Execute GEOS via calling gcm_run.j + rename marine suites -- part 1, 2, & 3

src/swell/configuration/jedi/interfaces/geos_marine/model/background_error.yaml

@@ -12,9 +12,12 @@ saber central block:
     - sea_surface_height_above_geoid
   read:
     groups:
-    - variables: [sea_water_potential_temperature, sea_water_salinity]
+    - variables:
+      - sea_water_potential_temperature
+      - sea_water_salinity
       horizontal:
-        filepath: 'background_error_model/hz_rossby'
+        filepath: 'background_error_model/new_corr_1p0'
+        # filepath: 'background_error_model/hz_rossby'
       vertical:
         levels: {{vertical_resolution}}
         filepath: 'background_error_model/vt.{{local_background_time}}'
@@ -26,7 +29,8 @@ saber central block:
       - sea_ice_snow_thickness
     {% endif %}
       horizontal:
-        filepath: 'background_error_model/hz_rossby_1p5'
+        # filepath: 'background_error_model/hz_rossby_1p5'
+        filepath: 'background_error_model/new_corr_1p5'
 
 date: '{{local_background_time_iso}}'
 
@@ -43,6 +47,8 @@ saber outer blocks:
         variable: sst_bgerr
     unbalanced salinity: {} # use default values
     unbalanced ssh: {} # use default values
+    # save diagnostics:
+    #   filepath: parametric_ocean_stddev_diags
 
 linear variable change:
   input variables: {{analysis_variables}}

src/swell/deployment/create_experiment.py

@@ -230,7 +230,8 @@ def create_experiment_directory(
     # resolve the templates and write the suite file to the experiment suite directory.
     # --------------------------------------------------------------------------------------------
     swell_suite_path = os.path.join(get_swell_path(), 'suites', suite)
-    prepare_cylc_suite_jinja2(logger, swell_suite_path, exp_suite_path, experiment_dict, platform)
+    prepare_cylc_suite_jinja2(logger, swell_suite_path, exp_suite_path, experiment_dict,
+                              platform, exp_path)
 
     # Copy suite and platform files to experiment suite directory
     # -----------------------------------------------------------
@@ -424,7 +425,8 @@ def prepare_cylc_suite_jinja2(
     swell_suite_path: str,
     exp_suite_path: str,
     experiment_dict: dict,
-    platform: str
+    platform: str,
+    experiment_path: str
 ) -> None:
 
     # Open suite file from swell
@@ -436,6 +438,10 @@ def prepare_cylc_suite_jinja2(
     # ----------------------------------------------------------
     render_dictionary = copy.deepcopy(experiment_dict)
 
+    # Add experiment path to the rendering dictionary
+    # ----------------------------------------------------
+    render_dictionary['experiment_path'] = experiment_path
+
     # Get unique list of cycle times with model flags to render dictionary
     # --------------------------------------------------------------------
 

src/swell/deployment/launch_experiment.py

@@ -89,7 +89,7 @@ def cylc_run_experiment(self) -> None:  # NB: Could be a factory based on workfl
             self.logger.info(' ')
 
             # Launch the job monitor
-            self.logger.critical('Launching the TUI, press \'q\' at any time to exit the TUI')
+            self.logger.critical('Press any key to launch the TUI. To exit TUI, press \'q\' at any time.')
             input()
             self.logger.info(' ')
             self.logger.info('TUI can be relaunched with:')

src/swell/deployment/platforms/nccs_discover_sles15/task_questions.yaml

@@ -2,10 +2,10 @@ crtm_coeff_dir:
   default_value: /discover/nobackup/projects/gmao/advda/SwellStaticFiles/jedi/crtm_coefficients/2.4.1/
 
 existing_geos_gcm_build_path:
-  default_value: /discover/nobackup/projects/gmao/SIteam/Models/GEOSgcm-v11.6.0/install-SLES15
+  default_value: /discover/nobackup/projects/gmao/SIteam/Models/GEOSgcm-GCMv12-rc12/install
 
 existing_geos_gcm_source_path:
-  default_value: /discover/nobackup/projects/gmao/SIteam/Models/GEOSgcm-v11.6.0/
+  default_value: /discover/nobackup/projects/gmao/SIteam/Models/GEOSgcm-GCMv12-rc12/
 
 existing_jedi_build_directory:
   default_value: /discover/nobackup/projects/gmao/advda/swell/JediBundles/fv3_soca_SLES15_12092025/build-intel-release/
@@ -19,6 +19,9 @@ existing_jedi_source_directory:
 existing_jedi_source_directory_pinned:
   default_value: /discover/nobackup/projects/gmao/advda/jedi_bundles_sles15/current_pinned_jedi_bundle/source/
 
+geos_homdir:
+  default_value: /discover/nobackup/projects/gmao/advda/SwellStaticFiles/geos/homdirs/coupled_025deg
+
 geos_experiment_directory:
   default_value: 5deg_0701
 

src/swell/suites/3dfgat_coupled_cycle/eva/increment-geos_marine.yaml

@@ -0,0 +1,170 @@
+datasets:
+
+  - name: ocean_increment
+    type: SocaRestart
+    soca_filenames: {{increment_file_path}}
+    geometry_file: {{cycle_dir}}/INPUT/soca_gridspec.nc
+    variables: [Temp, Salt, ave_ssh]
+    coordinate variables: [lon, lat]
+
+{% if 'cice6' in marine_models %}
+  - name: seaice_increment
+    type: SocaRestart
+    soca_filenames: {{ice_increment_file_path}}
+    geometry_file: {{cycle_dir}}/INPUT/soca_gridspec.nc
+    variables: [aice_h]
+    coordinate variables: [lon, lat]
+{% endif %}
+
+graphics:
+
+  plotting_backend: Emcpy
+  figure_list:
+
+  - batch figure:
+      variables: [ave_ssh]
+    figure:
+      figure size: [20,10]
+      layout: [1,1]
+      title: 'SOCA Increment'
+      output name: '{{cycle_dir}}/eva/increment/map_plots/${variable}/inc_${variable}.png'
+    plots:
+      - mapping:
+          projection: plcarr
+          domain: global
+        add_map_features: ['coastline']
+        add_colorbar:
+          label: SSH Increment
+        add_grid:
+        layers:
+        - type: MapGridded
+          longitude:
+            variable: ocean_increment::SOCAgrid::lon
+          latitude:
+            variable: ocean_increment::SOCAgrid::lat
+          data:
+            variable: ocean_increment::SOCAVars::ave_ssh
+          label: ave_ssh increment
+          colorbar: true
+          cmap: 'bwr'
+          vmin: -0.25
+          vmax: 0.25
+
+  - batch figure:
+      variables: [Temp]
+    figure:
+      figure size: [20,10]
+      layout: [1,1]
+      title: 'Soca Increment'
+      output name: '{{cycle_dir}}/eva/increment/map_plots/${variable}/inc_${variable}.png'
+    plots:
+      - mapping:
+          projection: plcarr
+          domain: global
+        add_map_features: ['coastline']
+        add_colorbar:
+          label: SST Increment
+        add_grid:
+        layers:
+        - type: MapGridded
+          longitude:
+            variable: ocean_increment::SOCAgrid::lon
+          latitude:
+            variable: ocean_increment::SOCAgrid::lat
+          data:
+            variable: ocean_increment::SOCAVars::Temp
+            slices: '[0,...]'
+          label: SST increment
+          colorbar: true
+          cmap: 'bwr'
+          vmin: -3
+          vmax: 3
+
+  - batch figure:
+      variables: [Salt]
+    figure:
+      figure size: [20,10]
+      layout: [1,1]
+      title: 'Soca Increment'
+      output name: '{{cycle_dir}}/eva/increment/map_plots/${variable}/inc_${variable}.png'
+    plots:
+      - mapping:
+          projection: plcarr
+          domain: global
+        add_map_features: ['coastline']
+        add_colorbar:
+          label: SSS Increment
+        add_grid:
+        layers:
+        - type: MapGridded
+          longitude:
+            variable: ocean_increment::SOCAgrid::lon
+          latitude:
+            variable: ocean_increment::SOCAgrid::lat
+          data:
+            variable: ocean_increment::SOCAVars::Salt
+            slices: '[0,...]'
+          label: SSS increment
+          colorbar: true
+          cmap: 'bwr'
+          vmin: -1
+          vmax: 1
+
+{% if 'cice6' in marine_models %}
+  - batch figure:
+      variables: [aice_h]
+    figure:
+      figure size: [20,10]
+      layout: [1,1]
+      title: 'Increment from JEDI'
+      output name: '{{cycle_dir}}/eva/increment/map_plots/${variable}/inc_s_${variable}.png'
+    plots:
+      - mapping:
+          projection: spstere
+          domain: south
+        add_map_features: ['coastline']
+        add_colorbar:
+          label: Sea-ice Concentration Increment
+        add_grid:
+        layers:
+        - type: MapGridded
+          longitude:
+            variable: seaice_increment::SOCAgrid::lon
+          latitude:
+            variable: seaice_increment::SOCAgrid::lat
+          data:
+            variable: seaice_increment::SOCAVars::aice_h
+          label: Sea ice concentration increment
+          colorbar: true
+          cmap: 'bwr'
+          vmin: -1
+          vmax: 1
+  - batch figure:
+      variables: [aice_h]
+    figure:
+      figure size: [20,10]
+      layout: [1,1]
+      title: 'Increment from JEDI'
+      output name: '{{cycle_dir}}/eva/increment/map_plots/${variable}/inc_n_${variable}.png'
+    plots:
+      - mapping:
+          projection: npstere
+          domain: north
+        add_map_features: ['coastline']
+        add_colorbar:
+          label: Sea-ice Concentration Increment
+        add_grid:
+        layers:
+        - type: MapGridded
+          longitude:
+            variable: seaice_increment::SOCAgrid::lon
+          latitude:
+            variable: seaice_increment::SOCAgrid::lat
+          data:
+            variable: seaice_increment::SOCAVars::aice_h
+          label: Sea-ice concentration increment
+          colorbar: true
+          cmap: 'bwr'
+          vmin: -1
+          vmax: 1
+{% endif %}

src/swell/suites/3dfgat_coupled_cycle/eva/jedi_log-geos_marine.yaml

@@ -0,0 +1,57 @@
+datasets:
+
+- type: JediLog
+  collection_name: jedi_log_test
+  jedi_log_to_parse: '{{cycle_dir}}/jedi_fgat_log.log'
+  data_to_parse:
+    convergence: true
+
+graphics:
+
+  plotting_backend: Emcpy
+  figure_list:
+
+  - figure:
+      layout: [3,1]
+      figure size: [12,10]
+      title: 'Residual Norm and Norm Reduction Plots'
+      output name: '{{cycle_dir}}/eva/jedi_log/convergence/residual_norm_reduction.png'
+    plots:
+      - add_xlabel: 'Total inner iteration number'
+        add_ylabel: 'Residual norm'
+        layers:
+        - type: LinePlot
+          x:
+            variable: jedi_log_test::convergence::total_iteration
+          y:
+            variable: jedi_log_test::convergence::residual_norm
+          color: 'black'
+
+      - add_xlabel: 'Total inner iteration number'
+        add_ylabel: 'Norm reduction'
+        layers:
+        - type: LinePlot
+          x:
+            variable: jedi_log_test::convergence::total_iteration
+          y:
+            variable: jedi_log_test::convergence::norm_reduction
+          color: 'black'
+
+      - add_xlabel: 'Total inner iteration number'
+        add_ylabel: 'Normalized Value'
+        add_legend:
+        layers:
+        - type: LinePlot
+          x:
+            variable: jedi_log_test::convergence::total_iteration
+          y:
+            variable: jedi_log_test::convergence::residual_norm_normalized
+          color: 'red'
+          label: 'Normalized residual norm'
+        - type: LinePlot
+          x:
+            variable: jedi_log_test::convergence::total_iteration
+          y:
+            variable: jedi_log_test::convergence::norm_reduction_normalized
+          color: 'blue'
+          label: 'Normalized norm reduction'