Merge branch 'seaice/develop' into release-v6.1

This merges in the seaice change since v6.0 that are needed for release.

* MPAS-Dev/MPAS-Model/seaice/develop:
  Removed reference to restartability_bgc in testing system.
  Added restart testing capability to restartability.py
  Added BGC testing and corrected 0 dimension
  Corrects iron uptake when carbon is active.
  Commented out two flags and updated bgc parameter defaults.

Author: matthewhoffman

src/core_seaice/Registry.xml

@@ -157,7 +157,7 @@
 			description="Number of dissolved organic carbon groups in use"
 		/>
 		<dim name="nDIC"
-			definition="0"
+			definition="1"
 			description="Number of dissolved inorganic carbon groups in use"
 		/>
 		<dim name="nDON"
@@ -779,7 +779,7 @@
 			possible_values="positive real number less than 1"
 			icepack_name="grid_o_t"
 		/>
-		<nml_option name="config_bio_gravity_drainage_length_scale" type="real" default_value="0.024" units="m"
+		<nml_option name="config_bio_gravity_drainage_length_scale" type="real" default_value="20." units="m"
 			description="positive real number less than 1"
 			possible_values="Sets the gravity drainage length scale in the biological transport model"
 			icepack_name="l_sk"
@@ -799,7 +799,7 @@
 			possible_values="real between 0 and 1 or negative.  If negative, compute porosity from snow density"
 			icepack_name="phi_snow"
 		/>
-		<nml_option name="config_new_ice_fraction_biotracer" type="real" default_value="0.80" units="unitless"
+		<nml_option name="config_new_ice_fraction_biotracer" type="real" default_value="1.0" units="unitless"
 			description="Fraction of biological tracer retained as new sea ice is formed from ocean water"
 			possible_values="positive real number less than or equal to 1"
 			icepack_name="initbio_frac"
@@ -889,17 +889,17 @@
 			possible_values="positive real less than one"
 			icepack_name="fr_resp"
 		/>
-		<nml_option name="config_rapid_mobile_to_stationary_time" type="real" default_value="5200.0" units="seconds"
+		<nml_option name="config_rapid_mobile_to_stationary_time" type="real" default_value="3600.0" units="seconds"
 			description="Rapid adsorption timescale  "
 			possible_values="zero or positive real number"
 			icepack_name="tau_min"
 		/>
-		<nml_option name="config_long_mobile_to_stationary_time" type="real" default_value="173000.0" units="seconds"
+		<nml_option name="config_long_mobile_to_stationary_time" type="real" default_value="7776000.0" units="seconds"
 			description="Slow adsorption timescale"
 			possible_values="zero or positive real number"
 			icepack_name="tau_max"
 		/>
-		<nml_option name="config_algal_maximum_velocity" type="real" default_value="0.0000000111" units="m/s"
+		<nml_option name="config_algal_maximum_velocity" type="real" default_value="0.0000001" units="m/s"
 			description="Maximum speed at which diatoms can move"
 			possible_values="zero or positive real number "
 			icepack_name="algal_vel"
@@ -929,32 +929,32 @@
 			possible_values="positive real"
 			icepack_name="chlabs_phaeo"
 		/>
-		<nml_option name="config_light_attenuation_diatoms" type="real" default_value="0.8" units="1/(W/m^2)"
+		<nml_option name="config_light_attenuation_diatoms" type="real" default_value="0.3" units="1/(W/m^2)"
 			description="Controls the ability of diatoms to utilize light"
 			possible_values="positive real less than 1"
 			icepack_name="alpha2max_low_diatoms"
 		/>
-		<nml_option name="config_light_attenuation_small_plankton" type="real" default_value="0.67" units="1/(W/m^2)"
+		<nml_option name="config_light_attenuation_small_plankton" type="real" default_value="0.2" units="1/(W/m^2)"
 			description="Controls the ability of small plankton to utilize light"
 			possible_values="positive real less than 1"
 			icepack_name="alpha2max_low_sp"
 		/>
-		<nml_option name="config_light_attenuation_phaeocystis" type="real" default_value="0.67" units="1/(W/m^2)"
+		<nml_option name="config_light_attenuation_phaeocystis" type="real" default_value="0.17" units="1/(W/m^2)"
 			description="Controls the ability of phaeocystis to utilize light"
 			possible_values="positive real less than 1"
 			icepack_name="alpha2max_low_phaeo"
 		/>
-		<nml_option name="config_light_inhibition_diatoms" type="real" default_value="0.018" units="1/(W/m^2)"
+		<nml_option name="config_light_inhibition_diatoms" type="real" default_value="0.001" units="1/(W/m^2)"
 			description="Controls the strength of light inhibition to growth for diatoms"
 			possible_values="positive real less than 1"
 			icepack_name="beta2max_diatoms"
 		/>
-		<nml_option name="config_light_inhibition_small_plankton" type="real" default_value="0.0025" units="1/(W/m^2)"
+		<nml_option name="config_light_inhibition_small_plankton" type="real" default_value="0.001" units="1/(W/m^2)"
 			description="Controls the strength of light inhibition to growth for small plankton"
 			possible_values="positive real less than 1"
 			icepack_name="beta2max_sp"
 		/>
-		<nml_option name="config_light_inhibition_phaeocystis" type="real" default_value="0.01" units="1/(W/m^2)"
+		<nml_option name="config_light_inhibition_phaeocystis" type="real" default_value="0.04" units="1/(W/m^2)"
 			description="Controls the strength of light inhibition to growth for phaeocystis"
 			possible_values="positive real less than 1"
 			icepack_name="beta2max_phaeo"
@@ -964,12 +964,12 @@
 			possible_values="positive real"
 			icepack_name="mu_max_diatoms"
 		/>
-		<nml_option name="config_maximum_growth_rate_small_plankton" type="real" default_value="0.851" units="1/day"
+		<nml_option name="config_maximum_growth_rate_small_plankton" type="real" default_value="0.41" units="1/day"
 			description="Maximum growth rate for small plankton"
 			possible_values="positive real"
 			icepack_name="mu_max_sp"
 		/>
-		<nml_option name="config_maximum_growth_rate_phaeocystis" type="real" default_value="0.851" units="1/day"
+		<nml_option name="config_maximum_growth_rate_phaeocystis" type="real" default_value="0.63" units="1/day"
 			description="Maximum growth rate for phaeocystis"
 			possible_values="positive real"
 			icepack_name="mu_max_phaeo"
@@ -994,12 +994,12 @@
 			possible_values="zero or positive real less than 1"
 			icepack_name="fr_graze_diatoms"
 		/>
-		<nml_option name="config_grazed_fraction_small_plankton" type="real" default_value="0.1" units="unitless"
+		<nml_option name="config_grazed_fraction_small_plankton" type="real" default_value="0.7" units="unitless"
 			description="Fraction of small plankton biomass grazed"
 			possible_values="zero or positive real less than 1"
 			icepack_name="fr_graze_sp"
 		/>
-		<nml_option name="config_grazed_fraction_phaeocystis" type="real" default_value="0.1" units="unitless"
+		<nml_option name="config_grazed_fraction_phaeocystis" type="real" default_value="0.7" units="unitless"
 			description="Fraction of phaeocystis biomass grazed"
 			possible_values="zero or positive real less than 1"
 			icepack_name="fr_graze_phaeo"
@@ -1179,12 +1179,12 @@
 			possible_values="zero or positive real less than 1"
 			icepack_name="fr_graze_e"
 		/>
-		<nml_option name="config_fraction_mortality_to_ammonium" type="real" default_value="0.5" units="unitless"
+		<nml_option name="config_fraction_mortality_to_ammonium" type="real" default_value="0.9" units="unitless"
 			description="Fraction of mortality to ammonium"
 			possible_values="zero or positive real less than 1"
 			icepack_name="fr_mort2min"
 		/>
-		<nml_option name="config_fraction_iron_remineralized" type="real" default_value="0.3" units="unitless"
+		<nml_option name="config_fraction_iron_remineralized" type="real" default_value="1.0" units="unitless"
 			description="Fraction of remineralized iron "
 			possible_values="zero or positive real less than or equal to 1"
 			icepack_name="fr_dFe"
@@ -1209,22 +1209,22 @@
 			possible_values="positive real"
 			icepack_name="max_dfe_doc1"
 		/>
-		<nml_option name="config_respiration_loss_to_DMSPd" type="real" default_value="0.75" units="unitless"
+		<nml_option name="config_respiration_loss_to_DMSPd" type="real" default_value="0.9" units="unitless"
 			description="Fraction of respiration loss as DMSPd"
 			possible_values="zero or positive real less than or equal to 1"
 			icepack_name="fr_resp_s"
 		/>
-		<nml_option name="config_DMSP_to_DMS_conversion_fraction" type="real" default_value="0.5" units="unitless"
+		<nml_option name="config_DMSP_to_DMS_conversion_fraction" type="real" default_value="0.7" units="unitless"
 			description="Fraction of conversion to DMS given high yield"
 			possible_values="zero or positive real less than or equal to 1"
 			icepack_name="y_sk_conv"
 		/>
-		<nml_option name="config_DMSP_to_DMS_conversion_time" type="real" default_value="3.0" units="day"
+		<nml_option name="config_DMSP_to_DMS_conversion_time" type="real" default_value="5.0" units="day"
 			description="Stefels conversion time"
 			possible_values="positive real"
 			icepack_name="t_sk_conv"
 		/>
-		<nml_option name="config_DMS_oxidation_time" type="real" default_value="10.0" units="day"
+		<nml_option name="config_DMS_oxidation_time" type="real" default_value="12.0" units="day"
 			description="DMS oxidation time"
 			possible_values="positive real"
 			icepack_name="t_sk_ox"
@@ -1234,12 +1234,12 @@
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="algaltype_diatoms"
 		/>
-		<nml_option name="config_mobility_type_small_plankton" type="real" default_value="0.5" units="unitless"
+		<nml_option name="config_mobility_type_small_plankton" type="real" default_value="0.0" units="unitless"
 			description="Transport type of small plankton"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="algaltype_sp"
 		/>
-		<nml_option name="config_mobility_type_phaeocystis" type="real" default_value="0.5" units="unitless"
+		<nml_option name="config_mobility_type_phaeocystis" type="real" default_value="0.0" units="unitless"
 			description="Transport type of phaeocystis"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="algaltype_phaeo"
@@ -1249,7 +1249,7 @@
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="nitratetype"
 		/>
-		<nml_option name="config_mobility_type_ammonium" type="real" default_value="1.0" units="unitless"
+		<nml_option name="config_mobility_type_ammonium" type="real" default_value="0.0" units="unitless"
 			description="Transport type of ammonium"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="ammoniumtype"
@@ -1264,32 +1264,32 @@
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="dmspptype"
 		/>
-		<nml_option name="config_mobility_type_DMSPd" type="real" default_value="-1.0" units="unitless"
+		<nml_option name="config_mobility_type_DMSPd" type="real" default_value="0.0" units="unitless"
 			description="Transport type of dissolved DMSP"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="dmspdtye"
 		/>
-		<nml_option name="config_mobility_type_humics" type="real" default_value="1.0" units="unitless"
+		<nml_option name="config_mobility_type_humics" type="real" default_value="0.0" units="unitless"
 			description="Transport type of humics"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="humtypes"
 		/>
-		<nml_option name="config_mobility_type_saccharids" type="real" default_value="0.5" units="unitless"
+		<nml_option name="config_mobility_type_saccharids" type="real" default_value="0.0" units="unitless"
 			description="Transport type of poly/saccharids"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="doctype_s"
 		/>
-		<nml_option name="config_mobility_type_lipids" type="real" default_value="0.5" units="unitless"
+		<nml_option name="config_mobility_type_lipids" type="real" default_value="0.0" units="unitless"
 			description="Transport type of lipids"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="doctype_l"
 		/>
-		<nml_option name="config_mobility_type_proteins" type="real" default_value="0.5" units="unitless"
+		<nml_option name="config_mobility_type_proteins" type="real" default_value="0.0" units="unitless"
 			description="Transport type of proteins"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="dontype_protein"
 		/>
-		<nml_option name="config_mobility_type_dissolved_iron" type="real" default_value="0.5" units="unitless"
+		<nml_option name="config_mobility_type_dissolved_iron" type="real" default_value="0.0" units="unitless"
 			description="Transport type of dissolved iron"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="fedtype_1"
@@ -1299,32 +1299,32 @@
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="feptype_1"
 		/>
-		<nml_option name="config_mobility_type_black_carbon1" type="real" default_value="1.0" units="unitless"
+		<nml_option name="config_mobility_type_black_carbon1" type="real" default_value="0.0" units="unitless"
 			description="Transport type of black carbon 1 pool"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="zaerotype_bc1"
 		/>
-		<nml_option name="config_mobility_type_black_carbon2" type="real" default_value="1.0" units="unitless"
+		<nml_option name="config_mobility_type_black_carbon2" type="real" default_value="0.0" units="unitless"
 			description="Transport type of black carbon 1 pool"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="zaerotype_bc2"
 		/>
-		<nml_option name="config_mobility_type_dust1" type="real" default_value="1.0" units="unitless"
+		<nml_option name="config_mobility_type_dust1" type="real" default_value="0.0" units="unitless"
 			description="Transport type of dust pool 1"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="zaerotype_dust1"
 		/>
-		<nml_option name="config_mobility_type_dust2" type="real" default_value="1.0" units="unitless"
+		<nml_option name="config_mobility_type_dust2" type="real" default_value="0.0" units="unitless"
 			description="Transport type of dust pool 2"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="zaerotype_dust2"
 		/>
-		<nml_option name="config_mobility_type_dust3" type="real" default_value="1.0" units="unitless"
+		<nml_option name="config_mobility_type_dust3" type="real" default_value="0.0" units="unitless"
 			description="Transport type of dust pool 3"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="zaerotype_dust3"
 		/>
-		<nml_option name="config_mobility_type_dust4" type="real" default_value="1.0" units="unitless"
+		<nml_option name="config_mobility_type_dust4" type="real" default_value="0.0" units="unitless"
 			description="Transport type of dust pool 4"
 			possible_values="-1 = entirely in the mobile phase; 0 = retention dominated; 1 = release dominated; 0.5 = equal but rapid exchange; 2 = equal but slow exchange"
 			icepack_name="zaerotype_dust4"

src/core_seaice/column/ice_algae.F90

@@ -1278,7 +1278,7 @@ subroutine z_biogeochemistry (n_cat,        dt,        &
                 call add_warning(warning)
                 write(warning,*)'Category,mm:',n_cat,mm
                 call add_warning(warning)
-                l_stop = .true.
+!                l_stop = .true.
                 stop_label = 'zbgc FCT tracer solution failed'
             endif
             if (l_stop) return
@@ -1351,7 +1351,7 @@ subroutine z_biogeochemistry (n_cat,        dt,        &
                 call add_warning(warning)
                 write(warning, *)  react(k,m),iphin_N(k),biomat_brine(k,m)
                 call add_warning(warning)
-                l_stop = .true.
+!                l_stop = .true.
                 stop_label = 'very large bgc value'
             elseif (bio_tmp < c0) then
                 write(warning, *) 'negative bgc'
@@ -2036,7 +2036,8 @@ subroutine algal_dyn (dt,           &
           enddo    
         endif
         endif !Docin(1) > c0
-      elseif (tr_bgc_Fe) then
+      endif
+      if (tr_bgc_Fe) then
         do n = 1,n_fed
            Fed_r(n) = Fed_r(n) + rFed(n)*Fed_tot_r          ! scavenging + uptake
         enddo 

testing_and_setup/seaice/configurations/standard_bgc/namelist.seaice

@@ -117,7 +117,7 @@
     config_use_vertical_tracers = true
     config_use_skeletal_biochemistry = false
     config_use_nitrate = true
-    config_use_carbon = true
+    config_use_carbon = false
     config_use_chlorophyll = false
     config_use_ammonium = true
     config_use_silicate = true

testing_and_setup/seaice/testing/tests/restartability.py

@@ -59,8 +59,18 @@ def restartability(mpasDevelopmentDir, domainsDir, domain, configuration, option
     # restart
     nProcs = 32
 
-    nmlChanges = {"seaice_model": {"config_start_time":"file"},
-                  "restart":    {"config_do_restart":True}}
+    bgcRestart = False
+    if ("bgc" in options.keys() and options["bgc"] == "True"):
+        bgcRestart = True
+
+    if (not bgcRestart):
+        nmlChanges = {"seaice_model": {"config_start_time":"file"},
+                      "restart": {"config_do_restart":True}}
+    else:
+        nmlChanges = {"seaice_model": {"config_start_time":"file"},
+                      "restart": {"config_do_restart":True,
+                                  "config_do_restart_bgc":True,
+                                  "config_do_restart_hbrine":True}}
     if (check):
         nmlChanges["unit_test"] = {"config_testing_system_test":True}
 

testing_and_setup/seaice/testing/testsuites/testsuite.standard_bgc.xml

@@ -4,7 +4,9 @@
 		<domain name="domain_QU240km">
 			<test name="regression"/>
 			<test name="parallelism"/>
-			<test name="restartability"/>
+			<test name="restartability">
+			      <option name="bgc" value="True"/>
+			    </test>
 		</domain>
 	</configuration>
 </testsuite>