Merge branch 'jonbob/mpaso/support-salinity-restoring' into next (PR #…

…1419)

This PR adds salinity restoring to C- and G-cases, when the appropriate data
file is available, through namelist and streams modifications. It adds a new
ocean bld variable, ocn_forcing, that has three valid options: active_atm;
core_forced; and core_forced_restoring. For grids with a valid monthly
salinity-restoring file (currently oEC60to30v3 and oRRS18to6v3), modifications
are made to mpas-o_in, streams.ocean, and mpas-o.input_data_list files. For
grids which do not yet have the required file, a warning is issued during the
case setup and the namelist/streams/input_data changes are not applied. This PR
also turns on the diurnal cycle for all C- and G-cases, regardless of the
availability of salinity-restoring files.

Note: because this codebase fails exact restart tests, it is off by default,
      even for situations in which it is fully supported. It will be made
      active by default once it does restart correctly (to be tracked by a
      separate issue).

Scripts tested with SMS.T62_oEC60to30v3.GMPAS-IAF.edison_intel and SMS.T62_oQU240.GMPAS-IAF.edison_intel.

Salinity-restoring namelist parameters tested for 250+ years with 20170320.beta0.GMPAS-IAF.T62_oECv3.anvil.

[NML]
[BFB]

cime/src/components/data_comps/datm/cime_config/namelist_definition_datm.xml

@@ -1944,6 +1944,7 @@
            steps, which is undesirable unless we truly want linear interpolation
            between multiple input values -->
       <value stream="topo.observed">lower</value>
+      <value stream="CORE2_IAF.GISS.SWDN">coszen</value>
     </values>
   </entry>
 

components/mpas-cice/bld/build-namelist

@@ -89,7 +89,7 @@ my %opts = ( help        => 0,
              preview     => 0,
              caseroot    => undef,
              casebuild   => undef,
-             cimeroot => undef,
+             cimeroot    => undef,
              inst_string => undef,
              ice_grid    => undef,
              date_stamp  => undef,

components/mpas-o/bld/build-namelist

@@ -45,6 +45,9 @@ OPTIONS
      -casebuild            CASEBUILD directory variable          
      -cimeroot             CIMEROOT directory variable
      -ocn_grid             OCN_GRID variable
+     -ocn_forcing          variable for defining if the ocn model is forced with an active atm
+                           or using CORE forcing.  
+                           Options are: active_atm, core_forced, core_forced_restoring
      -date_stamp           date_stamp variable
      -cfg_grid             Directory containing MPAS-O configuration scripts.
                            If not defined, location is set as \$ProgDir or \$cwd
@@ -87,10 +90,11 @@ my %opts = ( help        => 0,
              preview     => 0,
              caseroot    => undef,
              casebuild   => undef,
-             cimeroot => undef,
+             cimeroot    => undef,
              inst_string => undef,
              ocn_grid    => undef,
-             date_stamp    => undef,
+             ocn_forcing => undef,
+             date_stamp  => undef,
              cfg_dir     => $cfgdir,
            );
 
@@ -104,6 +108,7 @@ GetOptions(
     "cimeroot=s"    => \$opts{'cimeroot'},
     "inst_string=s" => \$opts{'inst_string'},	   
     "ocn_grid=s"    => \$opts{'ocn_grid'},
+    "ocn_forcing=s" => \$opts{'ocn_forcing'},
     "date_stamp=s"  => \$opts{'date_stamp'},
     "cfg_dir=s"     => \$opts{'cfg_dir'},
     "preview"       => \$opts{'preview'},
@@ -132,9 +137,10 @@ if ($print>=2) { print "Setting MPAS-O configuration script directory to $cfgdir
 
 my $CASEROOT    = $opts{'caseroot'};
 my $CASEBUILD   = $opts{'casebuild'};
-my $CIMEROOT = $opts{'cimeroot'};
+my $CIMEROOT    = $opts{'cimeroot'};
 my $inst_string = $opts{'inst_string'};
 my $OCN_GRID    = $opts{'ocn_grid'};
+my $OCN_FORCING = $opts{'ocn_forcing'};
 my $date_stamp  = $opts{'date_stamp'};
 $cfgdir         = $opts{'cfg_dir'};
 
@@ -1292,14 +1298,21 @@ add_default($nl, 'config_isomip_plus_effective_density');
 
 add_default($nl, 'config_use_activeTracers');
 add_default($nl, 'config_use_activeTracers_surface_bulk_forcing');
-add_default($nl, 'config_use_activeTracers_surface_restoring');
+if ($OCN_FORCING eq 'core_forced_restoring') {
+	add_default($nl, 'config_use_activeTracers_surface_restoring', 'val'=>".false.");
+	add_default($nl, 'config_use_surface_salinity_monthly_restoring', 'val'=>".false.");
+	add_default($nl, 'config_salinity_restoring_constant_piston_velocity', 'val'=>"1.585e-6");
+	add_default($nl, 'config_salinity_restoring_max_difference', 'val'=>"100.");
+} else {
+	add_default($nl, 'config_use_activeTracers_surface_restoring');
+	add_default($nl, 'config_use_surface_salinity_monthly_restoring');
+	add_default($nl, 'config_salinity_restoring_constant_piston_velocity');
+	add_default($nl, 'config_salinity_restoring_max_difference');
+}
 add_default($nl, 'config_use_activeTracers_interior_restoring');
 add_default($nl, 'config_use_activeTracers_exponential_decay');
 add_default($nl, 'config_use_activeTracers_idealAge_forcing');
 add_default($nl, 'config_use_activeTracers_ttd_forcing');
-add_default($nl, 'config_use_surface_salinity_monthly_restoring');
-add_default($nl, 'config_salinity_restoring_constant_piston_velocity');
-add_default($nl, 'config_salinity_restoring_max_difference');
 
 ###############################################
 # Namelist group: tracer_forcing_debugTracers #

components/mpas-o/cime_config/buildnml

@@ -8,20 +8,21 @@ if ($#ARGV == -1) {
 my ($CASEROOT) = @ARGV;
 chdir "${CASEROOT}";
 
-my $CIMEROOT            = `./xmlquery  CIMEROOT            -value`;
+my $CIMEROOT            = `./xmlquery  CIMEROOT			-value`;
 my $CASEROOT		= `./xmlquery  CASEROOT			-value`;
 my $CASEBUILD		= `./xmlquery  CASEBUILD		-value`;
 my $SRCROOT		= `./xmlquery  SRCROOT			-value`;
-my $OBJROOT		    = `./xmlquery  OBJROOT			-value`;
-my $COMP_INTERFACE	= `./xmlquery  COMP_INTERFACE	-value`;
-my $DIN_LOC_ROOT    = `./xmlquery  DIN_LOC_ROOT     -value`;
+my $OBJROOT		= `./xmlquery  OBJROOT			-value`;
+my $COMP_INTERFACE	= `./xmlquery  COMP_INTERFACE		-value`;
+my $DIN_LOC_ROOT	= `./xmlquery  DIN_LOC_ROOT		-value`;
 my $OCN_GRID		= `./xmlquery  OCN_GRID			-value`;
-my $OCN_MASK        = `./xmlquery  MASK_GRID            -value`;
+my $OCN_MASK		= `./xmlquery  MASK_GRID		-value`;
+my $OCN_FORCING		= `./xmlquery  MPASO_FORCING		-value`;
 my $NTASKS_OCN		= `./xmlquery  NTASKS_OCN		-value`;
 #my $NINST_OCN		= `./xmlquery  NINST_OCN		-value`;
 my $NINST_OCN = 1; # Change if you want multiple instances... though this isn't coded yet.
-my $RUNDIR		    = `./xmlquery  RUNDIR			-value`;
-my $STREAM_NAME     = 'streams.ocean';
+my $RUNDIR		= `./xmlquery  RUNDIR			-value`;
+my $STREAM_NAME		= 'streams.ocean';
 
 my @dirs = ("$CIMEROOT/utils/perl5lib");
 unshift @INC, @dirs;
@@ -42,6 +43,7 @@ my $grid_prefix = '';
 my $decomp_prefix = '';
 my $ic_date = '';
 my $ic_prefix = '';
+my $restoring_file = '';
 
 if ( $OCN_GRID eq 'oEC60to30' ) {
 	$grid_date .= '151031';
@@ -61,6 +63,7 @@ if ( $OCN_GRID eq 'oEC60to30' ) {
         $ic_date .= '161222';
         $ic_prefix .= 'oEC60to30v3';
         $decomp_prefix .= 'mpas-o.graph.info.';
+        $restoring_file .= 'sss.monthlyClimatology.PHC2_salx_040803.oEC60to30v3.nc';
 } elsif ( $OCN_GRID eq 'oEC60to30v3_ICG' ) {
         $grid_date .= '161222';
         $grid_prefix .= 'oEC60to30v3';
@@ -127,6 +130,7 @@ if ( $OCN_GRID eq 'oEC60to30' ) {
 	$ic_date .= '170111';
 	$ic_prefix .= 'oRRS18to6v3';
 	$decomp_prefix .= 'mpas-o.graph.info.';
+	$restoring_file .= 'sss.monthlyClimatology.PHC2_salx_040803.oRRS18to6v3.nc';
 } elsif ( $OCN_GRID eq 'oRRS18to6v3_ICG' ) {
 	$grid_date .= '170111';
 	$grid_prefix .= 'oRRS18to6v3';
@@ -143,13 +147,28 @@ if ( $OCN_GRID eq 'oEC60to30' ) {
 
 chdir "$CASEBUILD/mpas-oconf";
 
+#--------------------------------------------------------------------
+# Set OCN_FORCING = core_forced_restoring if restoring file is available
+#--------------------------------------------------------------------
+if ($OCN_FORCING eq 'core_forced') {
+	if ($restoring_file ne '') {
+		$OCN_FORCING = 'core_forced_restoring';
+	} else {
+		print "WARNING: Should be running with salinity restoring on!\n";
+		print "         But no file available for this grid.\n";
+	}
+}
+
 #--------------------------------------------------------------------
 # Generate input data file
 #--------------------------------------------------------------------
 
 open(my $input_list, "+>", "$CASEBUILD/mpas-o.input_data_list");
 print $input_list "mesh = $DIN_LOC_ROOT/ocn/mpas-o/$OCN_MASK/$grid_prefix.$grid_date.nc\n";
 print $input_list "ic = $DIN_LOC_ROOT/ocn/mpas-o/$OCN_MASK/$ic_prefix.$ic_date.nc\n";
+if ( $OCN_FORCING eq 'core_forced_restoring' ) {
+	print $input_list "sss = $DIN_LOC_ROOT/ocn/mpas-o/$OCN_MASK/$restoring_file\n";
+}
 #print $input_list "full_graph = $DIN_LOC_ROOT/ocn/mpas-o/$OCN_MASK/$decomp_prefix$grid_date\n";
 print $input_list "graph$NTASKS_OCN = $DIN_LOC_ROOT/ocn/mpas-o/$OCN_MASK/$decomp_prefix$grid_date.part.$NTASKS_OCN\n";
 close($input_list);
@@ -208,6 +227,7 @@ while ($inst_counter <= $NINST_OCN) {
 	$sysmod .= " -inst_string '$inst_string'";
 	$sysmod .= " -date_stamp '$grid_date'";
 	$sysmod .= " -ocn_grid '$OCN_MASK'";
+	$sysmod .= " -ocn_forcing '$OCN_FORCING'";
     # pass in OCN_MASK for now as a short-cut for the grid
     # at some point, we may want to pass both -- but for now this is simpler
 
@@ -376,6 +396,20 @@ if ( -e "$CASEROOT/SourceMods/src.mpaso/$STREAM_NAME" ) {
 	print $stream_file 'the analysis data.' . "\n";
 	print $stream_file '-->' . "\n";
 	print $stream_file '' . "\n";
+        if ($OCN_FORCING eq 'core_forced_restoring') {
+		print $stream_file '<stream name="surface_salinity_monthly_data"' . "\n";
+		print $stream_file '       type="input"' . "\n";
+		print $stream_file "       filename_template=" . '"'
+						. "$DIN_LOC_ROOT/ocn/mpas-o/$OCN_MASK/$restoring_file"
+						. '"' . "\n";
+		print $stream_file '       input_interval="none"' . "\n";
+		print $stream_file '       packages="activeTracersBulkRestoringPKG">' . "\n";
+		print $stream_file '' . "\n";
+		print $stream_file '       <var name="xtime"/>' . "\n";
+		print $stream_file '       <var name="surfaceSalinityMonthlyClimatologyValue"/>' . "\n";
+		print $stream_file '</stream>' . "\n";
+		print $stream_file '' . "\n";
+        }
 	print $stream_file '<stream name="globalStatsOutput"' . "\n";
 	print $stream_file '        type="output"' . "\n";
 	print $stream_file '        filename_template="mpaso.hist.am.globalStats.$Y-$M-$D.nc"' . "\n";

components/mpas-o/cime_config/config_component.xml

@@ -13,13 +13,26 @@
     <desc>Name of ocean component</desc>
   </entry>
 
+  <entry id="MPASO_FORCING">
+        <type>char</type>
+        <valid_values>active_atm,core_forced</valid_values>
+        <default_value>active_atm</default_value>
+        <values>
+           <value compset="MPASO_">active_atm</value>
+           <value compset="_MPASO%COREFORCED">core_forced</value>
+        </values>
+        <group>case_comp</group>
+        <file>env_case.xml</file>
+        <desc>Option to describe the MPASO surface forcing</desc>
+  </entry>
+
   <description>
     <desc compset="_MPASO">mpas ocean default:</desc>
   </description>
 
   <help>
     =========================================
-    POP naming conventions
+    MPAS-O naming conventions
     =========================================
   </help>
 

components/mpas-o/cime_config/config_compsets.xml

@@ -43,24 +43,24 @@
 
   <compset>
     <alias>CMPASO-NYF</alias>
-    <lname>2000_DATM%NYF_SLND_DICE%SSMI_MPASO_DROF%NYF_SGLC_SWAV</lname>
+    <lname>2000_DATM%NYF_SLND_DICE%SSMI_MPASO%COREFORCED_DROF%NYF_SGLC_SWAV</lname>
     <support_level>"Experimental, under development"</support_level>
   </compset>
 
   <compset>
     <alias>CMPASO-IAF</alias>
-    <lname>2000_DATM%IAF_SLND_DICE%SIAF_MPASO_DROF%IAF_SGLC_SWAV</lname>
+    <lname>2000_DATM%IAF_SLND_DICE%SIAF_MPASO%COREFORCED_DROF%IAF_SGLC_SWAV</lname>
     <support_level>Experimental, under development</support_level>
   </compset>
 
   <compset>
     <alias>GMPAS-NYF</alias>
-    <lname>2000_DATM%NYF_SLND_MPASCICE_MPASO_DROF%NYF_SGLC_SWAV</lname>
+    <lname>2000_DATM%NYF_SLND_MPASCICE_MPASO%COREFORCED_DROF%NYF_SGLC_SWAV</lname>
   </compset>
 
   <compset>
     <alias>GMPAS-IAF</alias>
-    <lname>2000_DATM%IAF_SLND_MPASCICE_MPASO_DROF%IAF_SGLC_SWAV</lname>
+    <lname>2000_DATM%IAF_SLND_MPASCICE_MPASO%COREFORCED_DROF%IAF_SGLC_SWAV</lname>
   </compset>
 
 </compsets>

components/mpas-o/driver/ocn_comp_mct.F

@@ -50,6 +50,7 @@ module ocn_comp_mct
    use ocn_frazil_forcing
    use ocn_surface_land_ice_fluxes
    use ocn_diagnostics
+   use ocn_tracer_surface_restoring
 
 !
 ! !PUBLIC MEMBER FUNCTIONS:
@@ -195,6 +196,9 @@ subroutine ocn_init_mct( EClock, cdata_o, x2o_o, o2x_o, NLFilename )!{{{
     logical, pointer :: tempLogicalConfig
     character(len=StrKIND), pointer :: tempCharConfig
 
+    logical, pointer :: config_use_activeTracers_surface_restoring
+    logical, pointer :: config_use_surface_salinity_monthly_restoring
+
     real (kind=RKIND) :: dt
     type (MPAS_timeInterval_type) :: timeStep
 
@@ -731,6 +735,17 @@ end subroutine xml_stream_get_attributes
     call mpas_get_time(curr_time=currTime, dateTimeString=timeStamp, ierr=ierr)
     call mpas_log_write( 'Initial time '//trim(timeStamp))
 
+    ! read initial data required for monthly surface salinity restoring
+    call mpas_pool_get_config(domain % configs, 'config_use_activeTracers_surface_restoring',  &
+                                                 config_use_activeTracers_surface_restoring)
+    call mpas_pool_get_config(domain % configs, 'config_use_surface_salinity_monthly_restoring',  &
+                                                 config_use_surface_salinity_monthly_restoring)
+    if (config_use_activeTracers_surface_restoring .and. config_use_surface_salinity_monthly_restoring) then
+      call mpas_timer_start('io_monthly_surface_salinity',.false.)
+      call ocn_get_surfaceSalinityData(domain_ptr % streamManager, domain, domain % clock, .true.)
+      call mpas_timer_stop('io_monthly_surface_salinity')
+    endif
+
     itimestep = 0
 
     ! Reset all output alarms, to prevent intial time step from writing any output, unless it's ringing.
@@ -799,7 +814,10 @@ subroutine ocn_run_mct( EClock, cdata_o, x2o_o, o2x_o)!{{{
       integer :: iam, ierr, streamDirection
       logical :: streamActive, debugOn
       logical, pointer :: config_write_output_on_startup
+      logical, pointer :: config_use_activeTracers_surface_restoring
+      logical, pointer :: config_use_surface_salinity_monthly_restoring
       character (len=StrKIND), pointer :: config_restart_timestamp_name
+      character (len=StrKIND), pointer :: config_forcing_restart_file
 
       ! Added for coupling interval initialization
       integer, pointer :: index_avgZonalSSHGradient, index_avgMeridionalSSHGradient
@@ -822,6 +840,7 @@ subroutine ocn_run_mct( EClock, cdata_o, x2o_o, o2x_o)!{{{
       if (debugOn) call mpas_log_write("=== Beginning ocn_run_mct ===")
 
       call mpas_pool_get_config(domain_ptr % configs, 'config_restart_timestamp_name', config_restart_timestamp_name)
+      call mpas_pool_get_config(domain_ptr % configs, 'config_forcing_restart_file', config_forcing_restart_file)
 
       ! Setup log information.
       call shr_file_getLogUnit (shrlogunit)
@@ -944,8 +963,24 @@ subroutine ocn_run_mct( EClock, cdata_o, x2o_o, o2x_o)!{{{
          call mpas_stream_mgr_reset_alarms(domain % streamManager, direction=MPAS_STREAM_OUTPUT, ierr=ierr)
          if (iam==0.and.debugOn) then
             call mpas_log_write('   Finished writing output streams')
+            call mpas_log_write('   Reading forcing streams')
+         endif
+
+         ! read next time level data required for monthly surface salinity restoring
+         call mpas_pool_get_config(domain % configs, 'config_use_activeTracers_surface_restoring',  &
+                                                      config_use_activeTracers_surface_restoring)
+         call mpas_pool_get_config(domain % configs, 'config_use_surface_salinity_monthly_restoring',  &
+                                                      config_use_surface_salinity_monthly_restoring)
+         if (config_use_activeTracers_surface_restoring .and. config_use_surface_salinity_monthly_restoring) then
+           call mpas_timer_start('io_monthly_surface_salinity',.false.)
+           call ocn_get_surfaceSalinityData(domain % streamManager, domain, domain % clock, .false.)
+           call mpas_timer_stop('io_monthly_surface_salinity')
+         endif
+         if (iam==0.and.debugOn) then
+            call mpas_log_write('   Finished reading forcing streams')
             call mpas_log_write('   Validating ocean state')
          endif
+
          call ocn_validate_state(domain, timeLevel=1)
          if (debugOn) call mpas_log_write('   Completed validating ocean state')
          if (debugOn) call mpas_log_write('Completed timestep '//trim(timeStamp))
@@ -997,7 +1032,14 @@ subroutine ocn_run_mct( EClock, cdata_o, x2o_o, o2x_o)!{{{
             open(22, file=config_restart_timestamp_name, form='formatted', status='replace')
             write(22, *) trim(timeStamp)
             close(22)
+
+            open(22, file=config_forcing_restart_file, form='formatted', status='replace')
+            close(22)
          end if
+
+         if (config_use_activeTracers_surface_restoring .and. config_use_surface_salinity_monthly_restoring)  &
+             call ocn_salinity_restoring_forcing_write_restart(domain_ptr)
+
          if (debugOn) call mpas_log_write('Finished writing restart streams')
       end if