Merge pull request #1247 from geoschem/feature/geoschem_14.5_and_dependencies

cam6_4_090: GEOS-Chem 14.5 and dependencies

This tag updates the following externals:
 - GEOS-Chem from version 14.4.3 to 14.5.3
 - Cloud-J from 7.7.3 to 8.0.1
 - HEMCO_CESM from 2.1.0 to 2.2.0
- HEMCO (external within HEMCO_CESM) from 3.9.0 to 3.10.3

All of these externals have their own Changelog listing changes between these versions.
There is also more information per version accessible from the GEOS-Chem versions page
(https://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_versions)
including benchmark results comparing GEOS-Chem 14.4 and 14.5.

The most notable changes are:

 - New chemistry features:
    - Added chemistry for RCOOH, monoterpenes, new PNs and ANs from Travis et al. (2024)
    - Added fixes for ALK4 and R4N2 chemistry from Brewer et al. (2023, JGR)
    - Added PPN photolysis from Horner et al (2024)
    - Added seasalt Ca, K, Mg in HETP aerosol thermodynamics
    - Added UV absorption by water in Cloud-J photolysis
 - HEMCO logging goes to atm.log rather than cesm.log
 - All camchem_hco tests (CAM-chem with HEMCO) pass (fixes #856 and #1018)
 - Bug fix for HEMCO vertical regridding (fixes #1282)

Note that GEOS-Chem will still fail restart tests. Updates to add additional arrays to
the restart file (known issue) will be a separate update later on.

Author: lizziel

.gitmodules

@@ -51,14 +51,14 @@
 	path = src/chemistry/geoschem/geoschem_src
 	url = https://github.com/geoschem/geos-chem.git
         fxrequired = AlwaysRequired
-        fxtag = 14.4.3
+        fxtag = 14.5.3
         fxDONOTUSEurl = https://github.com/geoschem/geos-chem.git
 
 [submodule "cloud_j"]
 	path = src/chemistry/cloud_j
 	url = https://github.com/geoschem/cloud-j.git
         fxrequired = AlwaysRequired
-        fxtag = 7.7.3
+        fxtag = 8.0.1
         fxDONOTUSEurl = https://github.com/geoschem/cloud-j.git
 
 [submodule "hetp"]
@@ -71,7 +71,7 @@
 [submodule "hemco"]
 	path = src/hemco
 	url = https://github.com/ESCOMP/HEMCO_CESM.git
-        fxtag = hemco-cesm2_1_0_hemco3_9_0
+        fxtag = hemco-cesm2_2_0_hemco3_10_3
         fxrequired = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/ESCOMP/HEMCO_CESM.git
 

bld/configure

@@ -1332,7 +1332,7 @@ if ($chem_pkg =~ '_mam3') {
 if ($chem_pkg =~ 'geoschem') {
     $chem_cppdefs .= ' -DEXTERNAL_GRID -DEXTERNAL_FORCING -DMODEL_CESM -DMODEL_GEOSCHEM';
     if ($chem_pkg =~ '_mam4') {
-        $chem_nadv = 269; # includes all GEOS-Chem advected species, CO2, and MAM aerosols
+        $chem_nadv = 312; # includes all GEOS-Chem advected species, CO2, and MAM aerosols
     }
 }
 # CARMA sectional microphysics

bld/namelist_files/geoschem_master_gas_drydep_list.xml

@@ -5,18 +5,45 @@
 <!-- gas-phase species -->
 <list id="gas_phase">
   ACET
+  ACR
   ACTA
+  AERI
   ALD2
+  ALK4N2
+  ALK4P
+  AONITA
+  APAN
+  APINN
+  APINP
+  AROMCHO
   AROMP4
   AROMP5
+  AROMPN
+  ASOA1
+  ASOA2
+  ASOA3
+  ASOAN
+  ASOG1
+  ASOG2
+  ASOG3
   ATOOH
   BALD
   BENZP
+  BPINN
+  BPINO
+  BPINON
+  BPINOOH
+  BPINP
   BR2
   BRCL
   BRNO3
+  BRSALA
+  BRSALC
+  BUTN
   BZCO3H
   BZPAN
+  C96N
+  C96O2H
   CH2O
   CL2
   CLNO2
@@ -35,6 +62,7 @@
   GLYX
   H2O2
   HAC
+  HACTA
   HBR
   HC5A
   HCL
@@ -73,14 +101,26 @@
   IHN2
   IHN3
   IHN4
+  INDIOL
   INPB
   INPD
+  IONITA
   IONO
   IONO2
   IPRNO3
+  ISALA
+  ISALC
   ITCN
   ITHN
+  LIMAL
+  LIMKB
+  LIMKET
+  LIMN
+  LIMNB
   LIMO
+  LIMO2H
+  LIMO3H
+  LIMPAN
   LVOC
   LVOCOA
   MACR
@@ -92,12 +132,15 @@
   MCRHNB
   MCRHP
   MCT
+  MEKPN
   MENO3
   MGLY
   MOH
+  MONITA
   MONITS
   MONITU
   MPAN
+  MSA
   MTPA
   MTPO
   MVK
@@ -107,56 +150,52 @@
   MVKHP
   MVKN
   MVKPC
+  MYRCO
   N2O5
   NH3
+  NH4
+  NIT
+  NITS
   NO2
   NPHEN
   NPRNO3
   O3
   PAN
+  PFE
+  PHAN
   PHEN
+  PIN
+  PINAL
+  PINO3H
+  PINONIC
+  PINPAN
   PP
   PPN
   PROPNN
   PRPN
   PYAC
   R4N2
   R4P
+  R7N2
+  R7P
   RA3P
   RB3P
+  RCOOH
   RIPA
   RIPB
   RIPC
   RIPD
+  RNO3
   RP
-  SO2
-  AERI
-  AONITA
-  ASOA1
-  ASOA2
-  ASOA3
-  ASOAN
-  ASOG1
-  ASOG2
-  ASOG3
-  BRSALA
-  BRSALC
-  INDIOL
-  IONITA
-  ISALA
-  ISALC
-  MONITA
-  MSA
-  NH4
-  NIT
-  NITS
   SALAAL
   SALACL
   SALCAL
   SALCCL
+  SO2
   SO4S
   SOAGX
   SOAIE
+  TLFUONE
   TSOA0
   TSOA1
   TSOA2
@@ -165,7 +204,6 @@
   TSOG1
   TSOG2
   TSOG3
-  PFE
 </list>
 
 </drydep_list_definition>

bld/namelist_files/geoschem_master_gas_wetdep_list.xml

@@ -3,16 +3,42 @@
 <!-- list of gas phase species that undergo wet deposition -->
 <list id="gas">
   ACTA
+  AERI
   ALD2
+  ALK4N2
+  ALK4P
+  AONITA
+  APAN
+  APINN
+  APINP
+  AROMCHO
   AROMP4
   AROMP5
+  AROMPN
+  ASOA1
+  ASOA2
+  ASOA3
+  ASOAN
+  ASOG1
+  ASOG2
+  ASOG3
   ATOOH
   BALD
   BENZP
+  BPINN
+  BPINO
+  BPINON
+  BPINOOH
+  BPINP
   BR2
   BRCL
+  BRSALA
+  BRSALC
+  BUTN
   BZCO3H
   BZPAN
+  C96N
+  C96O2H
   CH2O
   CSL
   EOH
@@ -25,6 +51,7 @@
   GLYX
   H2O2
   HAC
+  HACTA
   HBR
   HC5A
   HCL
@@ -58,13 +85,25 @@
   IHN2
   IHN3
   IHN4
+  INDIOL
   INPB
   INPD
+  IONITA
   IONO
   IONO2
+  ISALA
+  ISALC
   ITCN
   ITHN
+  LIMAL
+  LIMKB
+  LIMKET
+  LIMN
+  LIMNB
   LIMO
+  LIMO2H
+  LIMO3H
+  LIMPAN
   LVOC
   LVOCOA
   MACR1OOH
@@ -76,13 +115,16 @@
   MCRHP
   MCT
   MEK
+  MEKPN
   MGLY
   MOH
+  MONITA
   MONITS
   MONITU
   MP
   MPAN
   MPN
+  MSA
   MTPA
   MTPO
   MVK
@@ -92,10 +134,21 @@
   MVKHP
   MVKN
   MVKPC
+  MYRCO
   NH3
+  NH4
+  NIT
+  NITS
   NPHEN
   PAN
+  PFE
+  PHAN
   PHEN
+  PIN
+  PINAL
+  PINO3H
+  PINONIC
+  PINPAN
   PP
   PPN
   PROPNN
@@ -104,41 +157,26 @@
   PYAC
   R4N2
   R4P
+  R7N2
+  R7P
   RA3P
   RB3P
+  RCOOH
   RIPA
   RIPB
   RIPC
   RIPD
+  RNO3
   RP
-  SO2
-  AERI
-  AONITA
-  ASOA1
-  ASOA2
-  ASOA3
-  ASOAN
-  ASOG1
-  ASOG2
-  ASOG3
-  BRSALA
-  BRSALC
-  INDIOL
-  IONITA
-  ISALA
-  ISALC
-  MONITA
-  MSA
-  NH4
-  NIT
-  NITS
   SALAAL
   SALACL
   SALCAL
   SALCCL
+  SO2
   SO4S
   SOAGX
   SOAIE
+  TLFUONE
   TSOA0
   TSOA1
   TSOA2
@@ -147,7 +185,6 @@
   TSOG1
   TSOG2
   TSOG3
-  PFE
 </list>
 
 </gas_wetdep_list_definition>