column/forward.py  | 15 ++++++-
 .../tasks/ocean/single_column/forward.yaml    | 43 +++++++++++++++----
 .../ocean/single_column/inertial/forward.yaml |  4 +-
 polaris/tasks/ocean/single_column/init.py     |  6 +--
 6 files changed, 73 insertions(+), 29 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/cvmix/forward.yaml b/polaris/tasks/ocean/single_column/cvmix/forward.yaml
index 51336d619d..17fa423635 100644
--- a/polaris/tasks/ocean/single_column/cvmix/forward.yaml
+++ b/polaris/tasks/ocean/single_column/cvmix/forward.yaml
@@ -1,9 +1,18 @@
-mpas-ocean:
+ocean:
   time_management:
     config_run_duration: 0010_00:00:00
   hmix_del4:
     config_use_mom_del4: true
     config_mom_del4: 2.0e14
+  cvmix:
+    config_use_cvmix_convection: true
+    config_use_cvmix_shear: true
+  eos:
+    config_eos_type: linear
+  eos_linear:
+    config_eos_linear_beta: 0.01
+
+mpas-ocean:
   frazil_ice:
     config_use_frazil_ice_formation: true
   tracer_forcing_activeTracers:
@@ -11,15 +20,9 @@ mpas-ocean:
     config_use_activeTracers_surface_restoring: true
     config_use_activeTracers_interior_restoring: true
   cvmix:
-    config_use_cvmix_convection: true
-    config_use_cvmix_shear: true
     config_cvmix_shear_mixing_scheme: KPP
     config_use_cvmix_kpp: true
     config_cvmix_kpp_matching: MatchBoth
     config_cvmix_kpp_interpolationOMLType: cubic
-  eos:
-    config_eos_type: linear
-  eos_linear:
-    config_eos_linear_beta: 0.01
   streams:
     KPP_testing: {}
diff --git a/polaris/tasks/ocean/single_column/ekman/forward.yaml b/polaris/tasks/ocean/single_column/ekman/forward.yaml
index 85740192a9..51aadb9789 100644
--- a/polaris/tasks/ocean/single_column/ekman/forward.yaml
+++ b/polaris/tasks/ocean/single_column/ekman/forward.yaml
@@ -1,24 +1,27 @@
-mpas-ocean:
+ocean:
   time_management:
     config_run_duration: 0005_00:00:00
   hmix_del4:
     config_use_mom_del4: false
-  frazil_ice:
-    config_use_frazil_ice_formation: false
-  bottom_drag:
-    config_implicit_constant_bottom_drag_coeff: 0.0
   cvmix:
-    config_cvmix_background_scheme: constant
     config_cvmix_background_diffusion: 0.0
     config_use_cvmix_convection: false
     config_use_cvmix_shear: false
-    config_use_cvmix_kpp: false
   eos:
     config_eos_type: linear
   eos_linear:
     config_eos_linear_beta: 0.01
   forcing:
     config_use_bulk_wind_stress: true
+
+mpas-ocean:
+  bottom_drag:
+    config_implicit_constant_bottom_drag_coeff: 0.0
+  frazil_ice:
+    config_use_frazil_ice_formation: false
+  cvmix:
+    config_cvmix_background_scheme: constant
+    config_use_cvmix_kpp: false
   tracer_forcing_activeTracers:
     config_use_activeTracers_surface_bulk_forcing: false
     config_use_activeTracers_surface_restoring: false
diff --git a/polaris/tasks/ocean/single_column/forward.py b/polaris/tasks/ocean/single_column/forward.py
index 1cb40ecea7..71d3f41799 100644
--- a/polaris/tasks/ocean/single_column/forward.py
+++ b/polaris/tasks/ocean/single_column/forward.py
@@ -63,6 +63,8 @@ def __init__(
         task_name : str, optional
             the name of the test case
         """
+        if not enable_vadv:
+            name = f'{name}_no_vadv'
         super().__init__(
             component=component,
             name=name,
@@ -76,9 +78,8 @@ def __init__(
         self.add_yaml_file('polaris.ocean.config', 'output.yaml')
 
         self.add_input_file(
-            filename='initial_state.nc', target='../init/initial_state.nc'
+            filename='init.nc', target='../init/initial_state.nc'
         )
-        self.add_input_file(filename='forcing.nc', target='../init/forcing.nc')
         self.add_input_file(
             filename='graph.info', target='../init/culled_graph.info'
         )
@@ -96,6 +97,16 @@ def __init__(
 
         self.enable_vadv = enable_vadv
 
+    def setup(self):
+        """
+        TEMP: symlink initial condition to name hard-coded in Omega
+        """
+        super().setup()
+        model = self.config.get('ocean', 'model')
+        # TODO: remove as soon as Omega no longer hard-codes this file
+        if model == 'omega':
+            self.add_input_file(filename='OmegaMesh.nc', target='init.nc')
+
     def dynamic_model_config(self, at_setup):
         if self.task_name == 'ekman':
             nu = self.config.getfloat(
diff --git a/polaris/tasks/ocean/single_column/forward.yaml b/polaris/tasks/ocean/single_column/forward.yaml
index 8d349a8394..6b8b4af242 100644
--- a/polaris/tasks/ocean/single_column/forward.yaml
+++ b/polaris/tasks/ocean/single_column/forward.yaml
@@ -1,19 +1,21 @@
-mpas-ocean:
-  run_modes:
-    config_ocean_run_mode: forward
+ocean:
   time_management:
     config_stop_time: none
   time_integration:
     config_dt: 00:10:00
-  split_explicit_ts:
-    config_btr_dt: 0000_00:00:30
   forcing:
     config_use_bulk_wind_stress: true
+
+mpas-ocean:
+  run_modes:
+    config_ocean_run_mode: forward
+  split_explicit_ts:
+    config_btr_dt: 0000_00:00:30
   streams:
     mesh:
-      filename_template: initial_state.nc
+      filename_template: init.nc
     input:
-      filename_template: initial_state.nc
+      filename_template: init.nc
     restart: {}
     mixedLayerDepthsOutput:
       contents:
@@ -44,7 +46,7 @@ mpas-ocean:
       - frazilSalinityTendency
     forcing_data:
       type: input
-      filename_template: forcing.nc
+      filename_template: init.nc
       input_interval: initial_only
       contents:
       - tracersSurfaceRestoringFields
@@ -65,3 +67,28 @@ mpas-ocean:
       - icebergFreshWaterFlux
       - riverRunoffFlux
       - iceRunoffFlux
+
+Omega:
+  IOStreams:
+    InitialVertCoord:
+      Filename: init.nc
+    InitialState:
+      UsePointerFile: false
+      Filename: init.nc
+      Contents:
+      - State
+      - WindStressZonal
+      - WindStressMeridional
+    History:
+      Filename: output.nc
+      Freq: 1
+      FreqUnits: Seconds
+      IfExists: append
+      # effectively never
+      FileFreq: 9999
+      FileFreqUnits: years
+      Contents:
+      - AuxiliaryState
+      - State
+      - Tracers
+      - SshCell
diff --git a/polaris/tasks/ocean/single_column/inertial/forward.yaml b/polaris/tasks/ocean/single_column/inertial/forward.yaml
index ba694874f9..ca5fd87c5a 100644
--- a/polaris/tasks/ocean/single_column/inertial/forward.yaml
+++ b/polaris/tasks/ocean/single_column/inertial/forward.yaml
@@ -1,6 +1,8 @@
-mpas-ocean:
+ocean:
   time_management:
     config_run_duration: 0010_00:00:00
+
+mpas-ocean:
   tracer_forcing_activeTracers:
     config_use_activeTracers_surface_bulk_forcing: false
     config_use_activeTracers_surface_restoring: false
diff --git a/polaris/tasks/ocean/single_column/init.py b/polaris/tasks/ocean/single_column/init.py
index c3c249e4b3..be33671986 100644
--- a/polaris/tasks/ocean/single_column/init.py
+++ b/polaris/tasks/ocean/single_column/init.py
@@ -33,7 +33,6 @@ def __init__(self, component, subdir):
             'culled_mesh.nc',
             'culled_graph.info',
             'initial_state.nc',
-            'forcing.nc',
         ]:
             self.add_output_file(file)
 
@@ -148,10 +147,9 @@ def run(self):
         ds.attrs['nx'] = nx
         ds.attrs['ny'] = ny
         ds.attrs['dc'] = dc
-        write_netcdf(ds, 'initial_state.nc')
 
         # create forcing stream
-        ds_forcing = xr.Dataset()
+        ds_forcing = ds.copy()
         forcing_array = xr.ones_like(temperature)
         forcing_array_surface = xr.ones_like(ds.bottomDepth)
         forcing_array_surface = forcing_array_surface.expand_dims(
@@ -234,4 +232,4 @@ def run(self):
         ds_forcing['icebergFreshWaterFlux'] = (
             iceberg_flux * forcing_array_surface
         )
-        write_netcdf(ds_forcing, 'forcing.nc')
+        write_netcdf(ds_forcing, 'initial_state.nc')

From 0a2800918c83284c61b5b29d3535ea737297d15d Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Sun, 4 Jan 2026 16:30:38 -0600
Subject: [PATCH 09/47] Add restart streams to forward.yaml's omega section

---
 .../tasks/ocean/single_column/forward.yaml    | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/polaris/tasks/ocean/single_column/forward.yaml b/polaris/tasks/ocean/single_column/forward.yaml
index 6b8b4af242..8161594588 100644
--- a/polaris/tasks/ocean/single_column/forward.yaml
+++ b/polaris/tasks/ocean/single_column/forward.yaml
@@ -77,6 +77,7 @@ Omega:
       Filename: init.nc
       Contents:
       - State
+      - Tracers
       - WindStressZonal
       - WindStressMeridional
     History:
@@ -92,3 +93,27 @@ Omega:
       - State
       - Tracers
       - SshCell
+    RestartRead:
+      UsePointerFile: true
+      PointerFilename: ocn.pointer
+      Mode: read
+      Precision: double
+      Freq: 1
+      FreqUnits: OnStartup
+      UseStartEnd: true
+      StartTime: 0001-01-01_00:00:01
+      EndTime: 99999-12-31_00:00:00
+      Contents:
+      - Restart
+    RestartWrite:
+      UsePointerFile: true
+      PointerFilename: ocn.pointer
+      Filename: ocn.restart.$Y-$M-$D_$h.$m.$s
+      Mode: write
+      IfExists: replace
+      Precision: double
+      Freq: 6
+      FreqUnits: months
+      UseStartEnd: false
+      Contents:
+      - Restart

From d5f45661c4f3ee46d74e17254d66ff2425b67239 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Sun, 4 Jan 2026 16:31:11 -0600
Subject: [PATCH 10/47] Add a bunch of tendency configs to cvmix forward.yaml's
 omega section

---
 .../ocean/single_column/cvmix/forward.yaml    | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/polaris/tasks/ocean/single_column/cvmix/forward.yaml b/polaris/tasks/ocean/single_column/cvmix/forward.yaml
index 17fa423635..08c8cff604 100644
--- a/polaris/tasks/ocean/single_column/cvmix/forward.yaml
+++ b/polaris/tasks/ocean/single_column/cvmix/forward.yaml
@@ -26,3 +26,22 @@ mpas-ocean:
     config_cvmix_kpp_interpolationOMLType: cubic
   streams:
     KPP_testing: {}
+
+Omega:
+  Tendencies:
+    ThicknessFluxTendencyEnable: true
+    PVTendencyEnable: false
+    KETendencyEnable: false
+    SSHTendencyEnable: false
+    VelDiffTendencyEnable: false
+    VelHyperDiffTendencyEnable: false
+    VelVertMixTendencyEnable: true
+    PresForceTendencyEnable: false
+    PresGradForceTendencyEnable: false
+    GeoptGradTendencyEnable: false
+    WindForcingTendencyEnable: true
+    BottomDragTendencyEnable: false
+    TracerHorzAdvTendencyEnable: false
+    TracerDiffTendencyEnable: false
+    TracerHyperDiffTendencyEnable: false
+    TracerVertMixTendencyEnable: true

From abcdf4e1f8e4e7c490a3e1370a801a838b5d6206 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Sun, 4 Jan 2026 16:31:56 -0600
Subject: [PATCH 11/47] Remove later: check out hyun's vmix tendency branch

---
 e3sm_submodules/Omega | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/e3sm_submodules/Omega b/e3sm_submodules/Omega
index f2e951ac69..1b4057ed7c 160000
--- a/e3sm_submodules/Omega
+++ b/e3sm_submodules/Omega
@@ -1 +1 @@
-Subproject commit f2e951ac69e0b5667900906ff22ebb1587040d91
+Subproject commit 1b4057ed7c8898d4022b5d10754c76e0dcec780b

From f08de5fb82ff8eaaace9919a9d3aedcbbe428cdc Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Thu, 8 Jan 2026 16:01:40 -0600
Subject: [PATCH 12/47] Add mapping for vmix tendency config

---
 polaris/ocean/model/mpaso_to_omega.yaml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/polaris/ocean/model/mpaso_to_omega.yaml b/polaris/ocean/model/mpaso_to_omega.yaml
index 359c02af47..24efc61c90 100644
--- a/polaris/ocean/model/mpaso_to_omega.yaml
+++ b/polaris/ocean/model/mpaso_to_omega.yaml
@@ -91,6 +91,11 @@ config:
   options:
     config_disable_vel_explicit_bottom_drag: BottomDragTendencyEnable
 
+- section:
+    debug: Tendencies
+  options:
+    config_disable_vel_vmix: VelVertMixTendencyEnable
+
 - section:
     bottom_drag: Tendencies
   options:

From 23325ce10422656481b87ef3fb64c1dedf6ebd6e Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Thu, 8 Jan 2026 16:07:33 -0600
Subject: [PATCH 13/47] WIP add stable and unstable versions of cvmix

---
 polaris/tasks/ocean/single_column/__init__.py | 34 +++++++++++++++++--
 1 file changed, 32 insertions(+), 2 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/__init__.py b/polaris/tasks/ocean/single_column/__init__.py
index 518eb0dab7..3ea3f27b66 100644
--- a/polaris/tasks/ocean/single_column/__init__.py
+++ b/polaris/tasks/ocean/single_column/__init__.py
@@ -17,7 +17,8 @@ def add_single_column_tasks(component):
 
     forcing = ['wind', 'evap']
     name = 'cvmix'
-    filepath = f'{component.name}/{group_name}/{name}/{name}.cfg'
+    indir = f'{group_name}_stable'
+    filepath = f'{component.name}/indir/{name}/{name}.cfg'
     config = PolarisConfigParser(filepath=filepath)
     config.add_from_package(
         'polaris.tasks.ocean.single_column', f'{group_name}.cfg'
@@ -40,7 +41,36 @@ def add_single_column_tasks(component):
             component=component,
             config=config,
             init=init_step,
-            indir=f'{group_name}',
+            indir=indir,
+        )
+    )
+
+    name = 'cvmix'
+    forcing_name = 'wind'
+    indir = group_name
+    filepath = f'{component.name}/indir/{name}/{name}_{forcing_name}.cfg'
+    config = PolarisConfigParser(filepath=filepath)
+    config.add_from_package(
+        'polaris.tasks.ocean.single_column', f'{group_name}.cfg'
+    )
+    config.add_from_package(
+        'polaris.tasks.ocean.single_column', f'{forcing_name}.cfg'
+    )
+    config.add_from_package(
+        'polaris.tasks.ocean.single_column', 'unstable_stratification.cfg'
+    )
+    init_step = component.get_or_create_shared_step(
+        step_cls=Init,
+        subdir=f'{group_name}/{forcing_name}/init_unstable',
+        config=config,
+        config_filename=f'{name}_{forcing_name}.cfg',
+    )
+    component.add_task(
+        CVMix(
+            component=component,
+            config=config,
+            init=init_step,
+            indir=indir,
         )
     )
 

From fd4e014fa0749fa111657b3b81a9a3811ac707d1 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Thu, 8 Jan 2026 16:13:21 -0600
Subject: [PATCH 14/47] Add name argument to cvmix and fixup comparison
 filepath

---
 polaris/tasks/ocean/single_column/cvmix/__init__.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/cvmix/__init__.py b/polaris/tasks/ocean/single_column/cvmix/__init__.py
index d5d48de246..3d13fbc9de 100644
--- a/polaris/tasks/ocean/single_column/cvmix/__init__.py
+++ b/polaris/tasks/ocean/single_column/cvmix/__init__.py
@@ -9,7 +9,7 @@ class CVMix(Task):
     then performs a short forward run testing vertical mixing on 1 core.
     """
 
-    def __init__(self, component, config, init, indir):
+    def __init__(self, component, config, init, indir, name='cvmix'):
         """
         Create the test case
         Parameters
@@ -17,7 +17,6 @@ def __init__(self, component, config, init, indir):
         component : polaris.tasks.ocean.Ocean
             The ocean component that this task belongs to
         """
-        name = 'cvmix'
         super().__init__(component=component, name=name, indir=indir)
         config_filename = 'cvmix.cfg'
         self.set_shared_config(config, link=config_filename)
@@ -50,7 +49,7 @@ def __init__(self, component, config, init, indir):
             Viz(
                 component=component,
                 indir=self.subdir,
-                comparison_path=f'{self.subdir}/forward_no_vadv',
+                comparison_path='../forward_no_vadv',
             ),
             run_by_default=False,
         )

From d81281d788737566345a6f575af701820a60bd70 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Fri, 9 Jan 2026 11:40:46 -0600
Subject: [PATCH 15/47] Add utility for daysSinceStartOfSim

---
 polaris/ocean/time.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 polaris/ocean/time.py

diff --git a/polaris/ocean/time.py b/polaris/ocean/time.py
new file mode 100644
index 0000000000..38b61858e8
--- /dev/null
+++ b/polaris/ocean/time.py
@@ -0,0 +1,19 @@
+import numpy as np
+import pandas as pd
+
+
+def get_days_since_start(ds):
+    """
+    Ocean model output may or may not include 'daysSinceStartOfSim'. This
+    routine uses 'daysSinceStartOfSim' if available, otherwise it uses 'Time'
+    """
+    if 'daysSinceStartOfSim' in ds.keys():
+        t_arr = ds.daysSinceStartOfSim.values.astype(float)
+    elif 'Time' in ds.keys():
+        t_vals = ds['Time'].values
+        t_pd = pd.to_datetime(t_vals)
+        t_arr = 1.0e9 * (t_pd - t_pd[0]) / np.timedelta64(1, 's')
+        t_arr = t_arr.astype(float) / 86400.0
+    else:
+        raise ValueError('Could not find a time variable in dataset')
+    return t_arr

From fb03b48c67061eae15af8b86d6f693f72e385ab6 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Fri, 9 Jan 2026 11:46:30 -0600
Subject: [PATCH 16/47] WIP Support omega in single column viz step

---
 polaris/tasks/ocean/single_column/viz.py | 92 +++++++++++++++---------
 1 file changed, 57 insertions(+), 35 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/viz.py b/polaris/tasks/ocean/single_column/viz.py
index 5fcf165026..b30e66c24b 100644
--- a/polaris/tasks/ocean/single_column/viz.py
+++ b/polaris/tasks/ocean/single_column/viz.py
@@ -1,12 +1,13 @@
 import matplotlib.pyplot as plt
 import numpy as np
-import xarray as xr
 
-from polaris import Step
+from polaris.ocean.model import OceanIOStep
+from polaris.ocean.time import get_days_since_start
+from polaris.ocean.vertical.diagnostics import depth_from_thickness
 from polaris.viz import use_mplstyle
 
 
-class Viz(Step):
+class Viz(OceanIOStep):
     """
     A step for plotting the results of a single-column test
     """
@@ -49,33 +50,53 @@ def run(self):
         """
         use_mplstyle()
         ideal_age = self.ideal_age
-        ds = xr.load_dataset('output.nc')
+
+        ds_init = self.open_model_dataset('initial_state.nc')
+        ds_init = ds_init.isel(Time=0)
+
+        ds = self.open_model_dataset('output.nc')
+        t_arr = get_days_since_start(ds)
+        t_index = np.argmin(np.abs(t_arr - 1.0))  # index nearest 1 day
+        t_days = float(t_arr[t_index])
+        ds_final = ds.isel(Time=t_index)
+
         if self.comparison_path is not None:
-            ds_comp = xr.load_dataset('comparison.nc')
-        t_days = ds.daysSinceStartOfSim.values
-        t = t_days.astype('timedelta64[ns]')
-        t = t / np.timedelta64(1, 'D')
-        t_index = np.argmin(np.abs(t - 1.0))  # ds.sizes['Time'] - 1
-        t_days = t[t_index]
+            ds_comp = self.open_model_dataset('comparison.nc')
+            ds_comp = ds_comp.isel(Time=t_index)
 
         # Plot temperature and salinity profiles
-        title = f'final time = {t_days} days'
+        title = f'final time = {t_days:2.1g} days'
         fields = {'temperature': 'degC', 'salinity': 'PSU'}
         if ideal_age:
             # Include age tracer
             fields['iAge'] = 'seconds'
-        z_mid = ds['zMid'].mean(dim='nCells')
-        z_mid_init = z_mid.isel(Time=0)
-        z_mid_final = z_mid.isel(Time=t_index)
+        z_mid_init = depth_from_thickness(ds_init).mean(dim='nCells')
+        z_mid_final = depth_from_thickness(ds_final).mean(dim='nCells')
         for field_name, field_units in fields.items():
-            if field_name not in ds.keys():
+            if field_name not in ds_init.keys():
+                raise ValueError(
+                    f'{field_name} not present in initial_state.nc'
+                )
+            if field_name not in ds_final.keys():
                 raise ValueError(f'{field_name} not present in output.nc')
-            var = ds[field_name].mean(dim='nCells')
-            var_init = var.isel(Time=0)
-            var_final = var.isel(Time=t_index)
+            var_init = ds_init[field_name].mean(dim='nCells')
+            var_final = ds_final[field_name].mean(dim='nCells')
+            print('Size of variables to plot')
+            print(t_arr)
+            print(f't_index = {t_index}')
+            print(
+                f'Change of {field_name} at the surface: '
+                f'{var_final.values[0] - var_init.values[0]}'
+            )
+            print(
+                f'Change of {field_name} at the bottom: '
+                f'{var_final.values[-1] - var_init.values[-1]}'
+            )
+
             if self.comparison_path is not None:
                 var_comp = ds_comp[field_name].mean(dim='nCells')
-                var_comp = var_comp.isel(Time=t_index)
+                if field_name not in ds_final.keys():
+                    raise ValueError(f'{field_name} not present in output.nc')
             plt.figure(figsize=(3, 5))
             ax = plt.subplot(111)
             ax.plot(var_init, z_mid_init, '--k', label='initial')
@@ -84,25 +105,26 @@ def run(self):
                 ax.plot(var_comp, z_mid_final, '-r', label='comparison')
             ax.set_xlabel(f'{field_name} ({field_units})')
             ax.set_ylabel('z (m)')
-            ax.legend()
+            # ax.legend()
             plt.title(title)
             plt.tight_layout(pad=0.5)
             plt.savefig(f'{field_name}.png')
             plt.close()
 
         # Plot velocity profiles
-        u = ds['velocityZonal'].mean(dim='nCells')
-        v = ds['velocityMeridional'].mean(dim='nCells')
-        u_final = u.isel(Time=t_index)
-        v_final = v.isel(Time=t_index)
-        plt.figure(figsize=(3, 5))
-        ax = plt.subplot(111)
-        ax.plot(u_final, z_mid_final, '-k', label='u')
-        ax.plot(v_final, z_mid_final, '-b', label='v')
-        ax.set_xlabel('Velocity (m/s)')
-        ax.set_ylabel('z (m)')
-        ax.legend()
-        plt.title(title)
-        plt.tight_layout(pad=0.5)
-        plt.savefig('velocity.png')
-        plt.close()
+        if 'velocityZonal' and 'velocityMeridional' in ds.keys():
+            u = ds['velocityZonal'].mean(dim='nCells')
+            v = ds['velocityMeridional'].mean(dim='nCells')
+            u_final = u.isel(Time=t_index)
+            v_final = v.isel(Time=t_index)
+            plt.figure(figsize=(3, 5))
+            ax = plt.subplot(111)
+            ax.plot(u_final, z_mid_final, '-k', label='u')
+            ax.plot(v_final, z_mid_final, '-b', label='v')
+            ax.set_xlabel('Velocity (m/s)')
+            ax.set_ylabel('z (m)')
+            ax.legend()
+            plt.title(title)
+            plt.tight_layout(pad=0.5)
+            plt.savefig('velocity.png')
+            plt.close()

From 9f17f492bb67cb1806b35679ea228ad36289b3d2 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Fri, 9 Jan 2026 11:54:01 -0600
Subject: [PATCH 17/47] Unstable stratification config

---
 .../ocean/single_column/unstable_stratification.cfg  | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 polaris/tasks/ocean/single_column/unstable_stratification.cfg

diff --git a/polaris/tasks/ocean/single_column/unstable_stratification.cfg b/polaris/tasks/ocean/single_column/unstable_stratification.cfg
new file mode 100644
index 0000000000..0a3102f8b4
--- /dev/null
+++ b/polaris/tasks/ocean/single_column/unstable_stratification.cfg
@@ -0,0 +1,12 @@
+
+# config options for single column testcases
+[single_column]
+
+# Temperature gradient below the mixed layer
+temperature_gradient_interior = -0.01
+
+# Depth of the temperature mixed layer
+mixed_layer_depth_temperature =  25.0
+
+# The salinity below the mixed layer
+salinity_difference_across_mixed_layer = -1.0

From 494571b408380b3f7e66e29949590d64a10f4635 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Sat, 10 Jan 2026 14:36:13 -0600
Subject: [PATCH 18/47] Turn del4 off

---
 polaris/tasks/ocean/single_column/cvmix/forward.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/cvmix/forward.yaml b/polaris/tasks/ocean/single_column/cvmix/forward.yaml
index 08c8cff604..bffa1d70c0 100644
--- a/polaris/tasks/ocean/single_column/cvmix/forward.yaml
+++ b/polaris/tasks/ocean/single_column/cvmix/forward.yaml
@@ -2,8 +2,7 @@ ocean:
   time_management:
     config_run_duration: 0010_00:00:00
   hmix_del4:
-    config_use_mom_del4: true
-    config_mom_del4: 2.0e14
+    config_use_mom_del4: false
   cvmix:
     config_use_cvmix_convection: true
     config_use_cvmix_shear: true

From c26f7a41ea30c2552813c17c44c726505b2fbee1 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Sat, 10 Jan 2026 14:36:48 -0600
Subject: [PATCH 19/47] Run with background diff, visc only

---
 polaris/tasks/ocean/single_column/cvmix/forward.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/cvmix/forward.yaml b/polaris/tasks/ocean/single_column/cvmix/forward.yaml
index bffa1d70c0..f5bddb4506 100644
--- a/polaris/tasks/ocean/single_column/cvmix/forward.yaml
+++ b/polaris/tasks/ocean/single_column/cvmix/forward.yaml
@@ -4,8 +4,8 @@ ocean:
   hmix_del4:
     config_use_mom_del4: false
   cvmix:
-    config_use_cvmix_convection: true
-    config_use_cvmix_shear: true
+    config_use_cvmix_convection: false
+    config_use_cvmix_shear: false
   eos:
     config_eos_type: linear
   eos_linear:

From a906b35c80a8ffef4950d42d19a1ec9cea864b39 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Sun, 11 Jan 2026 15:18:51 -0600
Subject: [PATCH 20/47] Reorganize and rename cvmix tests

---
 polaris/tasks/ocean/single_column/__init__.py | 76 +++++++++++--------
 polaris/tasks/ocean/single_column/forward.py  | 22 ++++++
 polaris/tasks/ocean/single_column/viz.py      | 43 ++++++-----
 .../single_column/{cvmix => vmix}/__init__.py | 33 +++++---
 .../{cvmix => vmix}/forward.yaml              |  5 +-
 .../{cvmix/cvmix.cfg => vmix/vmix.cfg}        |  0
 6 files changed, 117 insertions(+), 62 deletions(-)
 rename polaris/tasks/ocean/single_column/{cvmix => vmix}/__init__.py (59%)
 rename polaris/tasks/ocean/single_column/{cvmix => vmix}/forward.yaml (91%)
 rename polaris/tasks/ocean/single_column/{cvmix/cvmix.cfg => vmix/vmix.cfg} (100%)

diff --git a/polaris/tasks/ocean/single_column/__init__.py b/polaris/tasks/ocean/single_column/__init__.py
index 3ea3f27b66..808f791baa 100644
--- a/polaris/tasks/ocean/single_column/__init__.py
+++ b/polaris/tasks/ocean/single_column/__init__.py
@@ -1,9 +1,9 @@
 from polaris.config import PolarisConfigParser as PolarisConfigParser
-from polaris.tasks.ocean.single_column.cvmix import CVMix as CVMix
 from polaris.tasks.ocean.single_column.ekman import Ekman as Ekman
 from polaris.tasks.ocean.single_column.ideal_age import IdealAge as IdealAge
 from polaris.tasks.ocean.single_column.inertial import Inertial as Inertial
 from polaris.tasks.ocean.single_column.init import Init
+from polaris.tasks.ocean.single_column.vmix import VMix as VMix
 
 
 def add_single_column_tasks(component):
@@ -15,10 +15,10 @@ def add_single_column_tasks(component):
     """
     group_name = 'single_column'
 
-    forcing = ['wind', 'evap']
-    name = 'cvmix'
-    indir = f'{group_name}_stable'
-    filepath = f'{component.name}/indir/{name}/{name}.cfg'
+    name = 'vmix_stable'
+    forcing = ['wind']
+    forcing_dir = '_'.join(forcing) if forcing else 'no_forcing'
+    filepath = f'{component.name}/{group_name}/{name}/{name}.cfg'
     config = PolarisConfigParser(filepath=filepath)
     config.add_from_package(
         'polaris.tasks.ocean.single_column', f'{group_name}.cfg'
@@ -32,58 +32,62 @@ def add_single_column_tasks(component):
     )
     init_step = component.get_or_create_shared_step(
         step_cls=Init,
-        subdir=f'{group_name}/{"_".join(forcing)}/init_stable',
+        subdir=f'{group_name}/{forcing_dir}/init_stable',
         config=config,
         config_filename=f'{name}.cfg',
     )
     component.add_task(
-        CVMix(
+        VMix(
             component=component,
             config=config,
+            name=name,
             init=init_step,
-            indir=indir,
+            indir=group_name,
         )
     )
 
-    name = 'cvmix'
-    forcing_name = 'wind'
-    indir = group_name
-    filepath = f'{component.name}/indir/{name}/{name}_{forcing_name}.cfg'
+    name = 'vmix_unstable'
+    forcing = []
+    forcing_dir = '_'.join(forcing) if forcing else 'no_forcing'
+    filepath = f'{component.name}/{group_name}/{name}/{name}.cfg'
     config = PolarisConfigParser(filepath=filepath)
     config.add_from_package(
         'polaris.tasks.ocean.single_column', f'{group_name}.cfg'
     )
-    config.add_from_package(
-        'polaris.tasks.ocean.single_column', f'{forcing_name}.cfg'
-    )
+    for forcing_name in forcing:
+        config.add_from_package(
+            'polaris.tasks.ocean.single_column', f'{forcing_name}.cfg'
+        )
     config.add_from_package(
         'polaris.tasks.ocean.single_column', 'unstable_stratification.cfg'
     )
     init_step = component.get_or_create_shared_step(
         step_cls=Init,
-        subdir=f'{group_name}/{forcing_name}/init_unstable',
+        subdir=f'{group_name}/{forcing_dir}/init_unstable',
         config=config,
-        config_filename=f'{name}_{forcing_name}.cfg',
+        config_filename=f'{name}.cfg',
     )
     component.add_task(
-        CVMix(
+        VMix(
             component=component,
             config=config,
+            name=name,
             init=init_step,
-            indir=indir,
+            indir=group_name,
         )
     )
 
-    forcing_name = 'wind'
+    forcing = ['wind']
     name = 'ekman'
     filepath = f'{component.name}/{group_name}/{name}/{name}.cfg'
     config = PolarisConfigParser(filepath=filepath)
     config.add_from_package(
         'polaris.tasks.ocean.single_column', f'{group_name}.cfg'
     )
-    config.add_from_package(
-        'polaris.tasks.ocean.single_column', f'{forcing_name}.cfg'
-    )
+    for forcing_name in forcing:
+        config.add_from_package(
+            'polaris.tasks.ocean.single_column', f'{forcing_name}.cfg'
+        )
     init_step = component.get_or_create_shared_step(
         step_cls=Init,
         subdir=f'{group_name}/{forcing_name}/init',
@@ -95,25 +99,28 @@ def add_single_column_tasks(component):
             component=component,
             config=config,
             init=init_step,
-            indir=f'{group_name}',
+            indir=group_name,
         )
     )
 
     name = 'ideal_age'
+    forcing = ['evap']
+    forcing_dir = '_'.join(forcing) if forcing else 'no_forcing'
     filepath = f'{component.name}/{group_name}/{name}/{name}.cfg'
     config = PolarisConfigParser(filepath=filepath)
     config.add_from_package(
         'polaris.tasks.ocean.single_column', f'{group_name}.cfg'
     )
-    config.add_from_package(
-        'polaris.tasks.ocean.single_column', f'{forcing_name}.cfg'
-    )
+    for forcing_name in forcing:
+        config.add_from_package(
+            'polaris.tasks.ocean.single_column', f'{forcing_name}.cfg'
+        )
     config.add_from_package(
         'polaris.tasks.ocean.single_column', 'stable_stratification.cfg'
     )
     init_step = component.get_or_create_shared_step(
         step_cls=Init,
-        subdir=f'{group_name}/{forcing_name}/init_stable',
+        subdir=f'{group_name}/{forcing_dir}/init_stable',
         config=config,
         config_filename=f'{name}.cfg',
     )
@@ -122,23 +129,28 @@ def add_single_column_tasks(component):
             component=component,
             init=init_step,
             config=config,
-            indir=f'{group_name}',
+            indir=group_name,
         )
     )
 
-    forcing_name = 'no_forcing'
     name = 'inertial'
+    forcing = []
+    forcing_dir = '_'.join(forcing) if forcing else 'no_forcing'
     filepath = f'{component.name}/{group_name}/{name}/{name}.cfg'
     config = PolarisConfigParser(filepath=filepath)
     config.add_from_package(
         'polaris.tasks.ocean.single_column', f'{group_name}.cfg'
     )
+    for forcing_name in forcing:
+        config.add_from_package(
+            'polaris.tasks.ocean.single_column', f'{forcing_name}.cfg'
+        )
     config.add_from_package(
         'polaris.tasks.ocean.single_column', 'stable_stratification.cfg'
     )
     init_step = component.get_or_create_shared_step(
         step_cls=Init,
-        subdir=f'{group_name}/{forcing_name}/init_stable',
+        subdir=f'{group_name}/{forcing_dir}/init_stable',
         config=config,
         config_filename=f'{name}.cfg',
     )
@@ -147,6 +159,6 @@ def add_single_column_tasks(component):
             component=component,
             init=init_step,
             config=config,
-            indir=f'{group_name}',
+            indir=group_name,
         )
     )
diff --git a/polaris/tasks/ocean/single_column/forward.py b/polaris/tasks/ocean/single_column/forward.py
index 71d3f41799..0ecc92bb07 100644
--- a/polaris/tasks/ocean/single_column/forward.py
+++ b/polaris/tasks/ocean/single_column/forward.py
@@ -25,6 +25,7 @@ def __init__(
         validate_vars=None,
         task_name='',
         enable_vadv=True,
+        constant_diff=False,
     ):
         """
         Create a new test case
@@ -65,6 +66,8 @@ def __init__(
         """
         if not enable_vadv:
             name = f'{name}_no_vadv'
+        if constant_diff:
+            name = f'{name}_constant'
         super().__init__(
             component=component,
             name=name,
@@ -97,6 +100,8 @@ def __init__(
 
         self.enable_vadv = enable_vadv
 
+        self.constant_diff = constant_diff
+
     def setup(self):
         """
         TEMP: symlink initial condition to name hard-coded in Omega
@@ -125,3 +130,20 @@ def dynamic_model_config(self, at_setup):
                 },
                 config_model='mpas-ocean',
             )
+
+        if self.constant_diff:
+            self.add_model_config_options(
+                options={
+                    'config_use_cvmix_convection': False,
+                    'config_use_cvmix_shear': False,
+                },
+                config_model='ocean',
+            )
+        else:
+            self.add_model_config_options(
+                options={
+                    'config_use_cvmix_convection': True,
+                    'config_use_cvmix_shear': True,
+                },
+                config_model='ocean',
+            )
diff --git a/polaris/tasks/ocean/single_column/viz.py b/polaris/tasks/ocean/single_column/viz.py
index b30e66c24b..5da129e6a3 100644
--- a/polaris/tasks/ocean/single_column/viz.py
+++ b/polaris/tasks/ocean/single_column/viz.py
@@ -13,7 +13,11 @@ class Viz(OceanIOStep):
     """
 
     def __init__(
-        self, component, indir, ideal_age=False, comparison_path=None
+        self,
+        component,
+        indir,
+        ideal_age=False,
+        comparisons=None,
     ):
         """
         Create the step
@@ -32,16 +36,17 @@ def __init__(
         """
         super().__init__(component=component, name='viz', indir=indir)
         self.ideal_age = ideal_age
-        self.comparison_path = comparison_path
+        self.comparisons = comparisons if comparisons else dict()
         self.add_input_file(
             filename='initial_state.nc', target='../init/initial_state.nc'
         )
         self.add_input_file(
             filename='output.nc', target='../forward/output.nc'
         )
-        if comparison_path is not None:
+        for comparison_name, comparison_path in self.comparisons.items():
             self.add_input_file(
-                filename='comparison.nc', target=f'{comparison_path}/output.nc'
+                filename=f'{comparison_name}.nc',
+                target=f'{comparison_path}/output.nc',
             )
 
     def run(self):
@@ -54,18 +59,15 @@ def run(self):
         ds_init = self.open_model_dataset('initial_state.nc')
         ds_init = ds_init.isel(Time=0)
 
-        ds = self.open_model_dataset('output.nc')
+        ds = self.open_model_dataset('output.nc', decode_times=False)
         t_arr = get_days_since_start(ds)
         t_index = np.argmin(np.abs(t_arr - 1.0))  # index nearest 1 day
         t_days = float(t_arr[t_index])
         ds_final = ds.isel(Time=t_index)
 
-        if self.comparison_path is not None:
-            ds_comp = self.open_model_dataset('comparison.nc')
-            ds_comp = ds_comp.isel(Time=t_index)
-
         # Plot temperature and salinity profiles
         title = f'final time = {t_days:2.1g} days'
+        print(f't_index = {t_index}, t_days = {t_days}')
         fields = {'temperature': 'degC', 'salinity': 'PSU'}
         if ideal_age:
             # Include age tracer
@@ -82,8 +84,6 @@ def run(self):
             var_init = ds_init[field_name].mean(dim='nCells')
             var_final = ds_final[field_name].mean(dim='nCells')
             print('Size of variables to plot')
-            print(t_arr)
-            print(f't_index = {t_index}')
             print(
                 f'Change of {field_name} at the surface: '
                 f'{var_final.values[0] - var_init.values[0]}'
@@ -93,16 +93,25 @@ def run(self):
                 f'{var_final.values[-1] - var_init.values[-1]}'
             )
 
-            if self.comparison_path is not None:
-                var_comp = ds_comp[field_name].mean(dim='nCells')
-                if field_name not in ds_final.keys():
-                    raise ValueError(f'{field_name} not present in output.nc')
             plt.figure(figsize=(3, 5))
             ax = plt.subplot(111)
             ax.plot(var_init, z_mid_init, '--k', label='initial')
             ax.plot(var_final, z_mid_final, '-k', label='final')
-            if self.comparison_path is not None:
-                ax.plot(var_comp, z_mid_final, '-r', label='comparison')
+            for comparison_name, _ in self.comparisons.items():
+                ds_comp = self.open_model_dataset(
+                    f'{comparison_name}.nc', decode_times=False
+                )
+                t_arr = get_days_since_start(ds_comp)
+                t_index = np.argmin(np.abs(t_arr - 1.0))  # index nearest 1 day
+                t_days = float(t_arr[t_index])
+                print(f't_index = {t_index}, t_days = {t_days}')
+                ds_comp = ds_comp.isel(Time=t_index)
+                if field_name not in ds_comp.keys():
+                    raise ValueError(
+                        f'{field_name} not present in {comparison_name}.nc'
+                    )
+                var_comp = ds_comp[field_name].mean(dim='nCells')
+                ax.plot(var_comp, z_mid_final, '-r', label=comparison_name)
             ax.set_xlabel(f'{field_name} ({field_units})')
             ax.set_ylabel('z (m)')
             # ax.legend()
diff --git a/polaris/tasks/ocean/single_column/cvmix/__init__.py b/polaris/tasks/ocean/single_column/vmix/__init__.py
similarity index 59%
rename from polaris/tasks/ocean/single_column/cvmix/__init__.py
rename to polaris/tasks/ocean/single_column/vmix/__init__.py
index 3d13fbc9de..e1317af197 100644
--- a/polaris/tasks/ocean/single_column/cvmix/__init__.py
+++ b/polaris/tasks/ocean/single_column/vmix/__init__.py
@@ -3,13 +3,13 @@
 from polaris.tasks.ocean.single_column.viz import Viz
 
 
-class CVMix(Task):
+class VMix(Task):
     """
-    The CVMix single-column test case creates the mesh and initial condition,
+    The VMix single-column test case creates the mesh and initial condition,
     then performs a short forward run testing vertical mixing on 1 core.
     """
 
-    def __init__(self, component, config, init, indir, name='cvmix'):
+    def __init__(self, component, config, init, indir, name='vmix'):
         """
         Create the test case
         Parameters
@@ -18,10 +18,10 @@ def __init__(self, component, config, init, indir, name='cvmix'):
             The ocean component that this task belongs to
         """
         super().__init__(component=component, name=name, indir=indir)
-        config_filename = 'cvmix.cfg'
+        config_filename = 'vmix.cfg'
         self.set_shared_config(config, link=config_filename)
         self.config.add_from_package(
-            'polaris.tasks.ocean.single_column.cvmix', config_filename
+            'polaris.tasks.ocean.single_column.vmix', config_filename
         )
         self.add_step(init, symlink='init')
 
@@ -35,21 +35,36 @@ def __init__(self, component, config, init, indir, name='cvmix'):
             self.add_step(
                 Forward(
                     component=component,
-                    indir=self.subdir,
+                    indir=f'{indir}/{name}',
                     ntasks=1,
                     min_tasks=1,
                     openmp_threads=1,
                     validate_vars=validate_vars,
-                    task_name=name,
+                    task_name='vmix',
                     enable_vadv=enable_vadv,
                 )
             )
+        self.add_step(
+            Forward(
+                component=component,
+                indir=f'{indir}/{name}',
+                ntasks=1,
+                min_tasks=1,
+                openmp_threads=1,
+                validate_vars=validate_vars,
+                task_name='vmix',
+                constant_diff=True,
+            )
+        )
 
         self.add_step(
             Viz(
                 component=component,
-                indir=self.subdir,
-                comparison_path='../forward_no_vadv',
+                indir=f'{indir}/{name}',
+                comparisons={
+                    'no_vadv': '../forward_no_vadv',
+                    'constant': '../forward_constant',
+                },
             ),
             run_by_default=False,
         )
diff --git a/polaris/tasks/ocean/single_column/cvmix/forward.yaml b/polaris/tasks/ocean/single_column/vmix/forward.yaml
similarity index 91%
rename from polaris/tasks/ocean/single_column/cvmix/forward.yaml
rename to polaris/tasks/ocean/single_column/vmix/forward.yaml
index f5bddb4506..7002e64b06 100644
--- a/polaris/tasks/ocean/single_column/cvmix/forward.yaml
+++ b/polaris/tasks/ocean/single_column/vmix/forward.yaml
@@ -3,9 +3,6 @@ ocean:
     config_run_duration: 0010_00:00:00
   hmix_del4:
     config_use_mom_del4: false
-  cvmix:
-    config_use_cvmix_convection: false
-    config_use_cvmix_shear: false
   eos:
     config_eos_type: linear
   eos_linear:
@@ -38,7 +35,7 @@ Omega:
     PresForceTendencyEnable: false
     PresGradForceTendencyEnable: false
     GeoptGradTendencyEnable: false
-    WindForcingTendencyEnable: true
+    WindForcingTendencyEnable: false
     BottomDragTendencyEnable: false
     TracerHorzAdvTendencyEnable: false
     TracerDiffTendencyEnable: false
diff --git a/polaris/tasks/ocean/single_column/cvmix/cvmix.cfg b/polaris/tasks/ocean/single_column/vmix/vmix.cfg
similarity index 100%
rename from polaris/tasks/ocean/single_column/cvmix/cvmix.cfg
rename to polaris/tasks/ocean/single_column/vmix/vmix.cfg

From 4a7083cbbd6441c90304fc5b74b6bd3c8f382921 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Mon, 12 Jan 2026 14:03:14 -0600
Subject: [PATCH 21/47] Fixup no vertical advection config options

---
 polaris/tasks/ocean/single_column/forward.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/polaris/tasks/ocean/single_column/forward.py b/polaris/tasks/ocean/single_column/forward.py
index 0ecc92bb07..083b320651 100644
--- a/polaris/tasks/ocean/single_column/forward.py
+++ b/polaris/tasks/ocean/single_column/forward.py
@@ -125,6 +125,7 @@ def dynamic_model_config(self, at_setup):
             self.add_model_config_options(
                 options={
                     'config_vert_coord_movement': 'impermeable_interfaces',
+                    'config_disable_thick_vadv': True,
                     'config_disable_vel_vadv': True,
                     'config_disable_tr_adv': True,
                 },

From 3fef2860107454b11eb63e13ceddbd64996cf6ff Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Sun, 11 Jan 2026 15:19:56 -0600
Subject: [PATCH 22/47] WIP fixup yaml

---
 polaris/tasks/ocean/single_column/forward.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/forward.yaml b/polaris/tasks/ocean/single_column/forward.yaml
index 8161594588..9a3eb770a2 100644
--- a/polaris/tasks/ocean/single_column/forward.yaml
+++ b/polaris/tasks/ocean/single_column/forward.yaml
@@ -2,9 +2,9 @@ ocean:
   time_management:
     config_stop_time: none
   time_integration:
-    config_dt: 00:10:00
+    config_dt: 0000_00:10:00
   forcing:
-    config_use_bulk_wind_stress: true
+    config_use_bulk_wind_stress: false
 
 mpas-ocean:
   run_modes:

From 9e132de37805cce1f2d548d8e9c89675b59c56b8 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Sun, 11 Jan 2026 18:13:35 -0600
Subject: [PATCH 23/47] Default duration of 1 day

---
 polaris/tasks/ocean/single_column/vmix/forward.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/polaris/tasks/ocean/single_column/vmix/forward.yaml b/polaris/tasks/ocean/single_column/vmix/forward.yaml
index 7002e64b06..0336232ebe 100644
--- a/polaris/tasks/ocean/single_column/vmix/forward.yaml
+++ b/polaris/tasks/ocean/single_column/vmix/forward.yaml
@@ -1,6 +1,6 @@
 ocean:
   time_management:
-    config_run_duration: 0010_00:00:00
+    config_run_duration: 0001_00:00:00
   hmix_del4:
     config_use_mom_del4: false
   eos:

From 5212ab5cdde35372ae6621c22a1038775db3c8f9 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Sun, 11 Jan 2026 20:02:59 -0600
Subject: [PATCH 24/47] WIP try different unstable stratification profiles

---
 .../ocean/single_column/unstable_stratification.cfg      | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/unstable_stratification.cfg b/polaris/tasks/ocean/single_column/unstable_stratification.cfg
index 0a3102f8b4..6221f1f66a 100644
--- a/polaris/tasks/ocean/single_column/unstable_stratification.cfg
+++ b/polaris/tasks/ocean/single_column/unstable_stratification.cfg
@@ -2,8 +2,13 @@
 # config options for single column testcases
 [single_column]
 
-# Temperature gradient below the mixed layer
-temperature_gradient_interior = -0.01
+temperature_difference_across_mixed_layer = -1.0
+
+# Salinity gradient below the mixed layer
+salinity_gradient_interior = 0.01
+
+# Depth of the temperature mixed layer
+mixed_layer_depth_salinity =  25.0
 
 # Depth of the temperature mixed layer
 mixed_layer_depth_temperature =  25.0

From 420043e038082bfbf8638192c67e652ed71e935f Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Mon, 12 Jan 2026 14:02:20 -0600
Subject: [PATCH 25/47] Use PP scheme for shear mixing

---
 polaris/tasks/ocean/single_column/vmix/forward.yaml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/vmix/forward.yaml b/polaris/tasks/ocean/single_column/vmix/forward.yaml
index 0336232ebe..4ccd814ce0 100644
--- a/polaris/tasks/ocean/single_column/vmix/forward.yaml
+++ b/polaris/tasks/ocean/single_column/vmix/forward.yaml
@@ -16,10 +16,8 @@ mpas-ocean:
     config_use_activeTracers_surface_restoring: true
     config_use_activeTracers_interior_restoring: true
   cvmix:
-    config_cvmix_shear_mixing_scheme: KPP
-    config_use_cvmix_kpp: true
-    config_cvmix_kpp_matching: MatchBoth
-    config_cvmix_kpp_interpolationOMLType: cubic
+    config_cvmix_shear_mixing_scheme: PP
+    config_use_cvmix_kpp: false
   streams:
     KPP_testing: {}
 

From 5ae958255854498fd1e8ba6512caa711862e1af7 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Tue, 13 Jan 2026 09:42:28 -0600
Subject: [PATCH 26/47] Output zMid instead of computing it from layerThickness

---
 polaris/ocean/model/mpaso_to_omega.yaml        | 3 +++
 polaris/tasks/ocean/single_column/forward.yaml | 1 +
 polaris/tasks/ocean/single_column/viz.py       | 5 ++---
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/polaris/ocean/model/mpaso_to_omega.yaml b/polaris/ocean/model/mpaso_to_omega.yaml
index 24efc61c90..9c7ac493a8 100644
--- a/polaris/ocean/model/mpaso_to_omega.yaml
+++ b/polaris/ocean/model/mpaso_to_omega.yaml
@@ -22,6 +22,9 @@ variables:
   cellsOnVertex: CellsOnVertex
   edgesOnVertex: EdgesOnVertex
 
+  # vertical
+  zMid: ZMid
+
   # tracers
   temperature: Temperature
   salinity: Salinity
diff --git a/polaris/tasks/ocean/single_column/forward.yaml b/polaris/tasks/ocean/single_column/forward.yaml
index 9a3eb770a2..71c8296f0f 100644
--- a/polaris/tasks/ocean/single_column/forward.yaml
+++ b/polaris/tasks/ocean/single_column/forward.yaml
@@ -91,6 +91,7 @@ Omega:
       Contents:
       - AuxiliaryState
       - State
+      - ZMid
       - Tracers
       - SshCell
     RestartRead:
diff --git a/polaris/tasks/ocean/single_column/viz.py b/polaris/tasks/ocean/single_column/viz.py
index 5da129e6a3..4a934b9b6e 100644
--- a/polaris/tasks/ocean/single_column/viz.py
+++ b/polaris/tasks/ocean/single_column/viz.py
@@ -3,7 +3,6 @@
 
 from polaris.ocean.model import OceanIOStep
 from polaris.ocean.time import get_days_since_start
-from polaris.ocean.vertical.diagnostics import depth_from_thickness
 from polaris.viz import use_mplstyle
 
 
@@ -72,8 +71,8 @@ def run(self):
         if ideal_age:
             # Include age tracer
             fields['iAge'] = 'seconds'
-        z_mid_init = depth_from_thickness(ds_init).mean(dim='nCells')
-        z_mid_final = depth_from_thickness(ds_final).mean(dim='nCells')
+        z_mid_init = ds['zMid'].isel(Time=0).mean(dim='nCells')
+        z_mid_final = ds_final['zMid'].mean(dim='nCells')
         for field_name, field_units in fields.items():
             if field_name not in ds_init.keys():
                 raise ValueError(

From de0ce29aaffafa3d40607dd40022abc7f726a4d1 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Tue, 13 Jan 2026 17:17:19 -0600
Subject: [PATCH 27/47] Provide ekman forward step path to analysis step

---
 .../ocean/single_column/ekman/__init__.py     | 24 +++++++++++--------
 .../ocean/single_column/ekman/analysis.py     | 13 +++++++---
 2 files changed, 24 insertions(+), 13 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/ekman/__init__.py b/polaris/tasks/ocean/single_column/ekman/__init__.py
index 17fbf32ad8..7c4e704540 100644
--- a/polaris/tasks/ocean/single_column/ekman/__init__.py
+++ b/polaris/tasks/ocean/single_column/ekman/__init__.py
@@ -40,20 +40,24 @@ def __init__(self, component, config, init, indir):
             'layerThickness',
             'normalVelocity',
         ]
+        forward_step = Forward(
+            component=component,
+            indir=self.subdir,
+            ntasks=1,
+            min_tasks=1,
+            openmp_threads=1,
+            validate_vars=validate_vars,
+            task_name=name,
+            constant_diff=True,
+        )
+        self.add_step(forward_step)
+
         self.add_step(
-            Forward(
-                component=component,
-                indir=self.subdir,
-                ntasks=1,
-                min_tasks=1,
-                openmp_threads=1,
-                validate_vars=validate_vars,
-                task_name=name,
+            Analysis(
+                component=component, indir=self.subdir, forward=forward_step
             )
         )
 
-        self.add_step(Analysis(component=component, indir=self.subdir))
-
         self.add_step(
             Viz(component=component, indir=self.subdir),
             run_by_default=False,
diff --git a/polaris/tasks/ocean/single_column/ekman/analysis.py b/polaris/tasks/ocean/single_column/ekman/analysis.py
index 299d6ed24e..93498bc4cb 100644
--- a/polaris/tasks/ocean/single_column/ekman/analysis.py
+++ b/polaris/tasks/ocean/single_column/ekman/analysis.py
@@ -14,7 +14,7 @@ class Analysis(Step):
     A step for comparing the velocity profile to an analytic solution
     """
 
-    def __init__(self, component, indir):
+    def __init__(self, component, indir, forward):
         """
         Create the step
 
@@ -27,13 +27,20 @@ def __init__(self, component, indir):
             The subdirectory that the task belongs to, that this step will
             go into a subdirectory of
 
+        forward : polaris.Step
+            The forward step for this test case
         """
         super().__init__(component=component, name='analysis', indir=indir)
+        self.forward = forward
+
+    def setup(self):
         self.add_input_file(
-            filename='init.nc', target='../forward/initial_state.nc'
+            filename='init.nc',
+            target=f'{self.base_work_dir}/{self.forward.path}/init.nc',
         )
         self.add_input_file(
-            filename='output.nc', target='../forward/output.nc'
+            filename='output.nc',
+            target=f'{self.base_work_dir}/{self.forward.path}/output.nc',
         )
 
     def run(self):

From 686e68d3bafd5f475c28f34466c2dcaf51ef83b5 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Tue, 13 Jan 2026 17:23:09 -0600
Subject: [PATCH 28/47] Provide consistent names for stream files

---
 polaris/tasks/ocean/single_column/ekman/forward.yaml | 4 ++--
 polaris/tasks/ocean/single_column/forward.py         | 8 ++++++++
 polaris/tasks/ocean/single_column/forward.yaml       | 4 ++--
 3 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/ekman/forward.yaml b/polaris/tasks/ocean/single_column/ekman/forward.yaml
index 51aadb9789..bcec302721 100644
--- a/polaris/tasks/ocean/single_column/ekman/forward.yaml
+++ b/polaris/tasks/ocean/single_column/ekman/forward.yaml
@@ -28,9 +28,9 @@ mpas-ocean:
     config_use_activeTracers_interior_restoring: false
   streams:
     mesh:
-      filename_template: initial_state.nc
+      filename_template: mesh.nc
     input:
-      filename_template: initial_state.nc
+      filename_template: init.nc
     restart: {}
     KPP_testing: {}
     mixedLayerDepthsOutput:
diff --git a/polaris/tasks/ocean/single_column/forward.py b/polaris/tasks/ocean/single_column/forward.py
index 083b320651..6431035ccc 100644
--- a/polaris/tasks/ocean/single_column/forward.py
+++ b/polaris/tasks/ocean/single_column/forward.py
@@ -80,12 +80,20 @@ def __init__(
 
         self.add_yaml_file('polaris.ocean.config', 'output.yaml')
 
+        self.add_input_file(
+            filename='mesh.nc',
+            target='../init/initial_state.nc',
+            # filename='mesh.nc', target='../init/culled_mesh.nc'
+        )
         self.add_input_file(
             filename='init.nc', target='../init/initial_state.nc'
         )
         self.add_input_file(
             filename='graph.info', target='../init/culled_graph.info'
         )
+        self.add_input_file(
+            filename='forcing.nc', target='../init/initial_state.nc'
+        )
 
         self.add_yaml_file('polaris.tasks.ocean.single_column', 'forward.yaml')
         self.add_yaml_file(
diff --git a/polaris/tasks/ocean/single_column/forward.yaml b/polaris/tasks/ocean/single_column/forward.yaml
index 71c8296f0f..4cda771245 100644
--- a/polaris/tasks/ocean/single_column/forward.yaml
+++ b/polaris/tasks/ocean/single_column/forward.yaml
@@ -4,7 +4,7 @@ ocean:
   time_integration:
     config_dt: 0000_00:10:00
   forcing:
-    config_use_bulk_wind_stress: false
+    config_use_bulk_wind_stress: true
 
 mpas-ocean:
   run_modes:
@@ -13,7 +13,7 @@ mpas-ocean:
     config_btr_dt: 0000_00:00:30
   streams:
     mesh:
-      filename_template: init.nc
+      filename_template: mesh.nc
     input:
       filename_template: init.nc
     restart: {}

From a603d6943a4afedbb0e3d438eb8e9d17ecc856d0 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Wed, 14 Jan 2026 13:27:01 -0600
Subject: [PATCH 29/47] Use viz argument to designate all output files

---
 .../ocean/single_column/ekman/__init__.py     |  6 +-
 .../tasks/ocean/single_column/ekman/ekman.cfg |  5 ++
 polaris/tasks/ocean/single_column/viz.py      | 89 +++++++++----------
 .../ocean/single_column/vmix/__init__.py      |  1 +
 .../ocean/single_column/vmix/forward.yaml     |  6 +-
 .../tasks/ocean/single_column/vmix/vmix.cfg   |  5 ++
 6 files changed, 63 insertions(+), 49 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/ekman/__init__.py b/polaris/tasks/ocean/single_column/ekman/__init__.py
index 7c4e704540..85c43af9ee 100644
--- a/polaris/tasks/ocean/single_column/ekman/__init__.py
+++ b/polaris/tasks/ocean/single_column/ekman/__init__.py
@@ -59,6 +59,10 @@ def __init__(self, component, config, init, indir):
         )
 
         self.add_step(
-            Viz(component=component, indir=self.subdir),
+            Viz(
+                component=component,
+                indir=self.subdir,
+                comparisons={'forward': '../forward_constant'},
+            ),
             run_by_default=False,
         )
diff --git a/polaris/tasks/ocean/single_column/ekman/ekman.cfg b/polaris/tasks/ocean/single_column/ekman/ekman.cfg
index 8720d2bb08..ac837d8541 100644
--- a/polaris/tasks/ocean/single_column/ekman/ekman.cfg
+++ b/polaris/tasks/ocean/single_column/ekman/ekman.cfg
@@ -3,6 +3,11 @@
 # Bottom depth
 bottom_depth = 100.
 
+[single_column]
+
+# Run duration in days
+run_duration = 5.
+
 [single_column_ekman]
 
 # Constant vertical eddy diffusivity
diff --git a/polaris/tasks/ocean/single_column/viz.py b/polaris/tasks/ocean/single_column/viz.py
index 4a934b9b6e..5de0fdbfd4 100644
--- a/polaris/tasks/ocean/single_column/viz.py
+++ b/polaris/tasks/ocean/single_column/viz.py
@@ -35,12 +35,13 @@ def __init__(
         """
         super().__init__(component=component, name='viz', indir=indir)
         self.ideal_age = ideal_age
-        self.comparisons = comparisons if comparisons else dict()
-        self.add_input_file(
-            filename='initial_state.nc', target='../init/initial_state.nc'
+        self.comparisons = (
+            dict(comparisons)
+            if comparisons
+            else {'forward': '../forward/output.nc'}
         )
         self.add_input_file(
-            filename='output.nc', target='../forward/output.nc'
+            filename='initial_state.nc', target='../init/initial_state.nc'
         )
         for comparison_name, comparison_path in self.comparisons.items():
             self.add_input_file(
@@ -57,51 +58,39 @@ def run(self):
 
         ds_init = self.open_model_dataset('initial_state.nc')
         ds_init = ds_init.isel(Time=0)
+        if 'zMid' in ds_init:
+            z_mid_init = ds_init['zMid'].mean(dim='nCells')
+        else:
+            comparison_name = next(iter(self.comparisons))
+            ds_comp = self.open_model_dataset(
+                f'{comparison_name}.nc', decode_times=False
+            )
+            z_mid_init = ds_comp['zMid'].isel(Time=0).mean(dim='nCells')
 
-        ds = self.open_model_dataset('output.nc', decode_times=False)
-        t_arr = get_days_since_start(ds)
-        t_index = np.argmin(np.abs(t_arr - 1.0))  # index nearest 1 day
-        t_days = float(t_arr[t_index])
-        ds_final = ds.isel(Time=t_index)
+        section = self.config['single_column']
+        t_target = section.getfloat('run_duration')
 
         # Plot temperature and salinity profiles
-        title = f'final time = {t_days:2.1g} days'
-        print(f't_index = {t_index}, t_days = {t_days}')
         fields = {'temperature': 'degC', 'salinity': 'PSU'}
         if ideal_age:
             # Include age tracer
             fields['iAge'] = 'seconds'
-        z_mid_init = ds['zMid'].isel(Time=0).mean(dim='nCells')
-        z_mid_final = ds_final['zMid'].mean(dim='nCells')
         for field_name, field_units in fields.items():
             if field_name not in ds_init.keys():
                 raise ValueError(
                     f'{field_name} not present in initial_state.nc'
                 )
-            if field_name not in ds_final.keys():
-                raise ValueError(f'{field_name} not present in output.nc')
             var_init = ds_init[field_name].mean(dim='nCells')
-            var_final = ds_final[field_name].mean(dim='nCells')
-            print('Size of variables to plot')
-            print(
-                f'Change of {field_name} at the surface: '
-                f'{var_final.values[0] - var_init.values[0]}'
-            )
-            print(
-                f'Change of {field_name} at the bottom: '
-                f'{var_final.values[-1] - var_init.values[-1]}'
-            )
 
             plt.figure(figsize=(3, 5))
             ax = plt.subplot(111)
-            ax.plot(var_init, z_mid_init, '--k', label='initial')
-            ax.plot(var_final, z_mid_final, '-k', label='final')
             for comparison_name, _ in self.comparisons.items():
                 ds_comp = self.open_model_dataset(
                     f'{comparison_name}.nc', decode_times=False
                 )
+                ax.plot(var_init, z_mid_init, '--k', label='initial')
                 t_arr = get_days_since_start(ds_comp)
-                t_index = np.argmin(np.abs(t_arr - 1.0))  # index nearest 1 day
+                t_index = np.argmin(np.abs(t_arr - t_target))
                 t_days = float(t_arr[t_index])
                 print(f't_index = {t_index}, t_days = {t_days}')
                 ds_comp = ds_comp.isel(Time=t_index)
@@ -110,29 +99,39 @@ def run(self):
                         f'{field_name} not present in {comparison_name}.nc'
                     )
                 var_comp = ds_comp[field_name].mean(dim='nCells')
+                z_mid_final = ds_comp['zMid'].mean(dim='nCells')
                 ax.plot(var_comp, z_mid_final, '-r', label=comparison_name)
+            title = f'final time = {t_days:2.1g} days'
             ax.set_xlabel(f'{field_name} ({field_units})')
             ax.set_ylabel('z (m)')
-            # ax.legend()
+            ax.legend(loc='lower right')
             plt.title(title)
             plt.tight_layout(pad=0.5)
             plt.savefig(f'{field_name}.png')
             plt.close()
 
         # Plot velocity profiles
-        if 'velocityZonal' and 'velocityMeridional' in ds.keys():
-            u = ds['velocityZonal'].mean(dim='nCells')
-            v = ds['velocityMeridional'].mean(dim='nCells')
-            u_final = u.isel(Time=t_index)
-            v_final = v.isel(Time=t_index)
-            plt.figure(figsize=(3, 5))
-            ax = plt.subplot(111)
-            ax.plot(u_final, z_mid_final, '-k', label='u')
-            ax.plot(v_final, z_mid_final, '-b', label='v')
-            ax.set_xlabel('Velocity (m/s)')
-            ax.set_ylabel('z (m)')
-            ax.legend()
-            plt.title(title)
-            plt.tight_layout(pad=0.5)
-            plt.savefig('velocity.png')
-            plt.close()
+        plt.figure(figsize=(3, 5))
+        ax = plt.subplot(111)
+        for comparison_name, _ in self.comparisons.items():
+            ds_comp = self.open_model_dataset(
+                f'{comparison_name}.nc', decode_times=False
+            )
+            t_arr = get_days_since_start(ds_comp)
+            t_index = np.argmin(np.abs(t_arr - t_target))
+            t_days = float(t_arr[t_index])
+            print(f't_index = {t_index}, t_days = {t_days}')
+            ds_comp = ds_comp.isel(Time=t_index)
+            z_mid_final = ds_comp['zMid'].mean(dim='nCells')
+            if 'velocityZonal' and 'velocityMeridional' in ds_comp.keys():
+                u_final = ds_comp['velocityZonal'].mean(dim='nCells')
+                v_final = ds_comp['velocityMeridional'].mean(dim='nCells')
+                ax.plot(u_final, z_mid_final, '-k', label='u')
+                ax.plot(v_final, z_mid_final, '-b', label='v')
+        ax.set_xlabel('Velocity (m/s)')
+        ax.set_ylabel('z (m)')
+        ax.legend()
+        plt.title(title)
+        plt.tight_layout(pad=0.5)
+        plt.savefig('velocity.png')
+        plt.close()
diff --git a/polaris/tasks/ocean/single_column/vmix/__init__.py b/polaris/tasks/ocean/single_column/vmix/__init__.py
index e1317af197..11411bd9e9 100644
--- a/polaris/tasks/ocean/single_column/vmix/__init__.py
+++ b/polaris/tasks/ocean/single_column/vmix/__init__.py
@@ -62,6 +62,7 @@ def __init__(self, component, config, init, indir, name='vmix'):
                 component=component,
                 indir=f'{indir}/{name}',
                 comparisons={
+                    'control': '../forward',
                     'no_vadv': '../forward_no_vadv',
                     'constant': '../forward_constant',
                 },
diff --git a/polaris/tasks/ocean/single_column/vmix/forward.yaml b/polaris/tasks/ocean/single_column/vmix/forward.yaml
index 4ccd814ce0..afd70c527d 100644
--- a/polaris/tasks/ocean/single_column/vmix/forward.yaml
+++ b/polaris/tasks/ocean/single_column/vmix/forward.yaml
@@ -1,6 +1,6 @@
 ocean:
   time_management:
-    config_run_duration: 0001_00:00:00
+    config_run_duration: 0010_00:00:00
   hmix_del4:
     config_use_mom_del4: false
   eos:
@@ -16,8 +16,8 @@ mpas-ocean:
     config_use_activeTracers_surface_restoring: true
     config_use_activeTracers_interior_restoring: true
   cvmix:
-    config_cvmix_shear_mixing_scheme: PP
     config_use_cvmix_kpp: false
+    config_cvmix_shear_mixing_scheme: PP
   streams:
     KPP_testing: {}
 
@@ -33,7 +33,7 @@ Omega:
     PresForceTendencyEnable: false
     PresGradForceTendencyEnable: false
     GeoptGradTendencyEnable: false
-    WindForcingTendencyEnable: false
+    WindForcingTendencyEnable: true
     BottomDragTendencyEnable: false
     TracerHorzAdvTendencyEnable: false
     TracerDiffTendencyEnable: false
diff --git a/polaris/tasks/ocean/single_column/vmix/vmix.cfg b/polaris/tasks/ocean/single_column/vmix/vmix.cfg
index 7394d9c777..937e6966fd 100644
--- a/polaris/tasks/ocean/single_column/vmix/vmix.cfg
+++ b/polaris/tasks/ocean/single_column/vmix/vmix.cfg
@@ -1,3 +1,8 @@
 # stable_stratification.cfg
 # evap.cfg
 # wind.cfg
+
+[single_column]
+
+# Run duration in days
+run_duration = 10.

From e086d2565188bf9989d0f9da07ce48b52cfe5988 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Wed, 14 Jan 2026 13:30:55 -0600
Subject: [PATCH 30/47] WIP troubleshoot vmix config options

---
 polaris/tasks/ocean/single_column/vmix/forward.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/vmix/forward.yaml b/polaris/tasks/ocean/single_column/vmix/forward.yaml
index afd70c527d..7e63a586f9 100644
--- a/polaris/tasks/ocean/single_column/vmix/forward.yaml
+++ b/polaris/tasks/ocean/single_column/vmix/forward.yaml
@@ -13,10 +13,11 @@ mpas-ocean:
     config_use_frazil_ice_formation: true
   tracer_forcing_activeTracers:
     config_use_activeTracers_surface_bulk_forcing: true
-    config_use_activeTracers_surface_restoring: true
-    config_use_activeTracers_interior_restoring: true
+    config_use_activeTracers_surface_restoring: false
+    config_use_activeTracers_interior_restoring: false
   cvmix:
     config_use_cvmix_kpp: false
+    config_cvmix_background_viscosity: 1e-2
     config_cvmix_shear_mixing_scheme: PP
   streams:
     KPP_testing: {}

From 5bf05ee3001fed2f267f80e9b9b6fea053f99958 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Wed, 14 Jan 2026 13:31:13 -0600
Subject: [PATCH 31/47] WIP troubleshoot vmix stable config options

---
 .../ocean/single_column/stable_stratification.cfg | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/stable_stratification.cfg b/polaris/tasks/ocean/single_column/stable_stratification.cfg
index 9f749bd918..9e2fe89b92 100644
--- a/polaris/tasks/ocean/single_column/stable_stratification.cfg
+++ b/polaris/tasks/ocean/single_column/stable_stratification.cfg
@@ -2,11 +2,18 @@
 # config options for single column testcases
 [single_column]
 
-# Temperature gradient below the mixed layer
-temperature_gradient_interior = 0.01
+# temperature gradient below the mixed layer
+temperature_gradient_interior = 0.005
 
 # Depth of the temperature mixed layer
-mixed_layer_depth_temperature =  25.0
+mixed_layer_depth_temperature =  0.0
 
 # The salinity below the mixed layer
-salinity_difference_across_mixed_layer = 1.0
+salinity_difference_across_mixed_layer = 0.0
+
+# Depth of the temperature mixed layer
+mixed_layer_depth_salinity =  0.0
+
+# Temperature gradient below the mixed layer
+#salinity_gradient_interior = -0.001
+salinity_gradient_interior = 0.0

From 1782615949761e72a3956c9cb72a76986d50fb0c Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Fri, 16 Jan 2026 13:54:43 -0600
Subject: [PATCH 32/47] Use mid-lat settings for stable stratification

---
 polaris/tasks/ocean/single_column/stable_stratification.cfg | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/stable_stratification.cfg b/polaris/tasks/ocean/single_column/stable_stratification.cfg
index 9e2fe89b92..3c965e67b7 100644
--- a/polaris/tasks/ocean/single_column/stable_stratification.cfg
+++ b/polaris/tasks/ocean/single_column/stable_stratification.cfg
@@ -3,7 +3,7 @@
 [single_column]
 
 # temperature gradient below the mixed layer
-temperature_gradient_interior = 0.005
+temperature_gradient_interior = 0.1
 
 # Depth of the temperature mixed layer
 mixed_layer_depth_temperature =  0.0
@@ -15,5 +15,4 @@ salinity_difference_across_mixed_layer = 0.0
 mixed_layer_depth_salinity =  0.0
 
 # Temperature gradient below the mixed layer
-#salinity_gradient_interior = -0.001
 salinity_gradient_interior = 0.0

From 953fc62da4fa750eaa9cda01937606ca0a521cb9 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Sun, 18 Jan 2026 17:17:29 -0600
Subject: [PATCH 33/47] WIP change unstable stratification settings

---
 .../tasks/ocean/single_column/unstable_stratification.cfg  | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/unstable_stratification.cfg b/polaris/tasks/ocean/single_column/unstable_stratification.cfg
index 6221f1f66a..d3831faafb 100644
--- a/polaris/tasks/ocean/single_column/unstable_stratification.cfg
+++ b/polaris/tasks/ocean/single_column/unstable_stratification.cfg
@@ -2,10 +2,13 @@
 # config options for single column testcases
 [single_column]
 
-temperature_difference_across_mixed_layer = -1.0
+# Use this to test temperature and salinity
+#temperature_difference_across_mixed_layer = 1.0
+#Use this to test salinity only
+temperature_difference_across_mixed_layer = 0.0
 
 # Salinity gradient below the mixed layer
-salinity_gradient_interior = 0.01
+salinity_gradient_interior = -0.01
 
 # Depth of the temperature mixed layer
 mixed_layer_depth_salinity =  25.0

From a72f422713c0cf7456ff916d7b6c4ce8c824745f Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Sun, 18 Jan 2026 17:24:55 -0600
Subject: [PATCH 34/47] Make comparison curves more differentiable

---
 polaris/tasks/ocean/single_column/viz.py | 45 +++++++++++++++++-------
 1 file changed, 33 insertions(+), 12 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/viz.py b/polaris/tasks/ocean/single_column/viz.py
index 5de0fdbfd4..4709d1af0a 100644
--- a/polaris/tasks/ocean/single_column/viz.py
+++ b/polaris/tasks/ocean/single_column/viz.py
@@ -82,17 +82,18 @@ def run(self):
                 )
             var_init = ds_init[field_name].mean(dim='nCells')
 
-            plt.figure(figsize=(3, 5))
-            ax = plt.subplot(111)
-            for comparison_name, _ in self.comparisons.items():
+            fig = plt.figure(figsize=(3, 5))
+            colors = ['b', 'r', 'darkgreen']
+            plt.plot(var_init, z_mid_init, '--k', label='initial')
+            for comparison_name, color in zip(
+                self.comparisons.keys(), colors, strict=False
+            ):
                 ds_comp = self.open_model_dataset(
                     f'{comparison_name}.nc', decode_times=False
                 )
-                ax.plot(var_init, z_mid_init, '--k', label='initial')
                 t_arr = get_days_since_start(ds_comp)
                 t_index = np.argmin(np.abs(t_arr - t_target))
                 t_days = float(t_arr[t_index])
-                print(f't_index = {t_index}, t_days = {t_days}')
                 ds_comp = ds_comp.isel(Time=t_index)
                 if field_name not in ds_comp.keys():
                     raise ValueError(
@@ -100,11 +101,17 @@ def run(self):
                     )
                 var_comp = ds_comp[field_name].mean(dim='nCells')
                 z_mid_final = ds_comp['zMid'].mean(dim='nCells')
-                ax.plot(var_comp, z_mid_final, '-r', label=comparison_name)
+                plt.plot(
+                    var_comp,
+                    z_mid_final,
+                    '-',
+                    color=color,
+                    label=comparison_name,
+                )
             title = f'final time = {t_days:2.1g} days'
-            ax.set_xlabel(f'{field_name} ({field_units})')
-            ax.set_ylabel('z (m)')
-            ax.legend(loc='lower right')
+            plt.xlabel(f'{field_name} ({field_units})')
+            plt.ylabel('z (m)')
+            fig.legend(loc='outside lower right')
             plt.title(title)
             plt.tight_layout(pad=0.5)
             plt.savefig(f'{field_name}.png')
@@ -113,7 +120,9 @@ def run(self):
         # Plot velocity profiles
         plt.figure(figsize=(3, 5))
         ax = plt.subplot(111)
-        for comparison_name, _ in self.comparisons.items():
+        for comparison_name, color in zip(
+            self.comparisons.keys(), colors, strict=False
+        ):
             ds_comp = self.open_model_dataset(
                 f'{comparison_name}.nc', decode_times=False
             )
@@ -126,8 +135,20 @@ def run(self):
             if 'velocityZonal' and 'velocityMeridional' in ds_comp.keys():
                 u_final = ds_comp['velocityZonal'].mean(dim='nCells')
                 v_final = ds_comp['velocityMeridional'].mean(dim='nCells')
-                ax.plot(u_final, z_mid_final, '-k', label='u')
-                ax.plot(v_final, z_mid_final, '-b', label='v')
+                ax.plot(
+                    u_final,
+                    z_mid_final,
+                    '-',
+                    color=color,
+                    label=f'u {comparison_name}',
+                )
+                ax.plot(
+                    v_final,
+                    z_mid_final,
+                    '--',
+                    color=color,
+                    label=f'v {comparison_name}',
+                )
         ax.set_xlabel('Velocity (m/s)')
         ax.set_ylabel('z (m)')
         ax.legend()

From 95591b7e6f043787b55cc0aef1ba8d9cf7a81695 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Wed, 21 Jan 2026 16:46:00 -0600
Subject: [PATCH 35/47] Update namelist options

---
 polaris/tasks/ocean/single_column/forward.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/polaris/tasks/ocean/single_column/forward.yaml b/polaris/tasks/ocean/single_column/forward.yaml
index 4cda771245..1a995a5fc0 100644
--- a/polaris/tasks/ocean/single_column/forward.yaml
+++ b/polaris/tasks/ocean/single_column/forward.yaml
@@ -11,6 +11,9 @@ mpas-ocean:
     config_ocean_run_mode: forward
   split_explicit_ts:
     config_btr_dt: 0000_00:00:30
+  forcing:
+    config_bulk_wind_stress_interp_isotropic: true
+    config_use_bulk_thickness_flux: true
   streams:
     mesh:
       filename_template: mesh.nc

From e0a99e3fe2fdaf26bc8d6e1bca3686a04e822004 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Wed, 21 Jan 2026 16:46:32 -0600
Subject: [PATCH 36/47] Use no_vadv with constant diffusivity tests

---
 polaris/tasks/ocean/single_column/vmix/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/polaris/tasks/ocean/single_column/vmix/__init__.py b/polaris/tasks/ocean/single_column/vmix/__init__.py
index 11411bd9e9..a9d9479c06 100644
--- a/polaris/tasks/ocean/single_column/vmix/__init__.py
+++ b/polaris/tasks/ocean/single_column/vmix/__init__.py
@@ -54,6 +54,7 @@ def __init__(self, component, config, init, indir, name='vmix'):
                 validate_vars=validate_vars,
                 task_name='vmix',
                 constant_diff=True,
+                enable_vadv=False,
             )
         )
 
@@ -64,7 +65,7 @@ def __init__(self, component, config, init, indir, name='vmix'):
                 comparisons={
                     'control': '../forward',
                     'no_vadv': '../forward_no_vadv',
-                    'constant': '../forward_constant',
+                    'constant': '../forward_no_vadv_constant',
                 },
             ),
             run_by_default=False,

From 1ad256c612d721cc1e1786577a0c975c9f34cfd9 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Wed, 21 Jan 2026 16:53:51 -0600
Subject: [PATCH 37/47] Make step with vadv optional

---
 polaris/tasks/ocean/single_column/viz.py      |  6 +++
 .../ocean/single_column/vmix/__init__.py      | 37 ++++++++++++-------
 2 files changed, 30 insertions(+), 13 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/viz.py b/polaris/tasks/ocean/single_column/viz.py
index 4709d1af0a..784e06b7bc 100644
--- a/polaris/tasks/ocean/single_column/viz.py
+++ b/polaris/tasks/ocean/single_column/viz.py
@@ -1,3 +1,5 @@
+import os
+
 import matplotlib.pyplot as plt
 import numpy as np
 
@@ -88,6 +90,8 @@ def run(self):
             for comparison_name, color in zip(
                 self.comparisons.keys(), colors, strict=False
             ):
+                if not os.path.exists(f'{comparison_name}.nc'):
+                    continue
                 ds_comp = self.open_model_dataset(
                     f'{comparison_name}.nc', decode_times=False
                 )
@@ -123,6 +127,8 @@ def run(self):
         for comparison_name, color in zip(
             self.comparisons.keys(), colors, strict=False
         ):
+            if not os.path.exists(f'{comparison_name}.nc'):
+                continue
             ds_comp = self.open_model_dataset(
                 f'{comparison_name}.nc', decode_times=False
             )
diff --git a/polaris/tasks/ocean/single_column/vmix/__init__.py b/polaris/tasks/ocean/single_column/vmix/__init__.py
index a9d9479c06..8151e15b54 100644
--- a/polaris/tasks/ocean/single_column/vmix/__init__.py
+++ b/polaris/tasks/ocean/single_column/vmix/__init__.py
@@ -31,19 +31,31 @@ def __init__(self, component, config, init, indir, name='vmix'):
             'layerThickness',
             'normalVelocity',
         ]
-        for enable_vadv in [True, False]:
-            self.add_step(
-                Forward(
-                    component=component,
-                    indir=f'{indir}/{name}',
-                    ntasks=1,
-                    min_tasks=1,
-                    openmp_threads=1,
-                    validate_vars=validate_vars,
-                    task_name='vmix',
-                    enable_vadv=enable_vadv,
-                )
+        self.add_step(
+            Forward(
+                component=component,
+                indir=f'{indir}/{name}',
+                ntasks=1,
+                min_tasks=1,
+                openmp_threads=1,
+                validate_vars=validate_vars,
+                task_name='vmix',
+                enable_vadv=True,
+            ),
+            run_by_default=False,
+        )
+        self.add_step(
+            Forward(
+                component=component,
+                indir=f'{indir}/{name}',
+                ntasks=1,
+                min_tasks=1,
+                openmp_threads=1,
+                validate_vars=validate_vars,
+                task_name='vmix',
+                enable_vadv=False,
             )
+        )
         self.add_step(
             Forward(
                 component=component,
@@ -63,7 +75,6 @@ def __init__(self, component, config, init, indir, name='vmix'):
                 component=component,
                 indir=f'{indir}/{name}',
                 comparisons={
-                    'control': '../forward',
                     'no_vadv': '../forward_no_vadv',
                     'constant': '../forward_no_vadv_constant',
                 },

From 9d04334fabcf438299bb9430374c2fb4a8bb2de1 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Wed, 21 Jan 2026 16:54:26 -0600
Subject: [PATCH 38/47] Always run viz step

---
 polaris/tasks/ocean/single_column/vmix/__init__.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/vmix/__init__.py b/polaris/tasks/ocean/single_column/vmix/__init__.py
index 8151e15b54..86150a02e9 100644
--- a/polaris/tasks/ocean/single_column/vmix/__init__.py
+++ b/polaris/tasks/ocean/single_column/vmix/__init__.py
@@ -78,6 +78,5 @@ def __init__(self, component, config, init, indir, name='vmix'):
                     'no_vadv': '../forward_no_vadv',
                     'constant': '../forward_no_vadv_constant',
                 },
-            ),
-            run_by_default=False,
+            )
         )

From 37ced8a54f67edd1fbc40ff5bdd77a554f43cfb3 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Mon, 26 Jan 2026 17:17:44 -0600
Subject: [PATCH 39/47] use zmid utility

---
 polaris/tasks/ocean/single_column/viz.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/viz.py b/polaris/tasks/ocean/single_column/viz.py
index 784e06b7bc..271d1e93b6 100644
--- a/polaris/tasks/ocean/single_column/viz.py
+++ b/polaris/tasks/ocean/single_column/viz.py
@@ -5,6 +5,7 @@
 
 from polaris.ocean.model import OceanIOStep
 from polaris.ocean.time import get_days_since_start
+from polaris.ocean.vertical.diagnostics import depth_from_thickness
 from polaris.viz import use_mplstyle
 
 
@@ -104,11 +105,13 @@ def run(self):
                         f'{field_name} not present in {comparison_name}.nc'
                     )
                 var_comp = ds_comp[field_name].mean(dim='nCells')
-                z_mid_final = ds_comp['zMid'].mean(dim='nCells')
+                # TODO use this line when Omega zMid is correct
+                # z_mid_final = ds_comp['zMid'].mean(dim='nCells')
+                z_mid_final = depth_from_thickness(ds_comp).mean(dim='nCells')
                 plt.plot(
                     var_comp,
                     z_mid_final,
-                    '-',
+                    '.',
                     color=color,
                     label=comparison_name,
                 )

From 64a138ad0495fb269853438898abc0c47dc5b04b Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Fri, 30 Jan 2026 12:27:34 -0600
Subject: [PATCH 40/47] Support fetching time from xtime variable

---
 polaris/ocean/time.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/polaris/ocean/time.py b/polaris/ocean/time.py
index 38b61858e8..8f2bf9e5a7 100644
--- a/polaris/ocean/time.py
+++ b/polaris/ocean/time.py
@@ -1,3 +1,5 @@
+from datetime import datetime
+
 import numpy as np
 import pandas as pd
 
@@ -9,6 +11,19 @@ def get_days_since_start(ds):
     """
     if 'daysSinceStartOfSim' in ds.keys():
         t_arr = ds.daysSinceStartOfSim.values.astype(float)
+    elif 'xtime' in ds.keys():
+        timestamps = []
+        for time_str in ds.xtime.values.astype(str):
+            try:
+                timestamp = datetime.strptime(time_str, '%Y-%m-%d_%H:%M:%S.%f')
+            except ValueError:
+                timestamp = datetime.strptime(time_str, '%Y-%m-%d_%H:%M:%S')
+            timestamps.append(timestamp)
+        # Calculate seconds since the first timestamp
+        seconds_since_start = [
+            (ts - timestamps[0]).total_seconds() for ts in timestamps
+        ]
+        t_arr = np.array(seconds_since_start, dtype=float) / 86400.0
     elif 'Time' in ds.keys():
         t_vals = ds['Time'].values
         t_pd = pd.to_datetime(t_vals)

From 4922ae3f69c05bc31b7acafec2609c7b52efe355 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Fri, 30 Jan 2026 17:22:56 -0600
Subject: [PATCH 41/47] Clean-up and generalize viz step

---
 polaris/tasks/ocean/single_column/viz.py | 224 ++++++++++++++---------
 1 file changed, 135 insertions(+), 89 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/viz.py b/polaris/tasks/ocean/single_column/viz.py
index 271d1e93b6..438f55983d 100644
--- a/polaris/tasks/ocean/single_column/viz.py
+++ b/polaris/tasks/ocean/single_column/viz.py
@@ -8,6 +8,8 @@
 from polaris.ocean.vertical.diagnostics import depth_from_thickness
 from polaris.viz import use_mplstyle
 
+# TODO import rho_0 from constants
+
 
 class Viz(OceanIOStep):
     """
@@ -20,6 +22,7 @@ def __init__(
         indir,
         ideal_age=False,
         comparisons=None,
+        variables=None,
     ):
         """
         Create the step
@@ -35,14 +38,31 @@ def __init__(
 
         ideal_age : bool, optional
             Whether the initial condition should include the ideal age tracer
+
+        comparisons : dict, optional
+            A dictionary of comparison datasets to use for validation
+
+        variables : dict, optional
+            A dictionary of variables to plot along with their units
         """
         super().__init__(component=component, name='viz', indir=indir)
-        self.ideal_age = ideal_age
+        if ideal_age:
+            # Include age tracer
+            variables['iAge'] = 'seconds'
         self.comparisons = (
             dict(comparisons)
             if comparisons
             else {'forward': '../forward/output.nc'}
         )
+        self.variables = (
+            dict(variables)
+            if variables
+            else {
+                'temperature': 'degC',
+                'salinity': 'PSU',
+                'velocity': 'm s$^{-1}$',
+            }
+        )
         self.add_input_file(
             filename='initial_state.nc', target='../init/initial_state.nc'
         )
@@ -51,13 +71,16 @@ def __init__(
                 filename=f'{comparison_name}.nc',
                 target=f'{comparison_path}/output.nc',
             )
+            self.add_input_file(
+                filename=f'{comparison_name}_diags.nc',
+                target=f'{comparison_path}/output/KPP_test.0001-01-01_00.00.00.nc',
+            )
 
     def run(self):
         """
         Run this step of the test case
         """
         use_mplstyle()
-        ideal_age = self.ideal_age
 
         ds_init = self.open_model_dataset('initial_state.nc')
         ds_init = ds_init.isel(Time=0)
@@ -72,96 +95,119 @@ def run(self):
 
         section = self.config['single_column']
         t_target = section.getfloat('run_duration')
+        # t_target = 0.
 
         # Plot temperature and salinity profiles
-        fields = {'temperature': 'degC', 'salinity': 'PSU'}
-        if ideal_age:
-            # Include age tracer
-            fields['iAge'] = 'seconds'
-        for field_name, field_units in fields.items():
-            if field_name not in ds_init.keys():
-                raise ValueError(
-                    f'{field_name} not present in initial_state.nc'
-                )
-            var_init = ds_init[field_name].mean(dim='nCells')
-
+        for field_name, field_units in self.variables.items():
             fig = plt.figure(figsize=(3, 5))
             colors = ['b', 'r', 'darkgreen']
-            plt.plot(var_init, z_mid_init, '--k', label='initial')
-            for comparison_name, color in zip(
-                self.comparisons.keys(), colors, strict=False
-            ):
-                if not os.path.exists(f'{comparison_name}.nc'):
+            if field_name == 'velocity':
+                if (
+                    'velocityZonal' not in ds_comp.keys()
+                    and 'velocityMeridional' not in ds_comp.keys()
+                ):
                     continue
-                ds_comp = self.open_model_dataset(
-                    f'{comparison_name}.nc', decode_times=False
-                )
-                t_arr = get_days_since_start(ds_comp)
-                t_index = np.argmin(np.abs(t_arr - t_target))
-                t_days = float(t_arr[t_index])
-                ds_comp = ds_comp.isel(Time=t_index)
-                if field_name not in ds_comp.keys():
-                    raise ValueError(
-                        f'{field_name} not present in {comparison_name}.nc'
+                ax = plt.subplot(111)
+                for comparison_name, color in zip(
+                    self.comparisons.keys(), colors, strict=False
+                ):
+                    if not os.path.exists(f'{comparison_name}.nc'):
+                        continue
+                    ds_comp = self.open_model_dataset(
+                        f'{comparison_name}.nc', decode_times=False
                     )
-                var_comp = ds_comp[field_name].mean(dim='nCells')
-                # TODO use this line when Omega zMid is correct
-                # z_mid_final = ds_comp['zMid'].mean(dim='nCells')
-                z_mid_final = depth_from_thickness(ds_comp).mean(dim='nCells')
-                plt.plot(
-                    var_comp,
-                    z_mid_final,
-                    '.',
-                    color=color,
-                    label=comparison_name,
-                )
-            title = f'final time = {t_days:2.1g} days'
-            plt.xlabel(f'{field_name} ({field_units})')
-            plt.ylabel('z (m)')
-            fig.legend(loc='outside lower right')
-            plt.title(title)
-            plt.tight_layout(pad=0.5)
-            plt.savefig(f'{field_name}.png')
-            plt.close()
-
-        # Plot velocity profiles
-        plt.figure(figsize=(3, 5))
-        ax = plt.subplot(111)
-        for comparison_name, color in zip(
-            self.comparisons.keys(), colors, strict=False
-        ):
-            if not os.path.exists(f'{comparison_name}.nc'):
-                continue
-            ds_comp = self.open_model_dataset(
-                f'{comparison_name}.nc', decode_times=False
-            )
-            t_arr = get_days_since_start(ds_comp)
-            t_index = np.argmin(np.abs(t_arr - t_target))
-            t_days = float(t_arr[t_index])
-            print(f't_index = {t_index}, t_days = {t_days}')
-            ds_comp = ds_comp.isel(Time=t_index)
-            z_mid_final = ds_comp['zMid'].mean(dim='nCells')
-            if 'velocityZonal' and 'velocityMeridional' in ds_comp.keys():
-                u_final = ds_comp['velocityZonal'].mean(dim='nCells')
-                v_final = ds_comp['velocityMeridional'].mean(dim='nCells')
-                ax.plot(
-                    u_final,
-                    z_mid_final,
-                    '-',
-                    color=color,
-                    label=f'u {comparison_name}',
-                )
-                ax.plot(
-                    v_final,
-                    z_mid_final,
-                    '--',
-                    color=color,
-                    label=f'v {comparison_name}',
-                )
-        ax.set_xlabel('Velocity (m/s)')
-        ax.set_ylabel('z (m)')
-        ax.legend()
-        plt.title(title)
-        plt.tight_layout(pad=0.5)
-        plt.savefig('velocity.png')
-        plt.close()
+                    t_arr = get_days_since_start(ds_comp)
+                    t_index = np.argmin(np.abs(t_arr - t_target))
+                    t_days = float(t_arr[t_index])
+                    title = f'final time = {t_days:2.1g} days'
+                    self.logger.info(
+                        f'Plot {field_name} for {comparison_name} at {t_days} '
+                        'days'
+                    )
+                    ds_comp = ds_comp.isel(Time=t_index)
+                    z_mid_final = ds_comp['zMid'].mean(dim='nCells')
+                    u_final = ds_comp['velocityZonal'].mean(dim='nCells')
+                    v_final = ds_comp['velocityMeridional'].mean(dim='nCells')
+                    ax.plot(
+                        u_final,
+                        z_mid_final,
+                        '-',
+                        color=color,
+                        label=f'u {comparison_name}',
+                    )
+                    ax.plot(
+                        v_final,
+                        z_mid_final,
+                        '--',
+                        color=color,
+                        label=f'v {comparison_name}',
+                    )
+                ax.set_xlabel('Velocity (m/s)')
+                ax.set_ylabel('z (m)')
+                ax.legend()
+                plt.title(title)
+                plt.tight_layout(pad=0.5)
+                plt.savefig('velocity.png')
+                plt.close()
+            else:
+                # Plot initial state if available
+                if field_name in ds_init.keys():
+                    var_init = ds_init[field_name].mean(dim='nCells')
+                    plt.plot(var_init, z_mid_init, '--k', label='initial')
+
+                for comparison_name, color in zip(
+                    self.comparisons.keys(), colors, strict=False
+                ):
+                    if not os.path.exists(f'{comparison_name}.nc'):
+                        continue
+                    # Look for field_name in either output file
+                    ds_comp = self.open_model_dataset(
+                        f'{comparison_name}.nc', decode_times=False
+                    )
+                    ds_diags = self.open_model_dataset(
+                        f'{comparison_name}_diags.nc', decode_times=False
+                    )
+                    if field_name in ds_comp.keys():
+                        ds = ds_comp
+                    elif field_name in ds_diags.keys():
+                        ds = ds_diags
+                    else:
+                        self.logger.warn(
+                            f'{field_name} not present in {comparison_name}.nc'
+                        )
+                        continue
+                    t_arr = get_days_since_start(ds)
+                    t_index = np.argmin(np.abs(t_arr - t_target))
+                    t_days = float(t_arr[t_index])
+                    ds_final = ds.isel(Time=t_index)
+                    var_comp = ds_final[field_name].mean(dim='nCells')
+                    if 'nVertLevelsP1' in var_comp.dims:
+                        var_comp = var_comp.isel(nVertLevelsP1=slice(0, -1))
+                    # TODO delete this line when MPAS-O bug is fixed
+                    if field_name == 'RiTopOfCell':
+                        var_comp[0] = np.nan
+                    # TODO use this line when Omega zMid is correct
+                    # z_mid_final = ds_comp['zMid'].mean(dim='nCells')
+                    z_mid_final = depth_from_thickness(ds_final).mean(
+                        dim='nCells'
+                    )
+                    plt.plot(
+                        var_comp,
+                        z_mid_final,
+                        '-',
+                        color=color,
+                        label=comparison_name,
+                    )
+                title = f'final time = {t_days:2.1g} days'
+                plt.ylim([-100, 0])
+                if field_name == 'temperature':
+                    plt.xlim([15, 20])
+                else:
+                    plt.xlim(auto=True)
+                plt.xlabel(f'{field_name} ({field_units})')
+                plt.ylabel('z (m)')
+                fig.legend(loc='center right')
+                plt.title(title)
+                plt.tight_layout(pad=0.5)
+                plt.savefig(f'{field_name}.png')
+                plt.close()

From 9585bed75a618ab323b902cf1d65e04a0c761db6 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Fri, 30 Jan 2026 17:33:28 -0600
Subject: [PATCH 42/47] Add analysis step for wind-driven mixing

---
 .../ocean/single_column/vmix/__init__.py      | 28 ++++++--
 .../ocean/single_column/vmix/analysis.py      | 72 +++++++++++++++++++
 2 files changed, 96 insertions(+), 4 deletions(-)
 create mode 100644 polaris/tasks/ocean/single_column/vmix/analysis.py

diff --git a/polaris/tasks/ocean/single_column/vmix/__init__.py b/polaris/tasks/ocean/single_column/vmix/__init__.py
index 86150a02e9..80be3c36cb 100644
--- a/polaris/tasks/ocean/single_column/vmix/__init__.py
+++ b/polaris/tasks/ocean/single_column/vmix/__init__.py
@@ -1,6 +1,7 @@
 from polaris import Task
 from polaris.tasks.ocean.single_column.forward import Forward
 from polaris.tasks.ocean.single_column.viz import Viz
+from polaris.tasks.ocean.single_column.vmix.analysis import Analysis
 
 
 class VMix(Task):
@@ -35,19 +36,20 @@ def __init__(self, component, config, init, indir, name='vmix'):
             Forward(
                 component=component,
                 indir=f'{indir}/{name}',
+                name='forward_kpp',
                 ntasks=1,
                 min_tasks=1,
                 openmp_threads=1,
                 validate_vars=validate_vars,
                 task_name='vmix',
-                enable_vadv=True,
+                enable_vadv=False,
             ),
-            run_by_default=False,
         )
         self.add_step(
             Forward(
                 component=component,
                 indir=f'{indir}/{name}',
+                name='forward_pp',
                 ntasks=1,
                 min_tasks=1,
                 openmp_threads=1,
@@ -75,8 +77,26 @@ def __init__(self, component, config, init, indir, name='vmix'):
                 component=component,
                 indir=f'{indir}/{name}',
                 comparisons={
-                    'no_vadv': '../forward_no_vadv',
-                    'constant': '../forward_no_vadv_constant',
+                    'kpp': '../forward_kpp_no_vadv',
+                    'pp': '../forward_pp_no_vadv',
+                },
+                variables={
+                    'temperature': 'degC',
+                    'salinity': 'PSU',
+                    'velocity': 'm s$^{-1}$',
+                    'RiTopOfCell': '',
+                    'BruntVaisalaFreqTop': '$s^{-2}$',
+                },
+            )
+        )
+
+        self.add_step(
+            Analysis(
+                component=component,
+                indir=f'{indir}/{name}',
+                comparisons={
+                    'kpp': '../forward_kpp_no_vadv',
+                    'pp': '../forward_pp_no_vadv',
                 },
             )
         )
diff --git a/polaris/tasks/ocean/single_column/vmix/analysis.py b/polaris/tasks/ocean/single_column/vmix/analysis.py
new file mode 100644
index 0000000000..5a4afb9c0c
--- /dev/null
+++ b/polaris/tasks/ocean/single_column/vmix/analysis.py
@@ -0,0 +1,72 @@
+import numpy as np
+
+from polaris.ocean.model import OceanIOStep
+from polaris.ocean.time import get_days_since_start
+
+# TODO import rho_0 from constants
+
+
+class Analysis(OceanIOStep):
+    """
+    A step for analyzing the results of a single-column wind-forced test
+    """
+
+    def __init__(
+        self,
+        component,
+        indir,
+        comparisons=None,
+    ):
+        super().__init__(component=component, name='analysis', indir=indir)
+        self.comparisons = (
+            dict(comparisons)
+            if comparisons
+            else {'forward': '../forward/output.nc'}
+        )
+        for comparison_name, comparison_path in self.comparisons.items():
+            self.add_input_file(
+                filename=f'{comparison_name}_diags.nc',
+                target=f'{comparison_path}/output/KPP_test.0001-01-01_00.00.00.nc',
+            )
+
+    def run(self):
+        """
+        Run this step of the test case
+        """
+        section = self.config['single_column_forcing']
+        wind_stress = np.sqrt(
+            section.getfloat('wind_stress_zonal') ** 2.0
+            + section.getfloat('wind_stress_meridional') ** 2.0
+        )
+        # u_star = 0.01
+        rho_0 = 1026.0
+        u_star = wind_stress / rho_0
+        # TODO why is this 0
+        # u_star = ds_diags_1day['surfaceFrictionVelocity'].mean(dim='nCells')
+        # TODO compute this based on config parameters
+        N_sq_init = 1.0e-4
+        for comparison_name in self.comparisons.keys():
+            ds_diags = self.open_model_dataset(
+                f'{comparison_name}_diags.nc', decode_times=False
+            )
+            t_target = 1.0  # empirical relationship hold for up to 30h
+            t_arr = get_days_since_start(ds_diags)
+            t_index = np.argmin(np.abs(t_arr - t_target))
+            t_days = float(t_arr[t_index])
+            if abs(t_days - t_target) > (1 / 24):
+                self.logger.warn(
+                    f'{comparison_name}: Time mismatch \n'
+                    f'expected {t_target}, got {t_days}'
+                )
+            bld_theory = u_star * (15.0 * t_days * 86400.0 / N_sq_init) ** (
+                1 / 3
+            )
+            ds_diags_1day = ds_diags.isel(Time=t_index)
+            z_top_final = ds_diags_1day['zTop'].mean(dim='nCells')
+            N_sq = ds_diags_1day['BruntVaisalaFreqTop'].mean(dim='nCells')
+            index_bld = int(np.nanargmax(N_sq.values))
+            bld = z_top_final.isel(nVertLevels=index_bld)
+            self.logger.info(
+                f'{comparison_name}: boundary layer depth '
+                f'expected {bld_theory}, actual {bld.values}'
+            )

From 7d587a20e68cc41adbbeb6b8cdb62f694a10abf1 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Fri, 30 Jan 2026 20:39:12 -0600
Subject: [PATCH 43/47] fixup viz

---
 polaris/tasks/ocean/single_column/viz.py | 24 ++++++++++++++++++------
 1 file changed, 18 insertions(+), 6 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/viz.py b/polaris/tasks/ocean/single_column/viz.py
index 438f55983d..4a05a18393 100644
--- a/polaris/tasks/ocean/single_column/viz.py
+++ b/polaris/tasks/ocean/single_column/viz.py
@@ -46,9 +46,6 @@ def __init__(
             A dictionary of variables to plot along with their units
         """
         super().__init__(component=component, name='viz', indir=indir)
-        if ideal_age:
-            # Include age tracer
-            variables['iAge'] = 'seconds'
         self.comparisons = (
             dict(comparisons)
             if comparisons
@@ -63,6 +60,9 @@ def __init__(
                 'velocity': 'm s$^{-1}$',
             }
         )
+        if ideal_age:
+            # Include age tracer
+            self.variables['iAge'] = 'seconds'
         self.add_input_file(
             filename='initial_state.nc', target='../init/initial_state.nc'
         )
@@ -179,6 +179,11 @@ def run(self):
                     t_arr = get_days_since_start(ds)
                     t_index = np.argmin(np.abs(t_arr - t_target))
                     t_days = float(t_arr[t_index])
+                    if abs(t_days - t_target) > (1 / 24):
+                        self.logger.warn(
+                            f'{comparison_name}: Time mismatch \n'
+                            f'expected {t_target}, got {t_days}'
+                        )
                     ds_final = ds.isel(Time=t_index)
                     var_comp = ds_final[field_name].mean(dim='nCells')
                     if 'nVertLevelsP1' in var_comp.dims:
@@ -188,9 +193,16 @@ def run(self):
                         var_comp[0] = np.nan
                     # TODO use this line when Omega zMid is correct
                     # z_mid_final = ds_comp['zMid'].mean(dim='nCells')
-                    z_mid_final = depth_from_thickness(ds_final).mean(
-                        dim='nCells'
-                    )
+                    if 'layerThickness' not in ds.keys():
+                        z_mid_final = z_mid_init
+                        self.logger.warn(
+                            'Using initial zMid values; may not represent '
+                            'plotted state'
+                        )
+                    else:
+                        z_mid_final = depth_from_thickness(ds_final).mean(
+                            dim='nCells'
+                        )
                     plt.plot(
                         var_comp,
                         z_mid_final,

From f7eebbba1e1264f6ea9268f2ba00cba2f9422bc5 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Fri, 30 Jan 2026 20:39:54 -0600
Subject: [PATCH 44/47] fixup analysis

---
 polaris/tasks/ocean/single_column/vmix/analysis.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/polaris/tasks/ocean/single_column/vmix/analysis.py b/polaris/tasks/ocean/single_column/vmix/analysis.py
index 5a4afb9c0c..d9f4dc7289 100644
--- a/polaris/tasks/ocean/single_column/vmix/analysis.py
+++ b/polaris/tasks/ocean/single_column/vmix/analysis.py
@@ -58,7 +58,7 @@ def run(self):
                     f'{comparison_name}: Time mismatch \n'
                     f'expected {t_target}, got {t_days}'
                 )
-            bld_theory = u_star * (15.0 * t_days * 86400.0 / N_sq_init) ** (
+            bld_theory = -u_star * (15.0 * t_days * 86400.0 / N_sq_init) ** (
                 1 / 3
             )
             ds_diags_1day = ds_diags.isel(Time=t_index)

From 417d5e68f63fa22872cd080760ef8d21878a39e6 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Fri, 30 Jan 2026 20:41:17 -0600
Subject: [PATCH 45/47] Do not use Ri smoothing

---
 .../ocean/single_column/vmix/forward.yaml     | 31 +++++++++++++++++--
 1 file changed, 29 insertions(+), 2 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/vmix/forward.yaml b/polaris/tasks/ocean/single_column/vmix/forward.yaml
index 7e63a586f9..ee492cb073 100644
--- a/polaris/tasks/ocean/single_column/vmix/forward.yaml
+++ b/polaris/tasks/ocean/single_column/vmix/forward.yaml
@@ -17,10 +17,37 @@ mpas-ocean:
     config_use_activeTracers_interior_restoring: false
   cvmix:
     config_use_cvmix_kpp: false
-    config_cvmix_background_viscosity: 1e-2
+    config_cvmix_background_diffusion: 0.
+    config_cvmix_background_viscosity: 0.
     config_cvmix_shear_mixing_scheme: PP
+    config_cvmix_num_ri_smooth_loops: 0
   streams:
-    KPP_testing: {}
+    KPP_testing:
+      contents:
+      - mesh
+      - layerThickness
+      - tracers
+      - vertNonLocalFlux
+      - xtime
+      - zMid
+      - zTop
+      - velocityZonal
+      - velocityMeridional
+      - bulkRichardsonNumber
+      - bulkRichardsonNumberBuoy
+      - potentialDensity
+      - unresolvedShear
+      - boundaryLayerDepth
+      - surfaceFrictionVelocity
+      - surfaceBuoyancyForcing
+      - windStressZonal
+      - windStressMeridional
+      - transportVelocityZonal
+      - transportVelocityMeridional
+      - RiTopOfCell
+      - BruntVaisalaFreqTop
+      - vertViscTopOfCell
+      - vertDiffTopOfCell
 
 Omega:
   Tendencies:

From f375266c3318a598639e53089fba2bed17b33006 Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Fri, 30 Jan 2026 20:43:17 -0600
Subject: [PATCH 46/47] Match parameter values from Van Roekel et al 2018 for
 vmix_stable

---
 polaris/tasks/ocean/single_column/stable_stratification.cfg | 2 +-
 polaris/tasks/ocean/single_column/vmix/vmix.cfg             | 2 +-
 polaris/tasks/ocean/single_column/wind.cfg                  | 3 ++-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/stable_stratification.cfg b/polaris/tasks/ocean/single_column/stable_stratification.cfg
index 3c965e67b7..92de3c84cb 100644
--- a/polaris/tasks/ocean/single_column/stable_stratification.cfg
+++ b/polaris/tasks/ocean/single_column/stable_stratification.cfg
@@ -3,7 +3,7 @@
 [single_column]
 
 # temperature gradient below the mixed layer
-temperature_gradient_interior = 0.1
+temperature_gradient_interior = 0.05
 
 # Depth of the temperature mixed layer
 mixed_layer_depth_temperature =  0.0
diff --git a/polaris/tasks/ocean/single_column/vmix/vmix.cfg b/polaris/tasks/ocean/single_column/vmix/vmix.cfg
index 937e6966fd..5f68cf311c 100644
--- a/polaris/tasks/ocean/single_column/vmix/vmix.cfg
+++ b/polaris/tasks/ocean/single_column/vmix/vmix.cfg
@@ -5,4 +5,4 @@
 [single_column]
 
 # Run duration in days
-run_duration = 10.
+run_duration = 1.
diff --git a/polaris/tasks/ocean/single_column/wind.cfg b/polaris/tasks/ocean/single_column/wind.cfg
index 9daa95b973..057c8c1258 100644
--- a/polaris/tasks/ocean/single_column/wind.cfg
+++ b/polaris/tasks/ocean/single_column/wind.cfg
@@ -1,4 +1,5 @@
 [single_column_forcing]
 
 # Zonal surface wind stress over the domain
-wind_stress_zonal = 0.1
+# corresponding to friction velocity of 0.01
+wind_stress_zonal = 10.26

From e853f41be4183871c24f6a593d450474cc050d8d Mon Sep 17 00:00:00 2001
From: Carolyn Begeman <cbegeman@lanl.gov>
Date: Fri, 30 Jan 2026 20:49:54 -0600
Subject: [PATCH 47/47] fixup analysis to revert to old comparisons

---
 .../tasks/ocean/single_column/vmix/__init__.py    | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/polaris/tasks/ocean/single_column/vmix/__init__.py b/polaris/tasks/ocean/single_column/vmix/__init__.py
index 80be3c36cb..8aa1c4dfe9 100644
--- a/polaris/tasks/ocean/single_column/vmix/__init__.py
+++ b/polaris/tasks/ocean/single_column/vmix/__init__.py
@@ -36,20 +36,19 @@ def __init__(self, component, config, init, indir, name='vmix'):
             Forward(
                 component=component,
                 indir=f'{indir}/{name}',
-                name='forward_kpp',
                 ntasks=1,
                 min_tasks=1,
                 openmp_threads=1,
                 validate_vars=validate_vars,
                 task_name='vmix',
-                enable_vadv=False,
+                enable_vadv=True,
             ),
+            run_by_default=False,
         )
         self.add_step(
             Forward(
                 component=component,
                 indir=f'{indir}/{name}',
-                name='forward_pp',
                 ntasks=1,
                 min_tasks=1,
                 openmp_threads=1,
@@ -77,8 +76,9 @@ def __init__(self, component, config, init, indir, name='vmix'):
                 component=component,
                 indir=f'{indir}/{name}',
                 comparisons={
-                    'kpp': '../forward_kpp_no_vadv',
-                    'pp': '../forward_pp_no_vadv',
+                    'standard': '../forward',
+                    'no_vadv': '../forward_no_vadv',
+                    'constant': '../forward_no_vadv_constant',
                 },
                 variables={
                     'temperature': 'degC',
@@ -95,8 +95,9 @@ def __init__(self, component, config, init, indir, name='vmix'):
                 component=component,
                 indir=f'{indir}/{name}',
                 comparisons={
-                    'kpp': '../forward_kpp_no_vadv',
-                    'pp': '../forward_pp_no_vadv',
+                    'standard': '../forward',
+                    'no_vadv': '../forward_no_vadv',
+                    'constant': '../forward_no_vadv_constant',
                 },
             )
         )