geoschem · yantosca · Feb 21, 2022 · May 23, 2022 · May 25, 2022 · Aug 15, 2022
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased 3.8.0] - TBD
+### Changed
+- Updated TOMAS_Jeagle sea salt extension
+
+### Fixed
+- Updated IsModelLevel check for CESM and WRF-GC
+
 ## [3.7.2] - 2023-12-01
 ### Added
 - Script `.release/changeVersionNumbers.sh` to change version numbers before a new HEMCO release
@@ -111,14 +118,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [3.5.2] - 2022-11-29
 ### Added
-- Added sanitizer option for detecting memory leaks in HEMCO
-    standalone during build
+- Added sanitizer option for detecting memory leaks in HEMCO standalone during build
 
 ### Changed
 - Remove unused, commented-out code in `src/Extensions/hcox_dustdead_mod.F`
-- Replaced placeholder error messages in
-    `src/Core/hco_config_mod.F90` with more informational messages
-    (often including the line of the HEMCO_Config.rc in the printout)
+- Replaced placeholder error messages in `src/Core/hco_config_mod.F90` with more informational messages (often including the line of the HEMCO_Config.rc in the printout)
 - Added improved documentation for time cycle flag `EFYO` in ReadTheDocs
 
 ### Fixed
@@ -132,8 +136,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Support for MAPL 2.16 (needed by GCHP and GEOS)
 - Bug fix for HEMCO standalone run directory creation
-- Bug fix: If HEMCO masks are specified as `lon1/lat1/lon2/lat2`,
-    then don't try to read from disk
+- Bug fix: If HEMCO masks are specified as `lon1/lat1/lon2/lat2`, then don't try to read from disk
 - Documentation from the GEOS-Chem wiki (now on ReadTheDocs)
 - Badges for the ReadTheDocs front page
 - Bug fix for masking issues in MPI environment (for WRF, CESM)
@@ -276,6 +279,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Bug fix for distributing emissions in the vertical dimension
 - New error checks in the HEMCO standalone module
 - Bug fix for `ifort` compiler in soil NOx extension
+
 ### Removed
 - Null string character from netCDF unit string
 
@@ -291,8 +295,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [2.1.004] - 2017-12-30
 ### Added
-- Updates to remove possible issues and excessive print statements when
-    operating in GEOS environment
+- Updates to remove possible issues and excessive print statements when operating in GEOS environment
 - Fixed possible tracer ID mismatch in sea salt extension
 - New option to normalize MEGAN LAI, HEMCO diagnostics
 - Now write multiple time slices into one file
@@ -375,8 +378,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [1.1.009] - 2015-09-10
 ### Added
-- Bug fixes to allow specifying flexible diagnostics output
-    frequencies.
+- Bug fixes to allow specifying flexible diagnostics output frequencies.
 
 ## [1.1.008] - 2015-07-06
 ### Added

diff --git a/src/Core/hco_arr_mod.F90 b/src/Core/hco_arr_mod.F90
@@ -1638,6 +1638,9 @@ SUBROUTINE HCO_ArrCleanup_2D_Hp( Arr, DeepClean )
        DEALLOCATE( Arr )
     ENDIF
 
+    ! Make sure we return a null pointer
+    Arr => NULL()
+
   END SUBROUTINE HCO_ArrCleanup_2D_Hp
 !EOC
 !------------------------------------------------------------------------------
@@ -1685,6 +1688,9 @@ SUBROUTINE HCO_ArrCleanup_2D_Sp( Arr, DeepClean )
        DEALLOCATE( Arr )
     ENDIF
 
+    ! Make sure we return a null pointer
+    Arr => NULL()
+
   END SUBROUTINE HCO_ArrCleanup_2D_Sp
 !EOC
 !------------------------------------------------------------------------------
@@ -1732,6 +1738,9 @@ SUBROUTINE HCO_ArrCleanup_2D_I( Arr, DeepClean )
        DEALLOCATE( Arr )
     ENDIF
 
+    ! Make sure we return a null pointer
+    Arr => NULL()
+
   END SUBROUTINE HCO_ArrCleanup_2D_I
 !EOC
 !------------------------------------------------------------------------------
@@ -1778,6 +1787,10 @@ SUBROUTINE HCO_ArrCleanup_3D_Hp( Arr, DeepClean )
        CALL HCO_ValCleanup( Arr%Val, Arr%Alloc, DeepClean=DC )
        DEALLOCATE( Arr )
     ENDIF
+
+    ! Make sure we return a null pointer
+    Arr => NULL()
+
   END SUBROUTINE HCO_ArrCleanup_3D_Hp
 !EOC
 !------------------------------------------------------------------------------
@@ -1825,6 +1838,9 @@ SUBROUTINE HCO_ArrCleanup_3D_Sp( Arr, DeepClean )
        DEALLOCATE( Arr )
     ENDIF
 
+    ! Make sure we return a null pointer
+    Arr => NULL()
+
   END SUBROUTINE HCO_ArrCleanup_3D_Sp
 !EOC
 !------------------------------------------------------------------------------
@@ -1876,6 +1892,9 @@ SUBROUTINE HCO_ArrVecCleanup_2D_Hp( ArrVec, DeepClean )
 
     ENDIF
 
+    ! Make sure we return a null pointer
+    ArrVec => NULL()
+
   END SUBROUTINE HCO_ArrVecCleanup_2D_Hp
 !EOC
 !------------------------------------------------------------------------------
@@ -1927,6 +1946,9 @@ SUBROUTINE HCO_ArrVecCleanup_2D_Sp( ArrVec, DeepClean )
 
     ENDIF
 
+    ! Make sure we return a null pointer
+    ArrVec => NULL()
+
   END SUBROUTINE HCO_ArrVecCleanup_2D_Sp
 !EOC
 !------------------------------------------------------------------------------
@@ -1978,6 +2000,9 @@ SUBROUTINE HCO_ArrVecCleanup_3D_Hp( ArrVec, DeepClean )
 
     ENDIF
 
+    ! Make sure we return a null pointer
+    ArrVec => NULL()
+
   END SUBROUTINE HCO_ArrVecCleanup_3D_Hp
 !EOC
 !------------------------------------------------------------------------------
@@ -2029,6 +2054,9 @@ SUBROUTINE HCO_ArrVecCleanup_3D_Sp( ArrVec, DeepClean )
 
     ENDIF
 
+    ! Make sure we return a null pointer
+    ArrVec => NULL()
+
   END SUBROUTINE HCO_ArrVecCleanup_3D_Sp
 !EOC
 !------------------------------------------------------------------------------

diff --git a/src/Core/hco_tidx_mod.F90 b/src/Core/hco_tidx_mod.F90
@@ -285,6 +285,7 @@ SUBROUTINE tIDx_Cleanup( AlltIDx )
     ! tIDx_Cleanup begins here!
     !======================================================================
 
+    ! Deallocate fields
     IF ( ASSOCIATED( AlltIDx ) ) THEN
 
        IF ( ASSOCIATED(AlltIDx%CONSTANT) ) THEN
@@ -307,9 +308,18 @@ SUBROUTINE tIDx_Cleanup( AlltIDx )
           DEALLOCATE(AlltIDx%MONTHLY)
        ENDIF
 
-       ! Also deallocate AlltIDx pointer
+       ! Nullify fields
+       AlltIDx%CONSTANT    => NULL()
+       AlltIDx%HOURLY      => NULL()
+       AlltIDx%HOURLY_GRID => NULL()
+       AlltIDx%WEEKDAY     => NULL()
+       AlltIDx%MONTHLY     => NULL()
+
+       ! Deallocate container
        DEALLOCATE( AlltIDx )
     ENDIF
+
+    ! Make sure we return a null pointer
     AlltIDx => NULL()
 
   END SUBROUTINE tIDx_Cleanup

diff --git a/src/Core/hcoio_read_std_mod.F90 b/src/Core/hcoio_read_std_mod.F90
@@ -695,12 +695,39 @@ SUBROUTINE HCOIO_Read( HcoState, Lct, RC )
        ! going to 72 levels. Otherwise, use MESSy (nbalasus, 8/24/2023).
        IF ( Lct%Dct%Dta%Levels == 0 ) THEN
 
+#if defined( MODEL_CESM ) || defined( MODEL_WRF )
+
+          ! In WRF/CESM, IsModelLevel has a different meaning of "GEOS-Chem levels"
+          ! because the models in WRF and CESM are user-defined and thus fixed input
+          ! files would never be on the model level. In this case, a check is added
+          ! in order to match the file with known GEOS-Chem levels, and if so, the
+          ! data will be handled later in this file accordingly to be vertically
+          ! regridded to the runtime model levels using MESSy.
+          ! This fixes a regression from the vertical regridding fixes in 3.7.1.
+          !
+          ! The meaning of "is model levels" in WRF and CESM are different.
+          ! Model levels can be changed and thus data is never on the model level.
+          ! In this case, IsModelLevel means that the data is on standard
+          ! GEOS-Chem levels, and if so, the data will be handled accordingly
+          ! using a hard-coded set of GEOS-Chem levels to be interpolated using MESSy.
+          ! (hplin, 10/15/23)
+          IF ( TRIM(LevUnit) == "level" .or. TRIM(LevUnit) == "GEOS-Chem level" ) THEN
+          ! the below check will be obsolete and is unmaintainable, but would be consistent with ModelLev_Check.
+          ! it is more robust to check for the explicit intention of LevUnit
+          !     nlev == 47 .or. nlev == 48 .or. nlev == 36 .or. nlev == 72 .or. nlev == 73 ) THEN
+              IsModelLevel = .true.
+          ENDIF
+
+#else
+
           CALL ModelLev_Check( HcoState, nlev, IsModelLevel, RC )
           IF ( RC /= HCO_SUCCESS ) THEN
               CALL HCO_ERROR( 'ERROR 3', RC, THISLOC=LOC )
               RETURN
           ENDIF
 
+#endif
+
           ! Set level indeces to be read
           lev1 = 1
           lev2 = nlev

diff --git a/src/Extensions/hcox_tomas_dustdead_mod.F b/src/Extensions/hcox_tomas_dustdead_mod.F
@@ -517,15 +517,15 @@ SUBROUTINE HCOX_TOMAS_DustDead_Run( ExtState, HcoState, RC )
 
 ! Get the proper species name
 !%%% This is a kludge, do better later %%%
-            IF ( N==1  ) SpcName = 'NK1'
-            IF ( N==2  ) SpcName = 'NK2'
-            IF ( N==3  ) SpcName = 'NK3'
-            IF ( N==4  ) SpcName = 'NK4'
-            IF ( N==5  ) SpcName = 'NK5'
-            IF ( N==6  ) SpcName = 'NK6'
-            IF ( N==7  ) SpcName = 'NK7'
-            IF ( N==8  ) SpcName = 'NK8'
-            IF ( N==9  ) SpcName = 'NK9'
+            IF ( N==1  ) SpcName = 'NK01'
+            IF ( N==2  ) SpcName = 'NK02'
+            IF ( N==3  ) SpcName = 'NK03'
+            IF ( N==4  ) SpcName = 'NK04'
+            IF ( N==5  ) SpcName = 'NK05'
+            IF ( N==6  ) SpcName = 'NK06'
+            IF ( N==7  ) SpcName = 'NK07'
+            IF ( N==8  ) SpcName = 'NK08'
+            IF ( N==9  ) SpcName = 'NK09'
             IF ( N==10 ) SpcName = 'NK10'
             IF ( N==11 ) SpcName = 'NK11'
             IF ( N==12 ) SpcName = 'NK12'