Merge branch 'eclare/seaice/deprecate_colpkg' (PR #7132)

Remove the old sea ice column package

Removes the old column package from MPAS-seaice, including changing the
BGC default to Icepack. Namelist option config_column_physics_type has
only one option (‘icepack’) and has been left in the code for now, but
most lines using it have been commented out.

Several options available in the old column package that were/are being
deprecated in Icepack have been removed, including zsalinity and CESM
melt ponds. There were also options to turn off individual thermodynamic
processes in the column package for testing, which now are no longer
available: config_use_congelation_basal_melt, config_use_lateral_melt,
config_use_latent_processes.

This PR changes the default column physics used for biogeochemistry from
column_package to icepack.

In ice_comp_mct.F, call the freezing temperature calculation from
Icepack instead of the column_package, in routine ice_import_moab. This
change might affect runs with a coupled ocean component.

MPAS-seaice documentation has been updated accordingly.

[NML]
[BFB] - except for seaice BGC tests

Author: jonbob

components/mpas-seaice/bld/build-namelist

@@ -509,14 +509,12 @@ add_default($nl, 'config_load_balance_timers');
 if ($CONTINUE_RUN eq 'TRUE') {
         add_default($nl, 'config_do_restart', 'val'=>".true.");
         add_default($nl, 'config_do_restart_hbrine', 'val'=>".true.");
-        add_default($nl, 'config_do_restart_zsalinity', 'val'=>".true.");
         add_default($nl, 'config_do_restart_bgc', 'val'=>".true.");
         add_default($nl, 'config_do_restart_snow_density', 'val'=>".true.");
         add_default($nl, 'config_do_restart_snow_grain_radius', 'val'=>".true.");
 } else {
         add_default($nl, 'config_do_restart', 'val'=>".false.");
         add_default($nl, 'config_do_restart_hbrine', 'val'=>".false.");
-        add_default($nl, 'config_do_restart_zsalinity', 'val'=>".false.");
         add_default($nl, 'config_do_restart_bgc', 'val'=>".false.");
         add_default($nl, 'config_do_restart_snow_density', 'val'=>".false.");
         add_default($nl, 'config_do_restart_snow_grain_radius', 'val'=>".false.");
@@ -585,9 +583,6 @@ add_default($nl, 'config_include_pond_freshwater_feedback');
 
 add_default($nl, 'config_use_test_ice_shelf');
 add_default($nl, 'config_testing_system_test');
-add_default($nl, 'config_use_congelation_basal_melt');
-add_default($nl, 'config_use_lateral_melt');
-add_default($nl, 'config_use_latent_processes');
 add_default($nl, 'config_limit_air_temperatures');
 
 ###################################
@@ -630,7 +625,7 @@ add_default($nl, 'config_recover_tracer_means_check');
 ##################################
 
 if ($ice_bgc eq 'ice_bgc') {
-        add_default($nl, 'config_column_physics_type', 'val'=>"column_package");
+        add_default($nl, 'config_column_physics_type', 'val'=>"icepack");
 } else {
         add_default($nl, 'config_column_physics_type');
 }
@@ -652,7 +647,6 @@ add_default($nl, 'config_use_column_snow_tracers');
 add_default($nl, 'config_use_ice_age');
 add_default($nl, 'config_use_first_year_ice');
 add_default($nl, 'config_use_level_ice');
-add_default($nl, 'config_use_cesm_meltponds');
 add_default($nl, 'config_use_level_meltponds');
 add_default($nl, 'config_use_topo_meltponds');
 add_default($nl, 'config_use_aerosols');
@@ -665,7 +659,6 @@ add_default($nl, 'config_use_floe_size_distribution');
 # Namelist group: biogeochemistry #
 ###################################
 
-add_default($nl, 'config_use_vertical_zsalinity');
 add_default($nl, 'config_use_shortwave_bioabsorption');
 add_default($nl, 'config_use_skeletal_biochemistry');
 if ($ice_bgc eq 'ice_bgc') {
@@ -708,8 +701,6 @@ add_default($nl, 'config_scale_initial_vertical_bgc');
 add_default($nl, 'config_biogrid_bottom_molecular_sublayer');
 add_default($nl, 'config_biogrid_top_molecular_sublayer');
 add_default($nl, 'config_bio_gravity_drainage_length_scale');
-add_default($nl, 'config_zsalinity_molecular_sublayer');
-add_default($nl, 'config_zsalinity_gravity_drainage_scale');
 add_default($nl, 'config_snow_porosity_at_ice_surface');
 add_default($nl, 'config_new_ice_fraction_biotracer');
 add_default($nl, 'config_fraction_biotracer_in_frazil');
@@ -891,6 +882,7 @@ add_default($nl, 'config_rapid_mode_aspect_ratio');
 add_default($nl, 'config_slow_mode_drainage_strength');
 add_default($nl, 'config_slow_mode_critical_porosity');
 add_default($nl, 'config_macro_drainage_timescale');
+add_default($nl, 'config_congelation_freezing_method');
 add_default($nl, 'config_congelation_ice_porosity');
 
 #######################

components/mpas-seaice/bld/build-namelist-section

@@ -44,21 +44,18 @@ add_default($nl, 'config_load_balance_timers');
 if ($CONTINUE_RUN eq 'TRUE') {
         add_default($nl, 'config_do_restart', 'val'=>".true.");
         add_default($nl, 'config_do_restart_hbrine', 'val'=>".true.");
-        add_default($nl, 'config_do_restart_zsalinity', 'val'=>".true.");
         add_default($nl, 'config_do_restart_bgc', 'val'=>".true.");
         add_default($nl, 'config_do_restart_snow_density', 'val'=>".true.");
         add_default($nl, 'config_do_restart_snow_grain_radius', 'val'=>".true.");
 } else {
         add_default($nl, 'config_do_restart', 'val'=>".false.");
         add_default($nl, 'config_do_restart_hbrine', 'val'=>".false.");
-        add_default($nl, 'config_do_restart_zsalinity', 'val'=>".false.");
         add_default($nl, 'config_do_restart_bgc', 'val'=>".false.");
         add_default($nl, 'config_do_restart_snow_density', 'val'=>".false.");
         add_default($nl, 'config_do_restart_snow_grain_radius', 'val'=>".false.");
 }
 add_default($nl, 'config_restart_timestamp_name');
 add_default($nl, 'config_do_restart_hbrine');
-add_default($nl, 'config_do_restart_zsalinity');
 add_default($nl, 'config_do_restart_bgc');
 add_default($nl, 'config_do_restart_snow_density');
 add_default($nl, 'config_do_restart_snow_grain_radius');
@@ -121,9 +118,6 @@ add_default($nl, 'config_include_pond_freshwater_feedback');
 
 add_default($nl, 'config_use_test_ice_shelf');
 add_default($nl, 'config_testing_system_test');
-add_default($nl, 'config_use_congelation_basal_melt');
-add_default($nl, 'config_use_lateral_melt');
-add_default($nl, 'config_use_latent_processes');
 add_default($nl, 'config_limit_air_temperatures');
 
 ###################################
@@ -180,7 +174,6 @@ add_default($nl, 'config_use_column_snow_tracers');
 add_default($nl, 'config_use_ice_age');
 add_default($nl, 'config_use_first_year_ice');
 add_default($nl, 'config_use_level_ice');
-add_default($nl, 'config_use_cesm_meltponds');
 add_default($nl, 'config_use_level_meltponds');
 add_default($nl, 'config_use_topo_meltponds');
 add_default($nl, 'config_use_aerosols');
@@ -195,7 +188,6 @@ add_default($nl, 'config_use_floe_size_distribution');
 
 add_default($nl, 'config_couple_biogeochemistry_fields');
 add_default($nl, 'config_use_brine');
-add_default($nl, 'config_use_vertical_zsalinity');
 add_default($nl, 'config_use_vertical_biochemistry');
 add_default($nl, 'config_use_shortwave_bioabsorption');
 add_default($nl, 'config_use_vertical_tracers');
@@ -220,8 +212,6 @@ add_default($nl, 'config_scale_initial_vertical_bgc');
 add_default($nl, 'config_biogrid_bottom_molecular_sublayer');
 add_default($nl, 'config_biogrid_top_molecular_sublayer');
 add_default($nl, 'config_bio_gravity_drainage_length_scale');
-add_default($nl, 'config_zsalinity_molecular_sublayer');
-add_default($nl, 'config_zsalinity_gravity_drainage_scale');
 add_default($nl, 'config_snow_porosity_at_ice_surface');
 add_default($nl, 'config_new_ice_fraction_biotracer');
 add_default($nl, 'config_fraction_biotracer_in_frazil');
@@ -403,6 +393,7 @@ add_default($nl, 'config_rapid_mode_aspect_ratio');
 add_default($nl, 'config_slow_mode_drainage_strength');
 add_default($nl, 'config_slow_mode_critical_porosity');
 add_default($nl, 'config_macro_drainage_timescale');
+add_default($nl, 'config_congelation_freezing_method');
 add_default($nl, 'config_congelation_ice_porosity');
 
 #######################

components/mpas-seaice/bld/namelist_files/namelist_defaults_mpassi.xml

@@ -61,7 +61,6 @@
 <config_do_restart>false</config_do_restart>
 <config_restart_timestamp_name>'rpointer.ice'</config_restart_timestamp_name>
 <config_do_restart_hbrine>false</config_do_restart_hbrine>
-<config_do_restart_zsalinity>false</config_do_restart_zsalinity>
 <config_do_restart_bgc>false</config_do_restart_bgc>
 <config_do_restart_snow_density>false</config_do_restart_snow_density>
 <config_do_restart_snow_grain_radius>false</config_do_restart_snow_grain_radius>
@@ -144,9 +143,6 @@
 <!-- testing -->
 <config_use_test_ice_shelf>false</config_use_test_ice_shelf>
 <config_testing_system_test>false</config_testing_system_test>
-<config_use_congelation_basal_melt>true</config_use_congelation_basal_melt>
-<config_use_lateral_melt>true</config_use_lateral_melt>
-<config_use_latent_processes>true</config_use_latent_processes>
 <config_limit_air_temperatures>true</config_limit_air_temperatures>
 
 <!-- velocity_solver -->
@@ -219,7 +215,6 @@
 <config_use_ice_age>false</config_use_ice_age>
 <config_use_first_year_ice>false</config_use_first_year_ice>
 <config_use_level_ice>true</config_use_level_ice>
-<config_use_cesm_meltponds>false</config_use_cesm_meltponds>
 <config_use_level_meltponds>true</config_use_level_meltponds>
 <config_use_topo_meltponds>false</config_use_topo_meltponds>
 <config_use_aerosols>false</config_use_aerosols>
@@ -231,7 +226,6 @@
 <!-- biogeochemistry -->
 <config_couple_biogeochemistry_fields>false</config_couple_biogeochemistry_fields>
 <config_use_brine>false</config_use_brine>
-<config_use_vertical_zsalinity>false</config_use_vertical_zsalinity>
 <config_use_vertical_biochemistry>false</config_use_vertical_biochemistry>
 <config_use_shortwave_bioabsorption>false</config_use_shortwave_bioabsorption>
 <config_use_vertical_tracers>false</config_use_vertical_tracers>
@@ -256,8 +250,6 @@
 <config_biogrid_bottom_molecular_sublayer>0.006</config_biogrid_bottom_molecular_sublayer>
 <config_biogrid_top_molecular_sublayer>0.006</config_biogrid_top_molecular_sublayer>
 <config_bio_gravity_drainage_length_scale>20.</config_bio_gravity_drainage_length_scale>
-<config_zsalinity_molecular_sublayer>0.0</config_zsalinity_molecular_sublayer>
-<config_zsalinity_gravity_drainage_scale>0.028</config_zsalinity_gravity_drainage_scale>
 <config_snow_porosity_at_ice_surface>-0.3</config_snow_porosity_at_ice_surface>
 <config_new_ice_fraction_biotracer>1.0</config_new_ice_fraction_biotracer>
 <config_fraction_biotracer_in_frazil>0.80</config_fraction_biotracer_in_frazil>

components/mpas-seaice/bld/namelist_files/namelist_definition_mpassi.xml

@@ -245,14 +245,6 @@ Valid values: true or false
 Default: Defined in namelist_defaults.xml
 </entry>
 
-<entry id="config_do_restart_zsalinity" type="logical"
-	category="restart" group="restart">
-Restart the z-salinity tracer
-
-Valid values: false
-Default: Defined in namelist_defaults.xml
-</entry>
-
 <entry id="config_do_restart_bgc" type="logical"
 	category="restart" group="restart">
 Restart the ice biogeochemistry
@@ -564,30 +556,6 @@ Valid values: true or false
 Default: Defined in namelist_defaults.xml
 </entry>
 
-<entry id="config_use_congelation_basal_melt" type="logical"
-	category="testing" group="testing">
-If true congelation and basal melt processes are active.
-
-Valid values: true or false
-Default: Defined in namelist_defaults.xml
-</entry>
-
-<entry id="config_use_lateral_melt" type="logical"
-	category="testing" group="testing">
-If true lateral melt process is active.
-
-Valid values: true or false
-Default: Defined in namelist_defaults.xml
-</entry>
-
-<entry id="config_use_latent_processes" type="logical"
-	category="testing" group="testing">
-If true latent heat processes are active.
-
-Valid values: true or false
-Default: Defined in namelist_defaults.xml
-</entry>
-
 <entry id="config_limit_air_temperatures" type="logical"
 	category="testing" group="testing">
 If true limit air temperatures above
@@ -809,7 +777,7 @@ Default: Defined in namelist_defaults.xml
 	category="column_package" group="column_package">
 Set column physics library.
 
-Valid values: 'icepack' and 'column_package'
+Valid values: 'icepack'
 Default: Defined in namelist_defaults.xml
 </entry>
 
@@ -888,14 +856,6 @@ Valid values: true or false
 Default: Defined in namelist_defaults.xml
 </entry>
 
-<entry id="config_use_cesm_meltponds" type="logical"
-	category="column_tracers" group="column_tracers">
-If true use the cesm meltponds tracers.
-
-Valid values: true or false
-Default: Defined in namelist_defaults.xml
-</entry>
-
 <entry id="config_use_level_meltponds" type="logical"
 	category="column_tracers" group="column_tracers">
 If true use the level ice meltponds tracers.
@@ -971,14 +931,6 @@ Valid values: true or false
 Default: Defined in namelist_defaults.xml
 </entry>
 
-<entry id="config_use_vertical_zsalinity" type="logical"
-	category="biogeochemistry" group="biogeochemistry">
-Use z-salinity (with Bitz and Lipscomb 1999 thermodynamics)
-
-Valid values: false
-Default: Defined in namelist_defaults.xml
-</entry>
-
 <entry id="config_use_vertical_biochemistry" type="logical"
 	category="biogeochemistry" group="biogeochemistry">
 Turn on the reaction terms for vertical biological tracers
@@ -1171,22 +1123,6 @@ Valid values: Sets the gravity drainage length scale in the biological transport
 Default: Defined in namelist_defaults.xml
 </entry>
 
-<entry id="config_zsalinity_molecular_sublayer" type="real"
-	category="biogeochemistry" group="biogeochemistry">
-Sets the ice/ocean molecular sublayer for the z-salinity model
-
-Valid values: zero or positive real number less than 1
-Default: Defined in namelist_defaults.xml
-</entry>
-
-<entry id="config_zsalinity_gravity_drainage_scale" type="real"
-	category="biogeochemistry" group="biogeochemistry">
-Sets the gravity drainage length scale in the z-salinity model
-
-Valid values: positive real number less than 1
-Default: Defined in namelist_defaults.xml
-</entry>
-
 <entry id="config_snow_porosity_at_ice_surface" type="real"
 	category="biogeochemistry" group="biogeochemistry">
 Specifies the snow porosity (volume of air/total volume) at the ice surface
@@ -2489,7 +2425,7 @@ Default: Defined in namelist_defaults.xml
 
 <entry id="config_congelation_freezing_method" type="char*1024"
 	category="thermodynamics" group="thermodynamics">
-Method used for congelation freezing.
+Method for congelation ice freezing.
 
 Valid values: 'one-step', 'two-step'
 Default: Defined in namelist_defaults.xml

components/mpas-seaice/docs/dev-guide/index.md

@@ -60,19 +60,17 @@ The following examples describe how to use the script for development in Icepack
 
 ### Set up and run baselines
 
-Create a file containing modified namelist options. The file ``nset01.nlk`` in this example creates baselines for two types of column physics and turns off the ``snicar_ad`` radiation scheme.
+Create a file containing modified namelist options. The file ``nset01.nlk`` in this example turns off the ``snicar_ad`` radiation scheme.
 
 ```text
 $ less nset01.nlk
 [mpassi]
-config_column_physics_type = {'column_package','icepack'}
 config_use_snicar_ad = {.false.}
 ```
 
 Notes:
 
 - A .nlk file without any config settings will create a baseline using default settings.
-- The ``column_package`` option is still available but is no longer being supported in MPAS-seaice.
 
 Fetch E3SM (choose any name for the directory baselines01):
 
@@ -92,7 +90,7 @@ Submit:
 ./E3SM-Polar-Developer.sh -s baselines01 -k nset01.nlk -e -q
 ```
 
-Examine the diagnostic output (compares the icepack run with the column_package run in this example):
+Examine the diagnostic output:
 
 ```text
 ./E3SM-Polar-Developer.sh -s baselines01 -k nset01.nlk -e -a -v

components/mpas-seaice/docs/index.md

@@ -37,7 +37,6 @@ Code structure within the ``mpas-seaice/``component-level directory:
 | ``driver``      | coupling modules |
 | ``src``         | source code for the model physics and output |
 | ``src/analysis_members`` | source code for model output |
-| ``src/column``           | source code for the (original) ``column_package`` |
 | ``src/icepack``          | link to the icepack submodule |
 | ``src/model_forward``    | top-level mpas-seaice modules |
 | ``src/shared``           | dynamics and general-purpose modules (e.g. mesh, constants) |

components/mpas-seaice/docs/tech-guide/index.md

@@ -54,8 +54,6 @@ With advanced physics and biogeochemistry (BGC) options, MPAS-Seaice can be conf
 
 ## Column Physics
 
-The Icepack software has replaced the original ``colpkg`` column physics code in MPAS-seaice. The ``config_column_physics_type = 'column_package'`` option is still available but is no longer being supported in MPAS-seaice.
-
 Because of the strong thermal gradients between the (cold) atmosphere and (relatively warm) oceans in polar regions, a large portion of the physics in sea ice models can be described in a vertical column, without reference to neighboring grid cells. MPAS-Seaice shares the same column physics code as CICE through the Icepack library (Hunke et al., 2018), which is maintained by the CICE Consortium. This code includes several options for simulating sea ice thermodynamics, mechanical redistribution (ridging) and associated area and thickness changes. In addition, the model supports a number of tracers, including thickness, enthalpy, ice age, first-year ice area, deformed ice area and volume, melt ponds, snow properties and biogeochemistry.
 
 Icepack is implemented in MPAS-seaice as a git submodule. Icepack consists of three independent parts, the column physics code, the Icepack driver that supports stand-alone testing of the column physics code, and the Icepack scripts that build and test the Icepack model.  E3SM uses only the column physics code, which is called for each ocean grid cell.  Icepack’s own driver and testing scripts are used when preparing new developments to be merged back to the CICE Consortium’s Icepack repository.

components/mpas-seaice/docs/user-guide/index.md

@@ -44,8 +44,6 @@ Related namelist variables are grouped according to their application.
 
 ## Icepack
 
-The Icepack software has replaced the original ``colpkg`` column physics code in MPAS-seaice. The ``column_package`` option is still available but is no longer being supported in MPAS-seaice.
-
 Full documentation for E3SM's version of Icepack can be found in [E3SM's Icepack readthedocs](<https://e3sm-icepack.readthedocs.io/en/latest>).  The most up-to-date documentation from the CICE Consortium's main Icepack repository is [here](<https://cice-consortium-icepack.readthedocs.io/en/main>).
 
 The MPAS-seaice driver for Icepack is