Merge pull request #14 from GEOS-ESM/feature/ewlundgr/hco_3.8.1

HEMCO 3.8.1
GEOS-ESM · Apr 5, 2024 · 80b9f40 · 80b9f40
2 parents ccbf008 + 2ab053a
commit 80b9f40
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diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,3 @@
-[submodule "docs/source/geos-chem-shared-docs"]
+[submodule "geos-chem-shared-docs"]
 	path = docs/source/geos-chem-shared-docs
 	url = https://github.com/geoschem/geos-chem-shared-docs.git
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,7 +5,16 @@ 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] - TBD
+## [3.8.1] - 2024-04-02
+### Changed
+- Now allow up to 10 nested brackets (`((( )))`) in the `HEMCO_Config.rc` file
+- Now use short submodule names (i.e. w/o path) in `.gitmodules`
+
+### Fixed
+- Limit volcano climatology file read message to root core
+- Updated `hco_interp_mod.F90` to handle 3D NEI emissions.
+
+## [3.8.0] - 2024-02-07
 ### Changed
 - Updated TOMAS_Jeagle sea salt extension
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,7 +1,7 @@
 # HEMCO/CMakeLists.txt
 
 cmake_minimum_required(VERSION 3.5)
-project(HEMCO VERSION 3.7.2 LANGUAGES Fortran)
+project(HEMCO VERSION 3.8.1 LANGUAGES Fortran)
 # Reminder: Make sure to also update version in src/Core/hco_error_mod.F90
 
 #-----------------------------------------------------------------------------

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -23,7 +23,7 @@
 author = 'GEOS-Chem Support Team'
 
 # The full version, including alpha/beta/rc tags
-release = '3.7.2'
+release = '3.8.1'
 
 # -- General configuration ---------------------------------------------------
 
@@ -82,8 +82,11 @@ def format_web_refs(self, e):
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
-
+exclude_patterns = [
+    'geos-chem-shared-docs/README.md',
+    'geos-chem-shared-docs/supplemental-guides/species-guide.rst',
+    'geos-chem-shared-docs/supplemental-guides/using-kpp-with-gc.rst',
+]
 
 # -- Options for HTML output -------------------------------------------------
 

diff --git a/docs/source/geos-chem-shared-docs b/docs/source/geos-chem-shared-docs
diff --git a/docs/source/hco-sa-guide/login-env.rst b/docs/source/hco-sa-guide/login-env.rst
@@ -255,8 +255,7 @@ These environment variables should be defined in your
 
    HEMCOc only requires the Fortran compiler.  But you will
    also need the C and C++ compilers if you plan to build other
-   software packages (:ref:`such as KPP <kppguide>`) or :ref:`install
-   libraries manually <build-libraries-with-spack>`.
+   software packages or :ref:`install libraries manually <spackguide>`.
 
    Also, older Intel compiler versions used :envvar:`icc` as the name
    for the C compiler and :envvar:`icpc` as the name of the C++ compiler.

diff --git a/src/Core/hco_config_mod.F90 b/src/Core/hco_config_mod.F90
@@ -1366,7 +1366,7 @@ SUBROUTINE BracketCheck( HcoConfig, STAT, LINE, SKIP, RC )
 ! !LOCAL VARIABLES:
 !
     ! Maximum number of nested brackets
-    INTEGER, PARAMETER            :: MAXBRACKNEST = 5
+    INTEGER, PARAMETER            :: MAXBRACKNEST = 10
     INTEGER                       :: IDX, STRLEN, ExtNr
     LOGICAL                       :: FOUND
     LOGICAL                       :: UseBracket, UseThis

diff --git a/src/Core/hco_error_mod.F90 b/src/Core/hco_error_mod.F90
@@ -105,7 +105,7 @@ MODULE HCO_Error_Mod
 #endif
 
   ! HEMCO version number.
-  CHARACTER(LEN=12), PARAMETER, PUBLIC :: HCO_VERSION = '3.7.2'
+  CHARACTER(LEN=12), PARAMETER, PUBLIC :: HCO_VERSION = '3.8.1'
 
   INTERFACE HCO_Error
      MODULE PROCEDURE HCO_ErrorNoErr

diff --git a/src/Core/hco_interp_mod.F90 b/src/Core/hco_interp_mod.F90
@@ -500,17 +500,17 @@ SUBROUTINE ModelLev_Check( HcoState, nLev, IsModelLev, RC )
     IF ( nlev == nz .OR. nlev == nz + 1 ) THEN
        IsModelLev = .TRUE.
 
-   ! If input is 72 layer (or 36 layer) and output is 47 layer
+   ! If input is 72 layer (or 3/11/36 layer) and output is 47 layer
     ELSEIF ( nz == 47 ) THEN
-       IsModelLev = ( nlev == 72 .OR. nlev == 73 .OR. nlev == 36)
+       IsModelLev = ( nlev == 72 .OR. nlev == 73 .OR. nlev == 36 .OR. nlev == 3 .OR. nlev == 11)
 
     ! If input is 102 layer and output is 74 layer
     ELSEIF ( nz == 74 ) THEN
        IsModelLev = ( nlev == 102 .OR. nlev == 103 )
 
-    ! If input is 47 layer (or 36 layer) and output is 72 layer
+    ! If input is 47 layer (or 3/11/36 layer) and output is 72 layer
     ELSEIF ( nz == 72 ) THEN
-       IsModelLev = ( nlev == 47 .OR. nlev == 48 .OR. nlev == 36)
+       IsModelLev = ( nlev == 47 .OR. nlev == 48 .OR. nlev == 36 .OR. nlev == 3 .OR. nlev == 11)
 
     ELSE
       IsModelLev = .FALSE.
@@ -543,18 +543,19 @@ END SUBROUTINE ModelLev_Check
 ! levels, this is interpreted as native data and will be collapsed onto the 
 ! reduced GISS grid. If the input holds 47/48 input levels, this is interpreted
 ! as reduced GEOS-5 data and it will be inflated to the native GEOS-5 grid
-! (with a warning, as this is not recommended). If the input holds 36 input levels,
-! this is assumed to be the first 36 levels of the GEOS-5 grid, meaning they will be
-! written as levels 1-36 of a 47 or 72 level output grid (with the remaining values
-! left to be zero) (nbalasus, 8/29/2023).
+! (with a warning, as this is not recommended). If the input holds N input levels,
+! (where N = 3, 11, or 36 to account for NEI and AEIC emissions), this is assumed 
+! to be the first N levels of the GEOS-5 grid, meaning they will be written as 
+! levels 1-N of a 47 or 72 level output grid (with the remaining values left to
+! be zero) (nbalasus, 8/29/2023).
 !
 !
 ! Currently, this routine can remap the following combinations:
 !
 ! * Native GEOS-5 onto reduced GEOS-5 (72 --> 47 levels, 73 --> 48 edges)
 ! * Native GISS onto reduced GISS (102 --> 74 levels, 103 --> 75 edges) 
 ! * Reduced GEOS-5 onto native GEOS-5 (47 --> 72 levels, 48 --> 73 edges)
-! * 36 levels onto native/reduced GEOS-5 (36 --> levels 1-36 levels of 47/72 level grid, rest are 0)
+! * N (N = 3/11/36) levels onto native/reduced GEOS-5 (N --> levels 1-N levels of 47/72 level grid, rest are 0)
 !
 ! !INTERFACE:
 !
@@ -638,8 +639,8 @@ SUBROUTINE ModelLev_Interpolate( HcoState, REGR_4D, Lct, RC )
     IF ( ( ( nlev == nz ) .OR. ( nlev == nz+1 ) ) .OR. &                          ! write data without doing anything
          ( ( nz == 47 ) .AND. ( ( nlev == 72 ) .OR. ( nlev == 73 ) ) ) .OR. &     ! collapse native to reduced GEOS-5
          ( ( nz == 74 ) .AND. ( ( nlev == 102 ) .OR. ( nlev == 103 ) ) ) .OR. &   ! collapse native to reduced GISS
-         ( ( nz == 72 ) .AND. ( ( nlev == 47 ) .OR. ( nlev == 48 ) ) ) .OR. &   ! inflate reduced to native GEOS-5
-         ( ( ( nz == 72 ) .OR. ( nz == 47 ) ) .AND. ( nlev == 36 ) ) ) THEN         ! write 36 levels to reduced/native GEOS-5
+         ( ( nz == 72 ) .AND. ( ( nlev == 47 ) .OR. ( nlev == 48 ) ) ) .OR. &     ! inflate reduced to native GEOS-5
+         ( ( ( nz == 72 ) .OR. ( nz == 47 ) ) .AND. ( ( nlev == 3 ) .OR. ( nlev == 11 ) .OR. ( nlev == 36 ) ) ) ) THEN  ! write 3/11/36 levels to reduced/native GEOS-5
          ! do nothing
     ELSE
       WRITE(MSG,*) 'ModelLev_Interpolate was called but MESSy should have been used: ',TRIM(Lct%Dct%cName)
@@ -694,15 +695,21 @@ SUBROUTINE ModelLev_Interpolate( HcoState, REGR_4D, Lct, RC )
           ELSEIF ( nlev == 73 ) THEN
              NL   = 37
              nout = 48
+          ELSEIF ( nlev == 3 ) THEN
+             NL   = 3
+             nout = 47
+          ELSEIF ( nlev == 11 ) THEN
+             NL   = 11
+             nout = 47
           ELSEIF ( nlev == 36 ) THEN
              NL   = 36
              nout = 47
           ELSE
              MSG = 'Can only remap from native onto reduced GEOS-5 if '// &
-                   'input data has exactly 72, 73, or 36 levels: '//TRIM(Lct%Dct%cName)
+                   'input data has exactly 72, 73, 3, 11, or 36 levels: '//TRIM(Lct%Dct%cName)
              CALL HCO_ERROR( MSG, RC )
              RETURN
-          ENDIF ! nlev == (72,73,36,ELSE)
+          ENDIF ! nlev == (72,73,3,11,36ELSE)
 
           ! Make sure output array is allocated
           CALL FileData_ArrCheck( HcoState%Config, Lct%Dct%Dta, nx, ny, nout, nt, RC )
@@ -743,7 +750,15 @@ SUBROUTINE ModelLev_Interpolate( HcoState, REGR_4D, Lct, RC )
                Lct%Dct%Dta%V3(T)%Val(:,:,46) = REGR_4D(:,:,65,T)
                Lct%Dct%Dta%V3(T)%Val(:,:,47) = REGR_4D(:,:,69,T)
                Lct%Dct%Dta%V3(T)%Val(:,:,48) = REGR_4D(:,:,73,T)
-            ! If the input is 36 levels, levels 37-47 are set to 0
+            ! If the input is N (N = 3/11/36) levels, levels N+1 to 47 are set to 0
+             ELSEIF ( nlev == 3 ) THEN
+               DO L = 4,47
+                  Lct%Dct%Dta%V3(T)%Val(:,:,L) = 0.0_hp
+               ENDDO !L
+             ELSEIF ( nlev == 11 ) THEN
+               DO L = 12,47
+                  Lct%Dct%Dta%V3(T)%Val(:,:,L) = 0.0_hp
+               ENDDO !L
              ELSEIF ( nlev == 36 ) THEN
                DO L = 37,47
                   Lct%Dct%Dta%V3(T)%Val(:,:,L) = 0.0_hp
@@ -756,8 +771,8 @@ SUBROUTINE ModelLev_Interpolate( HcoState, REGR_4D, Lct, RC )
           IF ( HCO_IsVerb( HcoState%Config%Err ) ) THEN
              WRITE(MSG,*) 'Mapped ', nlev, ' levels onto reduced GEOS-5 levels.'
              CALL HCO_MSG(HcoState%Config%Err,MSG)
-             IF ( nlev == 36 ) THEN
-               WRITE(MSG,*) 'The input variable has 36 L, which were written to be L 1-36 on the output 47 L grid (remaining values set to 0).'
+             IF ( nlev == 3 .OR. nlev == 11 .OR. nlev == 36 ) THEN
+               WRITE(MSG,*) 'The input variable has ', nlev, 'L, which were written to be L 1-', nlev, ' on the output 47 L grid (remaining values set to 0).'
              ELSE
                WRITE(MSG,*) 'Pressure-weighted vertical regridding was done - consider if this is appropriate for the variable units.'
              CALL HCO_MSG(HcoState%Config%Err,MSG)
@@ -857,15 +872,21 @@ SUBROUTINE ModelLev_Interpolate( HcoState, REGR_4D, Lct, RC )
           ELSEIF ( nlev == 48 ) THEN
              NL   = 37
              nout = 73
+          ELSEIF ( nlev == 3 ) THEN
+             NL   = 3
+             nout = 72
+          ELSEIF ( nlev == 11 ) THEN
+             NL   = 11
+             nout = 72
           ELSEIF ( nlev == 36 ) THEN
              NL   = 36
              nout = 72
           ELSE
              MSG = 'Can only remap from reduced onto native GEOS-5 if '// &
-                   'input data has exactly 47, 48, or 36 levels: '//TRIM(Lct%Dct%cName)
+                   'input data has exactly 47, 48, 3, 11, or 36 levels: '//TRIM(Lct%Dct%cName)
              CALL HCO_ERROR( MSG, RC )
              RETURN
-          ENDIF ! nlev == (48,48,36,ELSE)
+          ENDIF ! nlev == (48,48,3,11,36,ELSE)
 
           ! Make sure output array is allocated
           CALL FileData_ArrCheck( HcoState%Config, Lct%Dct%Dta, nx, ny, nout, nt, RC )
@@ -924,20 +945,30 @@ SUBROUTINE ModelLev_Interpolate( HcoState, REGR_4D, Lct, RC )
                    Lct%Dct%Dta%V3(T)%Val(:,:,fineIDX) = REGR_4D(:,:,coarseIDX,T)
                 ENDDO ! I
 
+             ELSEIF ( nlev == 3 ) THEN
+               DO L = 4,72
+                  Lct%Dct%Dta%V3(T)%Val(:,:,L) = 0.0_hp
+               ENDDO !L
+
+             ELSEIF ( nlev == 11 ) THEN
+               DO L = 12,72
+                  Lct%Dct%Dta%V3(T)%Val(:,:,L) = 0.0_hp
+               ENDDO !L
+
              ELSEIF ( nlev == 36 ) THEN
                DO L = 37,72
                   Lct%Dct%Dta%V3(T)%Val(:,:,L) = 0.0_hp
                ENDDO !L
 
-             ENDIF ! nlev == (47,48,36)
+             ENDIF ! nlev == (47,48,3,11,36)
           ENDDO ! T
 
           ! Verbose
           IF ( HCO_IsVerb(HcoState%Config%Err ) ) THEN
              WRITE(MSG,*) 'Mapped ', nlev, ' levels onto native GEOS-5 levels.'
              CALL HCO_MSG(HcoState%Config%Err,MSG)
-             IF ( nlev == 36 ) THEN
-               WRITE(MSG,*) 'The input variable has 36 L, which were written to be L 1-36 on the output 72 L grid (remaining values set to 0).'
+             IF ( nlev == 3 .OR. nlev == 11 .OR. nlev == 36 ) THEN
+               WRITE(MSG,*) 'The input variable has ', nlev, 'L, which were written to be L 1-', nlev, ' on the output 72 L grid (remaining values set to 0).'
              ELSE
                WRITE(MSG,*) 'Inflating from 47/48 to 72/73 levels is not recommended and is likely not mass-conserving.'
              ENDIF

diff --git a/src/Extensions/hcox_tomas_jeagle_mod.F90 b/src/Extensions/hcox_tomas_jeagle_mod.F90
@@ -281,7 +281,7 @@ SUBROUTINE HCOX_TOMAS_Jeagle_Run( ExtState, HcoState, RC )
     ! adjusting coeff
 
     !### Debug
-    print*, 'IN HCOX_TOMAS_Jeagle_Mod.F90'
+    !print*, 'IN HCOX_TOMAS_Jeagle_Mod.F90'
 
     ! Init
     ptr3D => NULL()
@@ -530,9 +530,9 @@ SUBROUTINE HCOX_TOMAS_Jeagle_Run( ExtState, HcoState, RC )
        ! HEMCO species ID
        HcoID = HCO_GetHcoID( TRIM(SpcName), HcoState )
 
-       !### Debug
-       print*, 'Aerosol number AT 50, 10,: ', Inst%TC1(ii,jj,1,k)
-       print*, 'HCO ID: ', K, SpcName, HcoID
+       !### Debug - comment out print over random oceen box - update indices if needed bc, 18/12/23
+       !!print*, 'Aerosol number AT 1, 1,: ', Inst%TC1(ii,jj,1,k)
+       !!print*, 'HCO ID: ', K, SpcName, HcoID
 
        ! Add number to the HEMCO data structure
        CALL HCO_EmisAdd( HcoState, Inst%TC1(:,:,:,K), HcoID, RC)
@@ -1052,29 +1052,33 @@ SUBROUTINE HCOX_TOMAS_Jeagle_Init( HcoState, ExtName, ExtState, RC )
        4.02325d-01, 5.06898d-01, 6.38652d-01, 8.04651d-01, 1.01380d+00 /)
 #endif
 
+
+    !bc, 10/01/24 - comment this out as coef is not being used
     !=======================================================================
     ! Allocate quantities depending on horizontal resolution
     !=======================================================================
-    IF ( TRIM( HcoState%Config%GridRes) == '4.0x5.0' ) THEN
-
-       !-----------------------------------------------------------------------
-       ! TOMAS simulations at 4 x 5 global resolution
-       !-----------------------------------------------------------------------
-       Inst%TOMAS_COEF = 1.d0
-
-    ELSE IF ( TRIM( HcoState%Config%GridRes) == '2.0x2.5' ) THEN
-
-       !-----------------------------------------------------------------------
-       ! TOMAS simulations at 2 x 2.5 global resolution
-       !-----------------------------------------------------------------------
-       Inst%TOMAS_COEF = 1.d0
-
-    ELSE
-
-       MSG = 'Adjust TOMAS_Jeagle emiss coeff (TOMAS_COEF) for your model res: SRCSALT30: hcox_TOMAS_jeagle_mod.F90'
-       CALL HCO_ERROR(MSG, RC )
-
-    ENDIF
+!    !IF ( TRIM( HcoState%Config%GridRes) == '4.0x5.0' ) THEN !comment out for
+!    resolution independence in code and consider implementing offline SS in
+!    TOMAS
+!
+!       !-----------------------------------------------------------------------
+!       ! TOMAS simulations at 4 x 5 global resolution
+!       !-----------------------------------------------------------------------
+!       Inst%TOMAS_COEF = 1.d0
+!
+!    ELSE IF ( TRIM( HcoState%Config%GridRes) == '2.0x2.5' ) THEN
+!
+!       !-----------------------------------------------------------------------
+!       ! TOMAS simulations at 2 x 2.5 global resolution
+!       !-----------------------------------------------------------------------
+!       Inst%TOMAS_COEF = 1.d0
+!
+!    ELSE
+!
+!       MSG = 'Adjust TOMAS_Jeagle emiss coeff (TOMAS_COEF) for your model res: SRCSALT30: hcox_TOMAS_jeagle_mod.F90'
+!       CALL HCO_ERROR(MSG, RC )
+!
+!    ENDIF
 
     !=======================================================================
     ! Activate this module and the fields of ExtState that it uses

diff --git a/src/Extensions/hcox_volcano_mod.F90 b/src/Extensions/hcox_volcano_mod.F90
@@ -651,9 +651,11 @@ SUBROUTINE ReadVolcTable( HcoState, ExtState, Inst, RC )
           INQUIRE( FILE=TRIM( ThisFile ), EXIST=FileExists )
 
           ! Write message to stdout and HEMCO log
-          MSG = 'Attempting to read volcano climatology file'
-          WRITE( 6,   300 ) TRIM( MSG )             
-          CALL HCO_MSG( HcoState%Config%Err, MSG )
+          IF ( Hcostate%amIRoot ) THEN
+             MSG = 'Attempting to read volcano climatology file'
+             WRITE( 6,   300 ) TRIM( MSG )             
+             CALL HCO_MSG( HcoState%Config%Err, MSG )
+          ENDIF
 
           ! Create a display string based on whether or not the file is found
           IF ( FileExists ) THEN
+6 −0		supplemental-guides/coards-guide.rst
+3 −2		supplemental-guides/error-guide.rst
+107 −101		supplemental-guides/netcdf-guide.rst