Merge branch 'cbegeman/ocn/mask-time-series-stats-vars' (PR #5325)

Mask ocean time series stats variables This PR applies fill value masking to non-restart time series stats streams in the ocean component. It also specifies the masking array for a subset of variables in the Registry. Fixes #5253 [BFB]
E3SM-Project · Dec 5, 2022 · 627683e · 627683e
2 parents 146732c + d0b11ef
commit 627683e
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Showing 15 changed files with 77 additions and 13 deletions.
diff --git a/components/mpas-ocean/cime_config/buildnml b/components/mpas-ocean/cime_config/buildnml
@@ -1058,6 +1058,7 @@ def buildnml(case, caseroot, compname):
         lines.append('        type="output"')
         lines.append('        precision="single"')
         lines.append('        io_type="{}"'.format(ocn_pio_typename))
+        lines.append('        useMissingValMask="true"')
         lines.append('        filename_template="{}.mpaso.hist.am.timeSeriesStatsDaily.$Y-$M-$D.nc"'.format(casename))
         lines.append('        filename_interval="00-01-00_00:00:00"')
         lines.append('        reference_time="01-01-01_00:00:00"')
@@ -1112,6 +1113,7 @@ def buildnml(case, caseroot, compname):
         else:
             lines.append('        io_type="{}"'.format(ocn_pio_typename))
 
+        lines.append('        useMissingValMask="true"')
         lines.append('        filename_template="{}.mpaso.hist.am.timeSeriesStatsMonthly.$Y-$M-$D.nc"'.format(casename))
         lines.append('        filename_interval="00-01-00_00:00:00"')
         lines.append('        reference_time="01-01-01_00:00:00"')
@@ -1347,6 +1349,7 @@ def buildnml(case, caseroot, compname):
         else:
             lines.append('        io_type="{}"'.format(ocn_pio_typename))
 
+        lines.append('        useMissingValMask="true"')
         lines.append('        filename_template="{}.mpaso.hist.am.timeSeriesStatsMonthlyMax.$Y-$M-$D.nc"'.format(casename))
         lines.append('        filename_interval="00-01-00_00:00:00"')
         lines.append('        reference_time="01-01-01_00:00:00"')
@@ -1408,6 +1411,7 @@ def buildnml(case, caseroot, compname):
         else:
             lines.append('        io_type="{}"'.format(ocn_pio_typename))
 
+        lines.append('        useMissingValMask="true"')
         lines.append('        filename_template="{}.mpaso.hist.am.timeSeriesStatsMonthlyMin.$Y-$M-$D.nc"'.format(casename))
         lines.append('        filename_interval="00-01-00_00:00:00"')
         lines.append('        reference_time="01-01-01_00:00:00"')
@@ -1465,6 +1469,7 @@ def buildnml(case, caseroot, compname):
         lines.append('        type="output"')
         lines.append('        precision="single"')
         lines.append('        io_type="{}"'.format(ocn_pio_typename))
+        lines.append('        useMissingValMask="true"')
         lines.append('        filename_template="{}.mpaso.hist.am.timeSeriesStatsClimatology.$Y-$M-$D.nc"'.format(casename))
         lines.append('        filename_interval="00-01-00_00:00:00"')
         lines.append('        reference_time="01-01-01_00:00:00"')
@@ -1479,6 +1484,7 @@ def buildnml(case, caseroot, compname):
         lines.append('        type="output"')
         lines.append('        precision="single"')
         lines.append('        io_type="{}"'.format(ocn_pio_typename))
+        lines.append('        useMissingValMask="true"')
         lines.append('        filename_template="{}.mpaso.hist.am.timeSeriesStatsCustom.$Y-$M-$D.nc"'.format(casename))
         lines.append('        filename_interval="00-01-00_00:00:00"')
         lines.append('        reference_time="01-01-01_00:00:00"')

diff --git a/components/mpas-ocean/src/Registry.xml b/components/mpas-ocean/src/Registry.xml
diff --git a/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_climatology.xml b/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_climatology.xml
@@ -80,6 +80,7 @@
 				type="output"
 				mode="forward;analysis"
 				io_type="pnetcdf"
+				useMissingValMask="true"
 				precision="single"
 				filename_template="analysis_members/mpaso.hist.am.timeSeriesStatsClimatology.$Y-$M-$D.nc"
 				reference_time="01-01-01_00:00:00"

diff --git a/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_custom.xml b/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_custom.xml
@@ -80,6 +80,7 @@
 				type="output"
 				mode="forward;analysis"
 				io_type="pnetcdf"
+				useMissingValMask="true"
 				precision="single"
 				filename_template="analysis_members/mpaso.hist.am.timeSeriesStatsCustom.$Y-$M-$D.nc"
 				reference_time="01-01-01_00:00:00"

diff --git a/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_daily.xml b/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_daily.xml
@@ -93,6 +93,7 @@
 				type="output"
 				mode="forward;analysis"
 				io_type="pnetcdf"
+				useMissingValMask="true"
 				precision="single"
 				filename_template="analysis_members/mpaso.hist.am.timeSeriesStatsDaily.$Y-$M-$D.nc"
 				reference_time="01-01-01_00:00:00"

diff --git a/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_monthly_max.xml b/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_monthly_max.xml
@@ -93,6 +93,7 @@
 				type="output"
 				mode="forward;analysis"
 				io_type="pnetcdf"
+				useMissingValMask="true"
 				precision="single"
 				filename_template="analysis_members/mpaso.hist.am.timeSeriesStatsMonthlyMax.$Y-$M-$D.nc"
 				filename_interval="00-01-00_00:00:00"

diff --git a/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_monthly_mean.xml b/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_monthly_mean.xml
@@ -93,6 +93,7 @@
 				type="output"
 				mode="forward;analysis"
 				io_type="pnetcdf"
+				useMissingValMask="true"
 				filename_template="analysis_members/mpaso.hist.am.timeSeriesStatsMonthly.$Y-$M-$D.nc"
 				filename_interval="00-01-00_00:00:00"
 				reference_time="01-01-01_00:00:00"

diff --git a/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_monthly_min.xml b/components/mpas-ocean/src/analysis_members/Registry_time_series_stats_monthly_min.xml
@@ -93,6 +93,7 @@
 				type="output"
 				mode="forward;analysis"
 				io_type="pnetcdf"
+				useMissingValMask="true"
 				precision="single"
 				filename_template="analysis_members/mpaso.hist.am.timeSeriesStatsMonthlyMin.$Y-$M-$D.nc"
 				filename_interval="00-01-00_00:00:00"

diff --git a/components/mpas-ocean/src/tracer_groups/Registry_CFC.xml b/components/mpas-ocean/src/tracer_groups/Registry_CFC.xml
@@ -49,7 +49,7 @@
 
 	<var_struct name="state" time_levs="2">
 		<var_struct name="tracers" time_levs="2">
-			<var_array name="CFCTracers" dimensions="nVertLevels nCells Time" type="real" packages="CFCTracersPKG"  default_value="0.0">
+			<var_array name="CFCTracers" dimensions="nVertLevels nCells Time" type="real" packages="CFCTracersPKG"  default_value="0.0" missing_value="FILLVAL" missing_value_mask="cellMask">
 				<!-- Add constituents of tracer group -->
 				<var name="CFC11" array_group="CFCGRP" units="mol m^{-3}"
 			description="CFC11"
@@ -63,7 +63,7 @@
 
 	<var_struct name="tend" time_levs="1">
 		<var_struct name="tracersTend" time_levs="1">
-			<var_array name="CFCTracersTend" type="real" dimensions="nVertLevels nCells Time" packages="CFCTracersPKG">
+			<var_array name="CFCTracersTend" type="real" dimensions="nVertLevels nCells Time" packages="CFCTracersPKG" missing_value="FILLVAL" missing_value_mask="cellMask">
 				<!-- Add constituents of tracer group -->
 				<var name="CFC11Tend" array_group="CFCGRP" units="mol m^{-3} s^{-1}"
 			description="CFC11 Tendency"

diff --git a/components/mpas-ocean/src/tracer_groups/Registry_DMS.xml b/components/mpas-ocean/src/tracer_groups/Registry_DMS.xml
@@ -49,7 +49,7 @@
 
 	<var_struct name="state" time_levs="2">
 		<var_struct name="tracers" time_levs="2">
-			<var_array name="DMSTracers" dimensions="nVertLevels nCells Time" type="real" packages="DMSTracersPKG" >
+			<var_array name="DMSTracers" dimensions="nVertLevels nCells Time" type="real" packages="DMSTracersPKG" missing_value="FILLVAL" missing_value_mask="cellMask">
 				<!-- Add constituents of tracer group -->
 				<var name="DMS" array_group="DMSGRP" units="mmol m^{-3}"
 			description="Dimethyl Sulfide"
@@ -63,7 +63,7 @@
 
 	<var_struct name="tend" time_levs="1">
 		<var_struct name="tracersTend" time_levs="1">
-			<var_array name="DMSTracersTend" type="real" dimensions="nVertLevels nCells Time" packages="DMSTracersPKG">
+			<var_array name="DMSTracersTend" type="real" dimensions="nVertLevels nCells Time" packages="DMSTracersPKG" missing_value="FILLVAL" missing_value_mask="cellMask">
 				<!-- Add constituents of tracer group -->
 				<var name="DMSTend" array_group="DMSGRP" units="mmol m^{-3} s^{-1}"
 			description="Dimethyl Sulfide Tendency"

diff --git a/components/mpas-ocean/src/tracer_groups/Registry_MacroMolecules.xml b/components/mpas-ocean/src/tracer_groups/Registry_MacroMolecules.xml
@@ -49,7 +49,7 @@
 
 	<var_struct name="state" time_levs="2">
 		<var_struct name="tracers" time_levs="2">
-			<var_array name="MacroMoleculesTracers" dimensions="nVertLevels nCells Time" type="real" packages="MacroMoleculesTracersPKG" >
+			<var_array name="MacroMoleculesTracers" dimensions="nVertLevels nCells Time" type="real" packages="MacroMoleculesTracersPKG" missing_value="FILLVAL" missing_value_mask="cellMask">
 				<!-- Add constituents of tracer group -->
 			<var name="PROT" array_group="MacroMoleculesGRP" units="mmol m^{-3}"
 				description="Proteins"
@@ -66,7 +66,7 @@
 
 	<var_struct name="tend" time_levs="1">
 		<var_struct name="tracersTend" time_levs="1">
-			<var_array name="MacroMoleculesTracersTend" type="real" dimensions="nVertLevels nCells Time" packages="MacroMoleculesTracersPKG">
+			<var_array name="MacroMoleculesTracersTend" type="real" dimensions="nVertLevels nCells Time" packages="MacroMoleculesTracersPKG" missing_value="FILLVAL" missing_value_mask="cellMask">
 				<!-- Add constituents of tracer group -->
 			<var name="PROTTend" array_group="MacroMoleculesGRP" units="mmol m^{-3} s^{-1}"
 				description="Proteins Tendency"

diff --git a/components/mpas-ocean/src/tracer_groups/Registry_activeTracers.xml b/components/mpas-ocean/src/tracer_groups/Registry_activeTracers.xml
@@ -74,7 +74,7 @@
 
 	<var_struct name="tend" time_levs="1">
 		<var_struct name="tracersTend" time_levs="1">
-			<var_array name="activeTracersTend" type="real" dimensions="nVertLevels nCells Time" packages="activeTracersPKG">
+			<var_array name="activeTracersTend" type="real" dimensions="nVertLevels nCells Time" packages="activeTracersPKG" missing_value="FILLVAL" missing_value_mask="cellMask">
 				<var name="temperatureTend" array_group="activeGRP" units="C s^-1"
 			 description="time tendency of potential temperature"
 				/>

diff --git a/components/mpas-ocean/src/tracer_groups/Registry_debugTracers.xml b/components/mpas-ocean/src/tracer_groups/Registry_debugTracers.xml
@@ -49,7 +49,7 @@
 
 	<var_struct name="state" time_levs="2">
 		<var_struct name="tracers" time_levs="2">
-			<var_array name="debugTracers" dimensions="nVertLevels nCells Time" type="real" packages="debugTracersPKG" default_value="1.0">
+			<var_array name="debugTracers" dimensions="nVertLevels nCells Time" type="real" packages="debugTracersPKG" default_value="1.0" missing_value="FILLVAL" missing_value_mask="cellMask">
 				<var name="tracer1" array_group="debugGRP"
 			 description="tracer for debugging purposes"
 				/>
@@ -65,7 +65,7 @@
 
 	<var_struct name="tend" time_levs="1">
 		<var_struct name="tracersTend" time_levs="1">
-			<var_array name="debugTracersTend" type="real" dimensions="nVertLevels nCells Time" packages="debugTracersPKG">
+			<var_array name="debugTracersTend" type="real" dimensions="nVertLevels nCells Time" packages="debugTracersPKG" missing_value="FILLVAL" missing_value_mask="cellMask">
 				<var name="tracer1Tend" array_group="debugGRP"
 			 description="Tendency for tracer1"
 				/>

diff --git a/components/mpas-ocean/src/tracer_groups/Registry_ecosys.xml b/components/mpas-ocean/src/tracer_groups/Registry_ecosys.xml
@@ -89,7 +89,7 @@
 
 	<var_struct name="state" time_levs="2">
 		<var_struct name="tracers" time_levs="2">
-			<var_array name="ecosysTracers" dimensions="nVertLevels nCells Time" type="real" packages="ecosysTracersPKG" >
+			<var_array name="ecosysTracers" dimensions="nVertLevels nCells Time" type="real" packages="ecosysTracersPKG" missing_value="FILLVAL" missing_value_mask="cellMask">
 				<!-- Add constituents of tracer group -->
 				<var name="PO4" array_group="ecosysGRP" units="mmol P m^{-3}"
 					description="Dissolved Inorganic Phosphate"
@@ -193,7 +193,7 @@
 
 	<var_struct name="tend" time_levs="1">
 		<var_struct name="tracersTend" time_levs="1">
-			<var_array name="ecosysTracersTend" type="real" dimensions="nVertLevels nCells Time" packages="ecosysTracersPKG">
+			<var_array name="ecosysTracersTend" type="real" dimensions="nVertLevels nCells Time" packages="ecosysTracersPKG" missing_value="FILLVAL" missing_value_mask="cellMask">
 				<!-- Add constituents of tracer group -->
 				<var name="PO4Tend" array_group="ecosysGRP" units="mmol P m^{-3} s^{-1}"
 					description="Dissolved Inorganic Phosphate Tendency"

diff --git a/components/mpas-ocean/src/tracer_groups/Registry_idealAge.xml b/components/mpas-ocean/src/tracer_groups/Registry_idealAge.xml
@@ -41,7 +41,7 @@
 
 	<var_struct name="state" time_levs="2">
 		<var_struct name="tracers" time_levs="2">
-			<var_array name="idealAgeTracers" dimensions="nVertLevels nCells Time" type="real" packages="idealAgeTracersPKG"  default_value="0.0">
+			<var_array name="idealAgeTracers" dimensions="nVertLevels nCells Time" type="real" packages="idealAgeTracersPKG"  default_value="0.0" missing_value="FILLVAL" missing_value_mask="cellMask">
 				<var name="iAge" array_group="iAgeGRP" units="seconds" description="tracer for ideal age"
 				/>
 			</var_array>
@@ -50,7 +50,7 @@
 
 	<var_struct name="tend" time_levs="1">
 		<var_struct name="tracersTend" time_levs="1">
-			<var_array name="idealAgeTracersTend" type="real" dimensions="nVertLevels nCells Time" packages="idealAgeTracersPKG">
+			<var_array name="idealAgeTracersTend" type="real" dimensions="nVertLevels nCells Time" packages="idealAgeTracersPKG" missing_value="FILLVAL" missing_value_mask="cellMask">
 				<var name="iAgeTend" array_group="iAgeGRP" units="seconds/second" description="Tendency for iAge"
 				/>
 			</var_array>