Add omega support for single column tests

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
 

polaris/ocean/model/mpaso_to_omega.yaml

@@ -22,6 +22,9 @@ variables:
   cellsOnVertex: CellsOnVertex
   edgesOnVertex: EdgesOnVertex
 
+  # vertical
+  zMid: ZMid
+
   # tracers
   temperature: Temperature
   salinity: Salinity
@@ -91,6 +94,11 @@ config:
   options:
     config_disable_vel_explicit_bottom_drag: BottomDragTendencyEnable
 
+- section:
+    debug: Tendencies
+  options:
+    config_disable_vel_vmix: VelVertMixTendencyEnable
+
 - section:
     bottom_drag: Tendencies
   options:
@@ -114,3 +122,24 @@ 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

polaris/ocean/time.py

@@ -0,0 +1,34 @@
+from datetime import datetime
+
+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 '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)
+        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

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

polaris/tasks/ocean/single_column/__init__.py

@@ -1,7 +1,9 @@
-from polaris.tasks.ocean.single_column.cvmix import CVMix as CVMix
+from polaris.config import PolarisConfigParser as PolarisConfigParser
 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):
@@ -11,7 +13,152 @@ 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'
+
+    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'
+    )
+    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_dir}/init_stable',
+        config=config,
+        config_filename=f'{name}.cfg',
+    )
+    component.add_task(
+        VMix(
+            component=component,
+            config=config,
+            name=name,
+            init=init_step,
+            indir=group_name,
+        )
+    )
+
+    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'
+    )
+    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_dir}/init_unstable',
+        config=config,
+        config_filename=f'{name}.cfg',
+    )
+    component.add_task(
+        VMix(
+            component=component,
+            config=config,
+            name=name,
+            init=init_step,
+            indir=group_name,
+        )
+    )
+
+    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'
+    )
+    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',
+        config=config,
+        config_filename=f'{name}.cfg',
+    )
+    component.add_task(
+        Ekman(
+            component=component,
+            config=config,
+            init=init_step,
+            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'
+    )
+    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_dir}/init_stable',
+        config=config,
+        config_filename=f'{name}.cfg',
+    )
+    component.add_task(
+        IdealAge(
+            component=component,
+            init=init_step,
+            config=config,
+            indir=group_name,
+        )
+    )
+
+    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_dir}/init_stable',
+        config=config,
+        config_filename=f'{name}.cfg',
+    )
+    component.add_task(
+        Inertial(
+            component=component,
+            init=init_step,
+            config=config,
+            indir=group_name,
+        )
+    )