Merge branch 'patch/13.3.1' into release

.github/ISSUE_TEMPLATE/report-a-bug-or-technical-issue.md

@@ -6,6 +6,10 @@ labels: bug
 assignees: ''
 
 ---
+
+### What institution are you from?
+Please tell us what institution you are from.
+
 ### Description of the problem
 Describe your problem here.  Describe the steps to reproduce the problem here, if possible.
 
@@ -26,4 +30,4 @@ Describe your modifications here.
 ### Software versions
 - CMake version:
 - Compilers (Intel or GNU, and version):
-- NetCDF version:
+- NetCDF version:

GeosCore/YuIMN_Code.F90

@@ -303,7 +303,7 @@ SUBROUTINE READJIMN5D( Input_Opt, RC )
   RC       = GC_SUCCESS
 
   ! Data directory path in shared disk space where files live
-  DATA_DIR = TRIM( Input_Opt%DATA_DIR ) // 'GEOS_NATIVE/TOMAS_201402/'
+  DATA_DIR = TRIM( Input_Opt%DATA_DIR ) // 'CHEM_INPUTS/TOMAS_201402/'
 
   WRITE(6,*) "Read IMN look-up tables"
 

GeosCore/planeflight_mod.F90

@@ -1546,6 +1546,11 @@ SUBROUTINE PLANEFLIGHT( Input_Opt,  State_Chm, State_Diag, &
 !  some of the legacy unit conversions were incorrect but have now been
 !  fixed. -- Bob Yantosca, 30 Jul 2021
 !
+!  Also note: The calls to Convert_Spc_Units were not necessary, and have
+!  since been removed.  Direct unit conversions for kg/kg dry -> v/v dry
+!  and kg/kg dry -> molec/cm3 are now done, which are more computationally
+!  efficient.  -- Bob Yantosca, 27 Oct 2021
+!
 ! !REVISION HISTORY:
 !  08 Jul 2002 - M. Evans - Initial version
 !  See https://github.com/geoschem/geos-chem for complete history
@@ -1700,10 +1705,6 @@ SUBROUTINE PLANEFLIGHT( Input_Opt,  State_Chm, State_Diag, &
           ! Initialize production count:
           PR = 0
 
-          ! Convert species units to [v/v]
-          CALL Convert_Spc_Units( Input_Opt, State_Chm, State_Grid, State_Met, &
-                                  'v/v dry', RC, OrigUnit=OrigUnit )
-
           ! Initialize GEOS-Chem species array
           Spc => State_Chm%Species
 
@@ -2272,7 +2273,7 @@ SUBROUTINE PLANEFLIGHT( Input_Opt,  State_Chm, State_Diag, &
                 MW_g    = State_Chm%SpcData(N)%Info%MW_g
                 VARI(V) = Spc(I,J,L,N) * ( AIRMW / MW_g )
 
-                IF ( VARI(V) < TINY ) VARI(V) = 0.e+0_fp
+                IF ( VARI(V) < TINY ) VARI(V) = 0.0_fp
 
 #ifdef TOMAS
 #ifdef BPCH_DIAG
@@ -2310,12 +2311,8 @@ SUBROUTINE PLANEFLIGHT( Input_Opt,  State_Chm, State_Diag, &
 
           ENDDO
 
-          ! Convert species units back to original unit
-          CALL Convert_Spc_Units( Input_Opt, State_Chm, State_Grid, State_Met, &
-                                  OrigUnit, RC )
-
           ! Free pointer
-          NULLIFY( Spc )
+          Spc => NULL()
 
           ! Write data for the Mth plane point out to disk
           CALL WRITE_VARS_TO_FILE( Input_Opt, State_Grid, State_Met, M, VARI )

Headers/diaglist_mod.F90

@@ -222,6 +222,7 @@ SUBROUTINE Init_DiagList ( am_I_Root, historyConfigFile, DiagList, RC )
     IsFullChem      = .FALSE.
     InDefSection    = .FALSE.
     InFieldsSection = .FALSE.
+    Name            =  ''
     LastCollName    =  ''
 
     ! Create DiagList object
@@ -259,11 +260,7 @@ SUBROUTINE Init_DiagList ( am_I_Root, historyConfigFile, DiagList, RC )
        IF ( INDEX( Line, 'Simulation name' ) > 0 ) THEN
           CALL StrSplit( Line, ':', SubStrs, N )
           SELECT CASE( To_UpperCase( ADJUSTL( SubStrs(2) ) ) )
-             CASE( 'ACIDUPTAKE', 'APM',              'BENCHMARK',            &
-                   'COMPLEXSOA', 'COMPLEXSOA_SVPOA', 'HEMCO',                &
-                   'MARINEPOA',  'RRTMG',            'STANDARD',             &
-                   'TROPCHEM',   'TOMAS12',          'TOMAS15',              &
-                   'TOMAS30',    'TOMAS40'                                  )
+             CASE( 'FULLCHEM' )
                 IsFullChem = .TRUE.
              CASE DEFAULT
                 IsFullChem = .FALSE.
@@ -274,7 +271,6 @@ SUBROUTINE Init_DiagList ( am_I_Root, historyConfigFile, DiagList, RC )
        IF ( INDEX( Line, 'Diag alt above sfc [m]' ) > 0 ) THEN
           CALL StrSplit( Line, ':', SubStrs, N )
           AltAboveSfc = TRIM( ADJUSTL( SubStrs(2) ) ) // 'm'
-          found       = .TRUE.
        ENDIF
 
        ! Update wavelength(s) with string in file
@@ -329,8 +325,13 @@ SUBROUTINE Init_DiagList ( am_I_Root, historyConfigFile, DiagList, RC )
           CALL GC_Error( ErrMsg, RC, ThisLoc, ErrorLine )
           RETURN
        ENDIF
+
+       ! Skip if there is a commment at the start of the line
        IF ( Line(1:1) == '#' ) CYCLE
 
+       ! Skip the EXPID tag at the top of the file
+       IF ( INDEX( Line, 'EXPID:' ) > 0 ) CYCLE
+
        !====================================================================
        ! Set collection name list (uncommented names only)
        !====================================================================
@@ -411,6 +412,7 @@ SUBROUTINE Init_DiagList ( am_I_Root, historyConfigFile, DiagList, RC )
           InDefSection    = .FALSE.
           InFieldsSection = .FALSE.
           LastCollName    = ''
+          CYCLE
        ENDIF
 
        !--------------------------------------------------------------------
@@ -518,7 +520,6 @@ SUBROUTINE Init_DiagList ( am_I_Root, historyConfigFile, DiagList, RC )
                 RETURN
              ENDIF
           ENDIF
-
        ENDIF
 
        !-----------------------------------------------------------------
@@ -534,7 +535,7 @@ SUBROUTINE Init_DiagList ( am_I_Root, historyConfigFile, DiagList, RC )
           IF ( AttName(1:LineInd-1) /= TRIM( LastCollName ) ) THEN
              ErrMsg = 'Attribute "' // TRIM( AttName ) // ' specifies a ' // &
                       'value for collection "'                            // &
-                      TRIM( AttName(1:LineInd-1) )                      // &
+                      TRIM( AttName(1:LineInd-1) )                        // &
                       '", but the expected collection name is "'          // &
                       TRIM( LastCollName ) // '".  This indicates that '  // &
                       'the end-of-collection delimiter (i.e. "::") is '   // &
@@ -603,8 +604,15 @@ SUBROUTINE Init_DiagList ( am_I_Root, historyConfigFile, DiagList, RC )
           name = CleanText( SubStrs(1) )
        ENDIF
 
-       ! Skip if diagnostic name is commented out
-       IF ( name(1:1) == '#' ) CYCLE
+       ! Sanity check! Skip to next line if the diagnostic name is
+       ! commented out, missing, or contains an attribute tag.
+       IF ( name(1:1)                   == '#' ) CYCLE
+       IF ( LEN_TRIM( name )            == 0   ) CYCLE
+       IF ( INDEX( name, '.template'  ) >  0   ) CYCLE
+       IF ( INDEX( name, '.frequency' ) >  0   ) CYCLE
+       IF ( INDEX( name, '.duration'  ) >  0   ) CYCLE
+       IF ( INDEX( name, '.format'    ) >  0   ) CYCLE
+       IF ( INDEX( name, '.mode'      ) >  0   ) CYCLE
 
        ! Skip if name is already in diag list
        CALL Search_DiagList( am_I_Root, DiagList, name, Found, RC )
@@ -658,12 +666,10 @@ SUBROUTINE Init_DiagList ( am_I_Root, historyConfigFile, DiagList, RC )
           CALL GC_Error( ErrMsg, RC, ThisLoc )
           RETURN
 #endif
-
           isWildcard = .TRUE.
           CALL StrSplit( name, '?', SubStrs, N )
           wildcard = SubStrs(N-1)
        ENDIF
-
        ! Get tag, if any
        isTagged  = .FALSE.
        tag = ''
@@ -672,13 +678,11 @@ SUBROUTINE Init_DiagList ( am_I_Root, historyConfigFile, DiagList, RC )
           IF ( TRIM(state) == 'DIAG' .AND. N == 2 ) THEN
              isTagged = .TRUE.
              tag = SubStrs(2)
-          ELSEIF ( TRIM(state) == 'CHEM' &
-                   .AND. N == 3 ) THEN
+          ELSE IF ( TRIM(state) == 'CHEM' .AND. N == 3 ) THEN
              isTagged = .TRUE.
              tag = SubStrs(3)
           ENDIF
        ENDIF
-
        ! Get registryID - start with the full name in HISTORY.rc
        registryID = TRIM(nameAllCaps)
        ! Then strip off the state prefix, if any
@@ -701,6 +705,7 @@ SUBROUTINE Init_DiagList ( am_I_Root, historyConfigFile, DiagList, RC )
 
        ! Get metadataID - start with the registry ID
        metadataID = registryID
+
        ! Then strip off the tag suffix, if any
        IF ( isTagged ) THEN
           LineInd = INDEX( TRIM(metadataID), '_' )

Headers/state_chm_mod.F90

@@ -2395,21 +2395,25 @@ SUBROUTINE Init_Hg_Simulation_Fields( Input_Opt, State_Chm, State_Grid,    &
 
     ! Index array: Hg0 species # <--> Hg0 category #
     ALLOCATE( State_Chm%Hg0_Id_List( State_Chm%N_Hg_CATS ), STAT=RC )
+    CALL GC_CheckVar( 'State_Chm%Hg0_Id_List', 0, RC )
     IF ( RC /= GC_SUCCESS ) RETURN
     State_Chm%Hg0_Id_List = 0
 
     ! Index array: Hg2 species # <--> Hg0 category #
     ALLOCATE( State_Chm%Hg2_Id_List( State_Chm%N_Hg_CATS ), STAT=RC )
+    CALL GC_CheckVar( 'State_Chm%Hg2_Id_List', 0, RC )
     IF ( RC /= GC_SUCCESS ) RETURN
     State_Chm%Hg2_Id_List = 0
 
     ! Index array: HgP species # <--> Hg0 category #
     ALLOCATE( State_Chm%HgP_Id_List( State_Chm%N_Hg_CATS ), STAT=RC )
+    CALL GC_CheckVar( 'State_Chm%HgP_Id_List', 0, RC )
     IF ( RC /= GC_SUCCESS ) RETURN
     State_Chm%HgP_Id_List = 0
 
     ! Hg category names
     ALLOCATE( State_Chm%Hg_Cat_Name( State_Chm%N_Hg_CATS ), STAT=RC )
+    CALL GC_CheckVar( 'State_Chm%Hg_Cat_Name', 0, RC )
     IF ( RC /= GC_SUCCESS ) RETURN
     State_Chm%Hg_Cat_Name = ''
 
@@ -2438,7 +2442,7 @@ SUBROUTINE Init_Hg_Simulation_Fields( Input_Opt, State_Chm, State_Grid,    &
        ThisSpc => NULL()
     ENDDO
 
-    ! Loop over Hg categories (except the first
+    ! Loop over Hg categories (except the first)
     DO C = 2, State_Chm%N_Hg_CATS
 
        ! Hg0 tracer number corresponding to this category
@@ -4559,7 +4563,7 @@ SUBROUTINE Init_and_Register_R8_3D( Input_Opt, State_Chm, State_Grid,      &
     CHARACTER(LEN=255) :: arrayId
 
     !========================================================================
-    ! Init_and_Register_R4_2D begins here!
+    ! Init_and_Register_R8_3D begins here!
     !========================================================================
 
     ! Initialize
@@ -4664,7 +4668,7 @@ SUBROUTINE Init_and_Register_R8_4D( Input_Opt, State_Chm, State_Grid,      &
     CHARACTER(LEN=255) :: arrayId
 
     !========================================================================
-    ! Init_and_Register_R4_2D begins here!
+    ! Init_and_Register_R8_4D begins here!
     !========================================================================
 
     ! Initialize
@@ -4846,11 +4850,11 @@ SUBROUTINE Get_Diagnostic_Name( State_Chm, perSpc,    N,        name,      &
        ! Hg simulation quantities
        !---------------------------------------------------------------------
 
-       ! Append the species name to the diagnostic name with an underscore
-       diagName = TRIM( name ) // '_' // TRIM( State_Chm%Hg_Cat_Name(N) )
+       ! Append the category name to the diagnostic name
+       diagName = TRIM( name ) // TRIM( State_Chm%Hg_Cat_Name(N) )
 
-       ! Append the species name to the diagnostic description
-       diagDesc = TRIM( desc ) // ' ' // TRIM( State_Chm%Hg_Cat_Name(N) )
+       ! Append the category name to the description
+       diagDesc = TRIM( desc ) // TRIM( State_Chm%Hg_Cat_Name(N) )
 
     ELSE
 

run/GCClassic/createRunDir.sh

@@ -976,7 +976,7 @@ if [[ "x${nested_sim}" == "xT" ]]; then
 	replace_colon_sep_val "--> NEI2011_MONMEAN" false HEMCO_Config.rc
 	replace_colon_sep_val "--> NEI2011_HOURLY"  false  HEMCO_Config.rc
     fi
-    
+
     printf "\n  -- Nested-grid simulations use global high-reoslution met fields"
     printf "\n     by default. To improve run time, you may choose to use cropped"
     printf "\n     met fields by modifying the file paths and names in HEMCO_Config.rc"
@@ -1002,17 +1002,39 @@ if [[ ${sim_name} =~ "POPs" ]]; then
 fi
 
 #--------------------------------------------------------------------
-# Change timesteps for nested-grid simulations
-# Transport should be 300s (5min); chemistry should be 600s (10min)
+# Nested-grid simulation timesteps:
+#
+# 0.25 x 0.3125 : Use reduced transport timestep = 300  s (5  min)
+#                 Use reduced chemistry timestep = 600  s (10 min)
+#
+# 0.5  x 0.625  : Use default transport timestep = 600  s (10 min)
+#                 Use default chemistry timestep = 1200 s (20 min)
+#
+# It has been shown that fullchem nested-grid simulations on 0.5 x
+# 0.625 grids will run more slowly if 300s/600s timesteps are used.
+# To avoid this slowdown, it is OK to use 600s/1200s timesteps.
+#
+# For the 0.25 x 0.3125 grids, it is necessary to use the 300s/600s
+# timesteps in order to avoid violating the Courant limit.
+#
+# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+# %%% EXCEPTION: 0.5 x 0.625 CH4 simulations will use 300s/600s %%%
+# %%% timesteps in order to avoid violating the Courant limit.  %%%
+# %%% The larger timesteps have proven to be problematic for    %%%
+# %%% CH4 simulations that are used to set up inversions.       %%%
+# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 #--------------------------------------------------------------------
-if [[ "x${domain_name}" == "xAS"     ]] || \
+if [[ "x${met_resolution}" == "x025x03125"                           ]] || \
+   [[ "x${met_resolution}" == "x05x0625" && "x${sim_name}" == "xCH4" ]];  then
+    if [[ "x${domain_name}" == "xAS"     ]] || \
        [[ "x${domain_name}" == "xEU"     ]] || \
        [[ "x${domain_name}" == "xNA"     ]] || \
        [[ "x${domain_name}" == "xcustom" ]]; then
-    cmd='s|\[sec\]: 600|\[sec\]: 300|'
-    sed_ie "$cmd" input.geos
-    cmd='s|\[sec\]: 1200|\[sec\]: 600|'
-    sed_ie "$cmd" input.geos
+	cmd='s|\[sec\]: 600|\[sec\]: 300|'
+	sed_ie "$cmd" input.geos
+	cmd='s|\[sec\]: 1200|\[sec\]: 600|'
+	sed_ie "$cmd" input.geos
+     fi
 fi
 
 # Modify default settings for GCAP simulations

run/GCHP/GCHP.rc.template

@@ -101,6 +101,11 @@ MEMORY_DEBUG_LEVEL:   0
 #
 WRITE_RESTART_BY_OSERVER: NO
 
+#
+# %%% Advection settings
+#
+EXCLUDE_ADVECTION_TRACERS: NO
+
 #
 # %%% Adjoint variables
 #

run/shared/cleanRunDir.sh

@@ -19,6 +19,8 @@ rm -fv slurm-*
 rm -fv 1
 rm -fv EGRESS
 rm -fv core.*
+rm -fv PET*.ESMF_LogFile
+rm -fv allPEs.log
 
 # Clean data too. Prompt user to confirm they want to do this.
 # perhaps asking if they want to archive before deletion.