Merge branch 'jonbob/ocean/CVMix_SmoothRi' into next (PR #1265)

Add Richardson number smoothing to CVMix in mpas-o

This PR implements @vanroekel's smoothing of the Richardson number profile prior
to computing LMD94 shear instability mixing (see MPAS 1219). This reduces the
frequency of 2 dz (grid-scale) noise in viscosity/diffusivity profiles.  It also
includes new default ICG files for the oEC60to30v3_ICG ice/ocn grid, which have
been spun-up with this fix, to provide consistent initial conditions for its
use.

A flag for the number of smoothing loops is also implemented, but should not
normally need to be changed from the default in registry.

Finally the limiting of the Ri profile to be positive is removed as this check
is also performed in CVMix.

Tested with SMS.ne30_oECv3_ICG.A_WCYCL2000S.edison_intel.

[CC]
[NML]

components/mpas-cice/cime_config/buildnml

@@ -62,8 +62,8 @@ if ( $ICE_GRID eq 'oEC60to30' ) {
 	$decomp_date .= '161222';
 	$decomp_prefix .= 'mpas-cice.graph.info.';
 } elsif ( $ICE_GRID eq 'oEC60to30v3_ICG' ) {
-        $grid_date .= '170111';
-	$grid_prefix .= 'seaice.EC60to30v3.ICG_a16q_yr60';
+        $grid_date .= '170213';
+	$grid_prefix .= 'seaice.EC60to30v3.a16q_smRi_yr102';
 	$decomp_date .= '161222';
 	$decomp_prefix .= 'mpas-cice.graph.info.';
 } elsif ( $ICE_GRID eq 'oEC60to30wLI' ) {

components/mpas-o/bld/build-namelist

@@ -638,6 +638,7 @@ add_default($nl, 'config_cvmix_convective_viscosity');
 add_default($nl, 'config_cvmix_convective_basedOnBVF');
 add_default($nl, 'config_cvmix_convective_triggerBVF');
 add_default($nl, 'config_use_cvmix_shear');
+add_default($nl, 'config_cvmix_num_ri_smooth_loops');
 add_default($nl, 'config_cvmix_shear_mixing_scheme');
 add_default($nl, 'config_cvmix_shear_PP_nu_zero');
 add_default($nl, 'config_cvmix_shear_PP_alpha');

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

@@ -225,6 +225,7 @@ add_default($nl, 'config_cvmix_convective_viscosity');
 add_default($nl, 'config_cvmix_convective_basedOnBVF');
 add_default($nl, 'config_cvmix_convective_triggerBVF');
 add_default($nl, 'config_use_cvmix_shear');
+add_default($nl, 'config_cvmix_num_ri_smooth_loops');
 add_default($nl, 'config_cvmix_shear_mixing_scheme');
 add_default($nl, 'config_cvmix_shear_PP_nu_zero');
 add_default($nl, 'config_cvmix_shear_PP_alpha');

components/mpas-o/bld/namelist_files/namelist_defaults_mpas-o.xml

@@ -197,6 +197,7 @@
 <config_cvmix_convective_basedOnBVF>.true.</config_cvmix_convective_basedOnBVF>
 <config_cvmix_convective_triggerBVF>0.0</config_cvmix_convective_triggerBVF>
 <config_use_cvmix_shear>.true.</config_use_cvmix_shear>
+<config_cvmix_num_ri_smooth_loops>2</config_cvmix_num_ri_smooth_loops>
 <config_cvmix_shear_mixing_scheme>'KPP'</config_cvmix_shear_mixing_scheme>
 <config_cvmix_shear_PP_nu_zero>0.005</config_cvmix_shear_PP_nu_zero>
 <config_cvmix_shear_PP_alpha>5.0</config_cvmix_shear_PP_alpha>

components/mpas-o/bld/namelist_files/namelist_definition_mpas-o.xml

@@ -937,6 +937,14 @@ Valid values: True or False
 Default: Defined in namelist_defaults.xml
 </entry>
 
+<entry id="config_cvmix_num_ri_smooth_loops" type="integer"
+	category="cvmix" group="cvmix">
+Number of smoothing passes over RiTopOfCell for LMD94 shear instability mixing
+
+Valid values: any integer
+Default: Defined in namelist_defaults.xml
+</entry>
+
 <entry id="config_cvmix_shear_mixing_scheme" type="char*1024"
 	category="cvmix" group="cvmix">
 Choose between Pacanowski/Philander or Large et al. shear mixing

components/mpas-o/cime_config/buildnml

@@ -64,8 +64,8 @@ if ( $OCN_GRID eq 'oEC60to30' ) {
 } elsif ( $OCN_GRID eq 'oEC60to30v3_ICG' ) {
         $grid_date .= '161222';
         $grid_prefix .= 'oEC60to30v3';
-        $ic_date .= '170111';
-        $ic_prefix .= 'oEC60to30v3.ICG_a16q_yr60';
+        $ic_date .= '170213';
+        $ic_prefix .= 'oEC60to30v3.a16q_smRi_yr102';
         $decomp_prefix .= 'mpas-o.graph.info.';
 } elsif ( $OCN_GRID eq 'oEC60to30wLI' ) {
         $grid_date .= '160830';
@@ -666,6 +666,21 @@ if ( -e "$CASEROOT/SourceMods/src.mpaso/$STREAM_NAME" ) {
 	print $stream_file '    <var name="vertTransportVelocityTop"/>' . "\n";
 	print $stream_file '    <var name="normalGMBolusVelocity"/>' . "\n";
 	print $stream_file '    <var name="vertGMBolusVelocityTop"/>' . "\n";
+	print $stream_file '    <var_struct name="tracersSurfaceFlux"/>' . "\n";
+	print $stream_file '    <var name="penetrativeTemperatureFlux"/>' . "\n";
+	print $stream_file '    <var name="latentHeatFlux"/>' . "\n";
+	print $stream_file '    <var name="sensibleHeatFlux"/>' . "\n";
+	print $stream_file '    <var name="longWaveHeatFluxUp"/>' . "\n";
+	print $stream_file '    <var name="longWaveHeatFluxDown"/>' . "\n";
+	print $stream_file '    <var name="seaIceHeatFlux"/>' . "\n";
+	print $stream_file '    <var name="shortWaveHeatFlux"/>' . "\n";
+	print $stream_file '    <var name="evaporationFlux"/>' . "\n";
+	print $stream_file '    <var name="seaIceSalinityFlux"/>' . "\n";
+	print $stream_file '    <var name="seaIceFreshWaterFlux"/>' . "\n";
+	print $stream_file '    <var name="riverRunoffFlux"/>' . "\n";
+	print $stream_file '    <var name="iceRunoffFlux"/>' . "\n";
+	print $stream_file '    <var name="rainFlux"/>' . "\n";
+	print $stream_file '    <var name="snowFlux"/>' . "\n";
 	print $stream_file '</stream>' . "\n";
 	print $stream_file '' . "\n";
         print $stream_file '<stream name="timeSeriesStatsClimatologyOutput"' . "\n";