Merging Feature/saraqzhang/ladasdev w/ latest branch of DAS - before going to develop

src/Applications/GEOSdas_App/CMakeLists.txt

@@ -11,7 +11,8 @@ set(dasscripts
     fvsens            
     fvsvec            
     g54dvar           
-    fp_seamless       
+    fp_seamless 
+    ldas_run.csh       
     read_HIST.csh )
 
 set(extraperlscripts

src/Applications/GEOSdas_App/GEOSdas.csm

@@ -1901,6 +1901,7 @@ exit 1
        /bin/cp $FVHOME/recycle/$EXPID.ana_radstat_rst.*.tar radstat
      endif
 
+
      # GAAS restart files
      #-------------------
      if ( ! $DO4DVAR ) then
@@ -3229,56 +3230,6 @@ endif
 
 #.............................................................................
 
-# ------------------------------
-  Sub LandAnalysisRun_() 
-# ------------------------------
-  if ( $?ECHO___ ) set echo
-
-  cd $FVWORK
-  set rstdate = ( `rst_date ./d_rst` )
-  set mydate = (`tick $rstdate -21600`)  # tick back 6 hours
-
-  set DURATION = "060000"
-  set SUBDIR = "ldas.$mydate[1].$mydate[2]"
-  set LDINPUT_FORCE = "$FVWORK"
-  set EXPDOMAIN = "GLOBAL"
-  set RESOLUTION = "144x91"
-  set THREEHOURS = 10800
-
-  ldsetup -expid $EXPID \
-          -nymd $mydate[1] \
-          -nhms $mydate[2] \
-          -duration $DURATION \
-          -fvroot $FVROOT \
-          -fvhome $FVHOME \
-          -fvwork $FVWORK \
-          -fvwork_subdir $SUBDIR \
-          -expdomain $EXPDOMAIN \
-          -resolution $RESOLUTION \
-          -ldinput_force $FVWORK \
-          -mettag $EXPID \
-          -forcedtstep $THREEHOURS \
-          -rstrtdir $FVWORK \
-          -rstrtid $EXPID \
-          -gid $GID \
-          -noprompt
-
-  echo y | lenkf.pl
-
-# Move output to top FVWORK directory
-# -----------------------------------
-  cd $FVWORK
-  foreach file ( `find $SUBDIR -name $EXPID\*.txt`)
-     /bin/mv $file .
-  end
-  foreach file ( `find $SUBDIR -name $EXPID\.ens\*`)
-     /bin/mv $file .
-  end
-
-                              # Last line of LandAnalysisRun_()
-\end
-
-#.............................................................................
 
 # ------------------------------
   Sub EvolveAinc0_( Viter_, Final_ )
@@ -5742,6 +5693,13 @@ endif
               /bin/cp $EXPID.ana_radstat_rst.$rtag.tar $RSTHOLD/ &
             endif
 
+        # hold lfo files for the next segment of ldas coupling
+        #----------------------------------------------------------
+           if  ( $LDAS_ANA ) then
+           mkdir -p       $FVHOME/recycle/holdforc
+          /bin/cp  *2d_lfo*nc4  $FVHOME/recycle/holdforc/.
+           endif
+
         # local copy to be moved by pesto, 2nd copy to be dealt w/ by recycle
         #--------------------------------------------------------------------
         if ( -e biasinp.$RSTSUFFIX ) then

src/Applications/GEOSdas_App/fvpsas

@@ -112,6 +112,7 @@
 #  30May2013 Todling    Add GetAODinfo4Fcst_ to retrieve AOD fields for fcsts
 #  13Jun2020 Todling    Time aerosol analysis
 #  19Oct2020 Todling    Call to JEDI analysis
+#  10Mar2021 sqzhang    Add call to LandAnalysis when coupling 
 #
 #-----------------------------------------------------------------------------
 
@@ -416,6 +417,24 @@
 
          endif
 
+#--------------------------------------
+#        Run Land analysis
+#        -----------------
+
+         if ( $LDAS_ANA ) then
+            echo "  LDAS coupling: fvpsas LDAS_ANA  run lenkf "
+                                                       zeit_ci.x ldasRun
+         ldas_run.csh 0 060000 |& tee -a ldasrun.log
+         if( $status) then
+            echo "ldasRun failed"
+            exit(1)
+         endif
+                                                       zeit_co.x ldasRun
+         endif
+
+##---------------------------------
+
+
 #        Run the analysis if not doing replay
 #        -----------------------------------
          if ( ! -e replay.acq ) then
@@ -474,6 +493,22 @@
             endif
          endif
 
+#------------------------------------------------
+#  check ldas job status and stage ldas increments 
+#--------------------------------------------------
+       if ( ( $LDAS_ANA ) && ( $LDASFDBK ) ) then
+        echo " LDAS coupling: stage 1"
+                                                      zeit_ci.x ldasStage
+       ldas_run.csh 1 060000 |& tee -a ldasrun.log
+      if( $status) then
+            echo "ldas_run stage 1  failed"
+            exit(1)
+         endif
+                                                       zeit_co.x ldasStage
+  endif
+
+#-----------------------
+
 #        Convert analysis eta file into GCM restart
 #        ------------------------------------------
                                                        zeit_ci.x AnaToGcm
@@ -511,14 +546,6 @@
          Call RenameRstCheckPoint_( 1 )
                                                        zeit_co.x RenameRstCheckPoint
 
-#        Run Land analysis
-#        -----------------
-         if ( $LDAS_ANA ) then         
-                                                       zeit_ci.x LandAnalysisRun
-              Call LandAnalysisRun_()
-                                                       zeit_co.x LandAnalysisRun
-         endif
-
 #        Run the vortex tracker
 #        ----------------------
                                                        zeit_ci.x VortexTrack

src/Applications/GEOSdas_App/fvsetup

@@ -375,7 +375,7 @@ my $SECS_PER_DAY = $SECS_PER_HR * $HRS_PER_DAY;
 
 my ($res, $hres);
 my ($g5hist_rc, $g5prog_rc);
-my ($gocart_tracers, $radcor, $emiss, $lsmodel_flag, $rroute_flag);
+my ($gocart_tracers, $radcor, $emiss, $lsmodel_flag, $ldas_flag, $rroute_flag);
 my ($agcm_rst_flg, $sensdeg, %setupfile, @otherheaders);
 my ($checkFLG, $dbqueue, $runjobFLG, $saveFLG, $stopFLG);
 my (@fvprompt, @fvANS1, @fvANS2, $fvsetupflags);
@@ -509,7 +509,7 @@ $ENV{"PATH"} = $FindBin::Bin .":$ENV{PATH}";
   while3 ( \&set_rcov );
   while3 ( \&set_acftbias );
   while3 ( \&set_newradbc ); 
-  while3 ( \&set_ldasANA  );
+  while3 ( \&set_ldasANA  );  
   while3 ( \&get_forecast );
   if ($DAO == 0) { while3 ( \&get_mhost ) }
   while3 ( \&get_output );
@@ -520,7 +520,7 @@ $ENV{"PATH"} = $FindBin::Bin .":$ENV{PATH}";
 
 # Create subdirectories in FVHOME
 # -------------------------------
-  mkdir_fvhome();
+  mkdir_fvhome(); 
 
 # Create Namelists/tables for main DAS run
 # ----------------------------------------
@@ -570,6 +570,20 @@ $ENV{"PATH"} = $FindBin::Bin .":$ENV{PATH}";
   $rc = system("$fvbin/fix_gocart_rc.csh $vres $fvhome/run/gocart");
   die "Failed to fix GOCART levels-referencing $!" if ( $rc );
 
+# LDAS Setup is done separately, follow instructions in GEOSldas/README.md   
+# ------------------------------------------------------------------------
+    print "\n checkprintout  ldas_ana == 1 ($ldas_ana)\n";
+    if ($ldas_ana == 1 ) {
+    print "\n Please run ldas_setup following instructions in GEOSldas/README.md\n";
+    print "\n requires config input files: YOUR_exeinp.txt, YOUR_batinp.txt.\n" ;
+    print "\n example LDROOT: /discover/nobackup/$user/GEOSldas\n" ;
+    print "\n example LDHOME: /discover/nobackup/$user/ldascoup_C180\n" ;
+    print "\n example cd $LDROOT/install/bin/ \n";
+    print "\n example salloc \n";
+    print "\n example source g5_modules \n" ;
+    print "\n example ldas_setup setup $LDHOME exp_exeinp.txt exp_batinp.txt \n" ;
+      }
+
 # Monthly Setup
 # -------------------------------------------------------------
 # [this must be after HISTORY.rc.tmpl and silo.arc are created]
@@ -3353,23 +3367,41 @@ sub set_newradbc {
 sub set_ldasANA {
 
     # initialize Land DAS processing flag
-    #------------------------------------
-    $ldasANA = 0;
-
-    # query for processing flag, if LDAS executable found
-    #----------------------------------------------------
-    if (-e "$fvbin/LDASsa_assim_seq.x") {
+    #------------------------------------ 
+    my($dflt, $ans1, $ans2, $ans3, $ans4);
+    $ldas_ana = 0;
+    $ldasfdbk = 0;
+    $ldas_flag = 0;
+    $dflt = "n";
 
         print "\n-------------\n";
         print   "LDAS Analysis\n";
         print   "-------------\n\n";
 
-        $ans = query("  Land DAS Analysis (y/n)?", "n");
-        $ldasANA = 1 if yes($ans);
-    }
+        $ans1 = query("  Land DAS Analysis (y/n)?", $dflt) ;
+        $ldas_ana = 1 if yes($ans1);
+        print " ldas_ana ($ldas_ana)\n " ;
+
+       if ($ldas_ana == 1) {
+          $ans2 = query("  Enable LDAS feedback to model y/n ? ", $dflt);
+          $ldasfdbk = 1 if yes($ans2);
+          print " ldasfdbk ($ldasfdbk)\n" ;
+
+          if ($ldasfdbk ==1 ) {
+          $ldas_flag = 1
+          }
+
+          $ans3 = query("LDAS HOME = /discover/nobackup/$user/$ldasexp, full path?  ");
+          $ldashome = $ans3 ;
+
+          $ans4 = query("LDAS HOME for atm_ens = /discover/nobackup/$user/$ldasexp4ens, full path?  ");
+          $ldashome4ens = $ans4 ;
+
+         } 
     return 0;
 }
 
+
 #=======================================================================
 sub get_setgsi {
 
@@ -3584,6 +3616,8 @@ EOF
   $replace{">>>EXPID<<<"} = $expid;
   $replace{">>>JOBNJ<<<"} = "$jobn.j";
   $replace{">>>FVHOME<<<"} = "$fvhome";
+  $replace{">>>LDAS_ANA<<<"} = $ldas_ana;
+  $replace{">>>LDHOME4ens<<<"} = "$ldashome4ens";
 
   $atm_ens_j = "$fvhome/run/atm_ens.j";
   $atm_ens_j_tilde = "${atm_ens_j}~";
@@ -4282,9 +4316,9 @@ sub get_history {
 
     # verify that HISTORY.rc.tmpl has collections needed by LDAS
     #-----------------------------------------------------------
-    if ( $ldasANA ) {
+    if ( $ldas_ana == 1 ) {
         $verify = 0;
-        @ldasinputs = qw / diag_sfc bkg.eta /;
+          @ldasinputs = qw / tavg1_2d_lfo inst1_2d_lfo /;
         foreach $prod ( @ldasinputs ) {
             open HIST, "< $fvroot/etc/$g5hist_rc";
             unless ( grep /$prod/, <HIST> ) {
@@ -4301,7 +4335,7 @@ sub get_history {
                 . "  2. Select again\n\n";
             $ans = query("  Choose option 1 or 2:", "2");
             return 1 unless $ans eq "1";
-        }          
+        }      
     }
     print "  Using HISTORY template: $g5hist_rc\n";
 
@@ -5206,12 +5240,11 @@ sub secs2hhmmss {
 
 #=========================================================================
 sub mkdir_fvhome {  # create directories on FVHOME
-
   print "\nSetting up FVHOME directory for $expid experiment ...\n";
   foreach $dir (qw(ana diag daotovs etc obs prog radmon)) {
       mkpath("$fvhome/$dir") or die ">>> ERROR <<< creating directory $fvhome/$dir;";
   }
-  foreach $dir (qw(rs run recycle fcst asens anasa)) {
+  foreach $dir (qw(rs run recycle fcst lana asens anasa)) {
       mkpath("$fvhome/$dir") or die ">>> ERROR <<< creating directory $fvhome/$dir;";
   }
   foreach $subdir (qw( gaas gocart )) {
@@ -7662,7 +7695,10 @@ print  SCRIPT <<"EOF";
   setenv GAAS_ANA $gaas_ana # 1 = aerosol analysis, 0 = disables it
   setenv GAASFDBK $gaasfdbk # 1 = feedback aerosol analysis into GCM, 0 = don't
   setenv SKIP_PSAS 0 #  sets do_you_want_to_skip_PSAS in ana.rc.tmpl; 0 = no, 1 = yes
-  setenv LDAS_ANA $ldasANA  # 0 = don't run Land DAS Analysis; 1 = run LDAS
+  setenv LDAS_ANA $ldas_ana # 1 = land analysis, 0 = disables it 
+  setenv LDASFDBK $ldasfdbk # 1 = read land analysis incr into GCM (feedback), 0 = don't 
+  setenv LDHOME  $ldashome  # land analysis home dir (ldas_exp/) for central 
+  setenv LDHOME4ens $ldashome4ens  # land analysis home dir for atm_ens  
   setenv IGNORE_0 1   # 1 = ignore 0 length obs files in acquire
   setenv ACFTBIAS $acftbias
   setenv USE_MODIS_STAGE 0  # 1 = use MODIS data from MODIS_STAGE_DIR; 0 = don't
@@ -9457,6 +9493,7 @@ sub init_agcm_rc {
     $flags{"iau"}            = $doiau;
     $flags{"pcp_forced"}     = $pcp_forced;
     $flags{"lsmodel_flag"}   = $lsmodel_flag;
+    $flags{"ldas_flag"}      = $ldas_flag;
     set_AGCM_flags(%flags);
 
     # $num_readers must divide evenly into $ny
@@ -9569,6 +9606,7 @@ sub init_agcm_rc {
     AGCM_label_subst("\@LSM_CHOICE" , $lsmodel_flag);
     AGCM_label_subst("\@RUN_ROUTE" , $rroute_flag);
     AGCM_label_subst("\@NUM_READERS" , "1");
+    AGCM_label_subst("\@LDAS_INCR"   , $ldas_flag);
 
     #  Choice of LSM parameters
     if ( "$landbcs" eq "Icarus-NLv3" ) {