Merge branch 'maltrud/ocean/add-carbon-conservation-check' into next …

…(PR #5151)

Add carbon to mpas-ocean conservation check analysis member

This PR adds carbon to the conservation check analysis member. Output is
written to both the log file and conservation check netcdf file. Carbon
variables are written to the netcdf file even if BGC is not turned on
(unless the user modifies streams.ocean), but not to the log file.

[BFB]

components/mpas-ocean/cime_config/buildnml

@@ -999,6 +999,14 @@ def buildnml(case, caseroot, compname):
         lines.append('<var name="accumulatedLandIceFlux"/>')
         lines.append('<var name="accumulatedLandIceFrazilFlux"/>')
         lines.append('<var name="accumulatedSeaIceSalinityFlux"/>')
+        lines.append('<var name="initialCarbon"/>')
+        lines.append('<var name="finalCarbon"/>')
+        lines.append('<var name="carbonChange"/>')
+        lines.append('<var name="netCarbonFlux"/>')
+        lines.append('<var name="absoluteCarbonError"/>')
+        lines.append('<var name="relativeCarbonError"/>')
+        lines.append('<var name="accumulatedAbsoluteCarbonError"/>')
+        lines.append('<var name="accumulatedRelativeCarbonError"/>')
         lines.append('</stream>')
         lines.append('')
         lines.append('<immutable_stream name="conservationCheckRestart"')

components/mpas-ocean/src/analysis_members/Registry_conservation_check.xml

@@ -198,6 +198,53 @@
 			 description="Salinity flux from frazil to Land Ice, given to coupler. Positive into the ocean."
 		/>
 	</var_struct>
+            <var_struct name="conservationCheckCarbonAM" time_levs="1" packages="conservationCheckAMPKG">
+                <var name="initialCarbon" type="real" dimensions="Time" units="kg"
+                     description="Total ocean carbon at start of conservation interval"
+                />
+                <var name="finalCarbon" type="real" dimensions="Time" units="kg"
+                     description="Total ocean carbon at end of conservation interval"
+                />
+                <var name="carbonChange" type="real" dimensions="Time" units="kg"
+                     description="Change in ocean carbon over conservation interval"
+                />
+                <var name="netCarbonFlux" type="real" dimensions="Time" units="kg"
+                     description="Net surface flux of ocean carbon over conservation interval"
+                />
+                <var name="absoluteCarbonError" type="real" dimensions="Time" units="kg"
+                     description="Absolute carbon conservation error over conservation interval"
+                />
+                <var name="relativeCarbonError" type="real" dimensions="Time" units="1"
+                     description="Relative carbon conservation error over conservation interval"
+                />
+                <var name="accumulatedAbsoluteCarbonError" type="real" default_value="0.0" dimensions="Time" units="kg"
+                     description="Accumulated absolute carbon conservation error over entire simulation"
+                />
+                <var name="accumulatedRelativeCarbonError" type="real" default_value="0.0" dimensions="Time" units="1"
+                     description="Accumulated relative carbon conservation error over entire simulation"
+                />
+                <var name="accumulatedCarbonSourceSink" type="real" dimensions="Time" units="kg"
+                     description="Volume integral of all carbon source-sink terms from MarBL"
+                />
+                <var name="accumulatedCarbonSedimentFlux" type="real" dimensions="Time" units="kg"
+                     description="Surface integral of all carbon sediment fluxes"
+                />
+                <var name="accumulatedCarbonSurfaceFlux" type="real" dimensions="Time" units="kg"
+                     description="Surface integral of all carbon ocean surface fluxes"
+                />
+                <var name="accumulatedCarbonTend" type="real" dimensions="Time" units="kg"
+                     description="Volume integral of all carbon-containing prognostic variable tendencies"
+                />
+                <var name="accumulatedCO2gasFlux" type="real" dimensions="Time" units="kg"
+                     description="Surface integral of air-sea CO2 gas flux"
+                />
+                <var name="accumulatedIceOceanOrganicCarbonFlux" type="real" dimensions="Time" units="kg"
+                     description="Surface integral of all organic ice-ocean carbon fluxes"
+                />
+                <var name="accumulatedIceOceanInorganicCarbonFlux" type="real" dimensions="Time" units="kg"
+                     description="Surface integral of all inorganic ice-ocean carbon fluxes"
+                />
+        </var_struct>
 	<streams>
 		<stream name="conservationCheckOutput" type="output"
 				mode="forward;analysis"
@@ -259,6 +306,14 @@
             <var name="accumulatedSeaIceSalinityFlux"/>
             <var name="accumulatedFrazilSalinityFlux"/>
             <var name="accumulatedLandIceFrazilSalinityFlux"/>
+            <var name="initialCarbon"/>
+            <var name="finalCarbon"/>
+            <var name="carbonChange"/>
+            <var name="netCarbonFlux"/>
+            <var name="absoluteCarbonError"/>
+            <var name="relativeCarbonError"/>
+            <var name="accumulatedAbsoluteCarbonError"/>
+            <var name="accumulatedRelativeCarbonError"/>
 		</stream>
 
 		<stream name="conservationCheckRestart"
@@ -308,5 +363,8 @@
             <var name="accumulatedSeaIceSalinityFlux"/>
             <var name="accumulatedFrazilSalinityFlux"/>
             <var name="accumulatedLandIceFrazilSalinityFlux"/>
+            <var name="initialCarbon"/>
+            <var name="accumulatedAbsoluteCarbonError"/>
+            <var name="accumulatedRelativeCarbonError"/>
 		</stream>
 	</streams>