From 333e3ff3a8b203e2909198b53295cf0408b5021c Mon Sep 17 00:00:00 2001
From: Xylar Asay-Davis <xylarstorm@gmail.com>
Date: Fri, 27 Sep 2024 07:59:29 -0500
Subject: [PATCH] Add Omega IOStreams to convergence and manufactured_solution

---
 polaris/ocean/convergence/forward.py          |  4 ++
 .../tasks/manufactured_solution/forward.py    | 11 -----
 .../tasks/manufactured_solution/forward.yaml  | 42 ++++++++++++++-----
 3 files changed, 36 insertions(+), 21 deletions(-)

diff --git a/polaris/ocean/convergence/forward.py b/polaris/ocean/convergence/forward.py
index 68c3c15c9..e0ca5416f 100644
--- a/polaris/ocean/convergence/forward.py
+++ b/polaris/ocean/convergence/forward.py
@@ -139,12 +139,16 @@ def dynamic_model_config(self, at_setup):
         output_interval_str = get_time_interval_string(
             seconds=output_interval * s_per_hour)
 
+        # For Omega, we want the output interval as a number of seconds
+        output_freq = int(output_interval * s_per_hour)
+
         replacements = dict(
             time_integrator=time_integrator,
             dt=dt_str,
             btr_dt=btr_dt_str,
             run_duration=run_duration_str,
             output_interval=output_interval_str,
+            output_freq=f'{output_freq}'
         )
 
         self.add_yaml_file(self.package, self.yaml_filename,
diff --git a/polaris/ocean/tasks/manufactured_solution/forward.py b/polaris/ocean/tasks/manufactured_solution/forward.py
index 62bd76a4d..fee1db144 100644
--- a/polaris/ocean/tasks/manufactured_solution/forward.py
+++ b/polaris/ocean/tasks/manufactured_solution/forward.py
@@ -44,17 +44,6 @@ def __init__(self, component, name, resolution, subdir, init):
                          output_filename='output.nc',
                          validate_vars=['layerThickness', 'normalVelocity'])
 
-    def setup(self):
-        """
-        TEMP: symlink initial condition to name hard-coded in Omega
-        """
-        super().setup()
-        config = self.config
-        model = config.get('ocean', 'model')
-        # TODO: remove as soon as Omega supports I/O streams
-        if model == 'omega':
-            self.add_input_file(filename='OmegaMesh.nc', target='init.nc')
-
     def compute_cell_count(self):
         """
         Compute the approximate number of cells in the mesh, used to constrain
diff --git a/polaris/ocean/tasks/manufactured_solution/forward.yaml b/polaris/ocean/tasks/manufactured_solution/forward.yaml
index f7aefa138..776359db2 100644
--- a/polaris/ocean/tasks/manufactured_solution/forward.yaml
+++ b/polaris/ocean/tasks/manufactured_solution/forward.yaml
@@ -5,6 +5,16 @@ ocean:
   time_integration:
     config_dt: {{ dt }}
     config_time_integrator: {{ time_integrator }}
+
+mpas-ocean:
+  bottom_drag:
+    config_bottom_drag_mode: implicit
+    config_implicit_bottom_drag_type: constant
+    config_implicit_constant_bottom_drag_coeff: 0.0
+  manufactured_solution:
+     config_use_manufactured_solution: true
+  debug:
+    config_disable_vel_hmix: true
   streams:
     mesh:
       filename_template: init.nc
@@ -22,19 +32,31 @@ ocean:
       - layerThickness
       - ssh
 
-mpas-ocean:
-  bottom_drag:
-    config_bottom_drag_mode: implicit
-    config_implicit_bottom_drag_type: constant
-    config_implicit_constant_bottom_drag_coeff: 0.0
-  manufactured_solution:
-     config_use_manufactured_solution: true
-  debug:
-    config_disable_vel_hmix: true
-
 Omega:
   Tendencies:
     VelDiffTendencyEnable: false
     VelHyperDiffTendencyEnable: false
   Dimension:
     NVertLevels: 1
+  IOStreams:
+    InitialState:
+      UsePointerFile: false
+      Filename: init.nc
+      Mode: read
+      Precision: double
+      Freq: 1
+      FreqUnits: OnStartup
+      UseStartEnd: false
+      Contents:
+        - Restart
+    History:
+      UsePointerFile: false
+      Filename: output.nc
+      Mode: write
+      IfExists: replace
+      Precision: double
+      Freq: {{ output_freq }}
+      FreqUnits: Seconds
+      UseStartEnd: false
+      Contents:
+        - Tracers