- use AerMass in OCPISOA to avoid unnecessary recalculation
- removed unnecessary OCPI reference when SVPOA is activated

- replace verbose representation of SOA and OCPI with OCPISOA

…nSVPOA

- also includes some rewrites for better readability

R4N2 was a common product of alkane, isoprene, and monoterpene oxidation
and produced organonitrate SOA but we don’t want ALK4 to produce
organonitrate SOA as discusses in #1625.
A fix from Jared Brewer is included here.

NOTE: The KPP fullchem mechanism has not been rebuilt with these fixes to
facilitate merging these updates up to the latest GEOS-Chem release. These
updates will also need to be added to the custom.eqn file.

Signed-off-by: Melissa Sulprizio <[email protected]>

run/shared/species_database.yml
run/shared/species_database_hg.yml
- Allow for KPP_AbsTol and KPP_RelTol tags.
- Set KPP_AbsTol to 1.0e25 for all dummy species, in order to prevent
  these from being considered when computing the error norm.

Headers/species_mod.F90
- Add KPP_AbsTol and KPP_RelTol to the Species derived type

Headers/species_database_mod.F90
- Add "KPP_AbsTol" and "KPP_RelTol" to the tags array
- Add code to parse KPP_AbsTol and KPP_RelTol tags
- Remove the "places" keyword and just pass the number of decimal
  places, for a consistent appearance
- Trimmed trailing whitespace
- Updated comments

Headers/state_chem_mod.F90
- Add KPP_AbsTol and KPP_RelTol 1-D arrays.  These are initialized
  at the same time as the Map_KppVar mapping array.  This will allow
  us to replace missing values at initialization, and just copy
  the values to ATOL and RTOL each timestep.  This is more efficient.

GeosCore/fullchem_mod.F90
GeosCore/mercury_mod.F90
- Replace missing values in State_Chm%KPP_AbsTol and State_Chm%KPP_RelTol
  with default values.  This preserves the absolute and relative
  tolerances for species that were specified in species_database.yml.
- Copy State_Chm%KPP_AbsTol to the KPP ATOL array
- Copy State_Chm%KPP_RelTol to the KPP RTOL array

Signed-off-by: Bob Yantosca <[email protected]>

CHANGELOG.md
- Added notes describing how we can now define KPP absolute and
  relative tolerances for species in species_database.yml

Signed-off-by: Bob Yantosca <[email protected]>

Headers/roundoff_mod.F90
- Bug fix: First cast to dble or flex.  Then round off if the places
  argument is > 0.  This allows us to just cast w/o rounding off
  if needed.

run/shared/species_database_mod.F90
- Changed 1.0e+25_8 to 1.0e+25 in for KPP_AbsTol (LBRO2H)

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>

GeosCore/fullchem_mod.F90
- Removed extraneous "<" character

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings PR #2359 (Allow per-species definition of KPP absolute
and relative solver tolerances; Set absolute tolerances of dummy species
to large value, by @yantosca) into the GEOS-Chem 14.5.0 development
stream.

This PR adds structural updates to allow per-species setting of the
KPP absolute & relative tolerances.  This now allows us to assign a
large absolute tolerance (1e25) to KPP dummy species, which excludes
them from the error norm computations.  This results in a faster
simulation at the cost of numerical noise.

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings the hotfix from PR #2363 (Update
setCommonRunSettings.template) on top of PR #2359.

This will allow GCHP benchmarks on the cloud to proceed.

Signed-off-by: Bob Yantosca <[email protected]

run/shared/species_database.yml
run/shared/species_database_hg.yml
- Allow for KPP_AbsTol and KPP_RelTol tags.
- Set KPP_AbsTol to 1.0e25 for all dummy species, in order to prevent
  these from being considered when computing the error norm.

Headers/species_mod.F90
- Add KPP_AbsTol and KPP_RelTol to the Species derived type

Headers/species_database_mod.F90
- Add "KPP_AbsTol" and "KPP_RelTol" to the tags array
- Add code to parse KPP_AbsTol and KPP_RelTol tags
- Remove the "places" keyword and just pass the number of decimal
  places, for a consistent appearance
- Trimmed trailing whitespace
- Updated comments

Headers/state_chem_mod.F90
- Add KPP_AbsTol and KPP_RelTol 1-D arrays.  These are initialized
  at the same time as the Map_KppVar mapping array.  This will allow
  us to replace missing values at initialization, and just copy
  the values to ATOL and RTOL each timestep.  This is more efficient.

GeosCore/fullchem_mod.F90
GeosCore/mercury_mod.F90
- Replace missing values in State_Chm%KPP_AbsTol and State_Chm%KPP_RelTol
  with default values.  This preserves the absolute and relative
  tolerances for species that were specified in species_database.yml.
- Copy State_Chm%KPP_AbsTol to the KPP ATOL array
- Copy State_Chm%KPP_RelTol to the KPP RTOL array

Signed-off-by: Bob Yantosca <[email protected]>

CHANGELOG.md
- Added notes describing how we can now define KPP absolute and
  relative tolerances for species in species_database.yml

Signed-off-by: Bob Yantosca <[email protected]>

Headers/roundoff_mod.F90
- Bug fix: First cast to dble or flex.  Then round off if the places
  argument is > 0.  This allows us to just cast w/o rounding off
  if needed.

run/shared/species_database_mod.F90
- Changed 1.0e+25_8 to 1.0e+25 in for KPP_AbsTol (LBRO2H)

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>

GeosCore/fullchem_mod.F90
- Removed extraneous "<" character

Signed-off-by: Bob Yantosca <[email protected]>

Fix typo for MassFlux_Entry

This merge brings PR #2315 (ix bugs in PDER, OCPISOA and TotalOC in
complexSOA, by @yuanjianz) into the GEOS-Chem 14.5.0 development stream.

This PR fixes several minor bugs in the complex SOA scheme as described
in issues #2314 and #2321.

Signed-off-by: Bob Yantosca <[email protected]>

Previously these values were zero due to an issue in ISORROPIA. With the
update to HETP we can now enable these cations.

Signed-off-by: Lizzie Lundgren <[email protected]>

This merge brings the GEOS-Chem 14.4.2 release into the GEOS-Chem
14.5.0 development stream.  14.4.2 is a zero-diff update.  The
CHANGELOG.md has been updated accordingly.

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings PR #2398 (Pass non-zero Ca2, Mg, and K cations
to HETP, by @lizziel) into the GEOS-Chem 14.5.0 development stream.

This PR uncomments setting Ca2+, K+, and Mg+ cation values passed
to HETP. Previously these values were zero due to an issue in ISORROPIA.
With the update to HETP we can enable these cations.

Signed-off-by: Bob Yantosca <[email protected]>

Resolved conflicts in:
	CHANGELOG.md
	KPP/fullchem/fullchem.eqn
	KPP/fullchem/fullchem.kpp
	run/shared/species_database.yml

Signed-off-by: Melissa Sulprizio <[email protected]>

This merge brings PR #2352 (Add fixes for ALK4 and R4N2 chemistry from
Brewer et al. (2023, JGR), by @msulprizio) into the GEOS-Chem 14.5.0
development stream.

R4N2 was a common product of alkane, isoprene, and monoterpene oxidation
and produced organonitrate SOA but we don’t want ALK4 to produce
organonitrate SOA as discusses in #1625. A fix from Jared Brewer is
included here.

Signed-off-by: Bob Yantosca <[email protected]>

Due to an oversight, we had forgotten to rebuild the KPP solver files
for PR #2352.  This has now been done.  We will re-tag this PR with
14.5.0-alpha.4 to re-trigger 1-month benchmarks.

Signed-off-by: Bob Yantosca <[email protected]>

run/GCClassic/HISTORY.rc.templates/HISTORY.rc.fullchem
- Change ##'DryDep' -> #'DryDep', which will activate this collection
  in benchmark simulations.

run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem
- Change @#'DryDep' -> #'DryDep', which will activate this collection
  in benchmark simulations.
- Also reduce the DryDep collection species to only those species
  we need for benchmark plots/tables

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>

CHANGELOG.md
- Restored missing line that was inadvertenly deleted
- Place `` around "State_Chm%CH4_EMIS"

run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem
- Removed extra slash in comments

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings all of the updates from the GEOS-Chem 14.4.3
"no-diff-to-benchmark" release back into the dev/14.5.0 branch.
We will test this merge with its own alpha benchmark.

Signed-off-by: Bob Yantosca <[email protected]>

…l NOx extension

Yi Wang updated the soil NOx algorithm in HEMCO to utilize soil
temperature as described in Yi Wang et al. (ERL, 2021). Those updates
require the addition of a new meteorology field, TSOIL1, for the soil
temperature in layer 1. This field has been added to State_Met.

Signed-off-by: Melissa Sulprizio <[email protected]>

CHANGELOG.md
- The entry for "Tropopause pressure field..." for 14.4.3 was located
  much further down than it should have been.  We have moved it back to
  to the 14.4.3 section at the top of the file.

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings PR # ( , by @) into

Signed-off-by: Bob Yantosca <[email protected]>

KPP/fullchem/gckpp*.F90
- GEOS-Chem "fullchem" chemistry mechanism files built with
  Kinetic PreProcessor version 3.1.1

KPP/custom/custom.eqn
- Now consistent with KPP/fullchem/fullchem

Signed-off-by: Bob Yantosca <[email protected]>

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
run/GCHP/ExtData.rc.templates/ExtData.rc.fullchem
- Add entries for new species (supplied by Kelvin Bates) that were
  introduced in the Travis et al 2023 chemistry.

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>

run/GCClassic/HEMCO_Config.templates/HEMCO_Config.rc.fullchem
run/GCHP/HEMCO_Config.templates/HEMCO_Config.rc.fullchem
- Bug fix: remove duplicate set of entries for CEDS_C6H14_* sectors.
  These should now be added to the ALK6 species instead of ALK4.

Signed-off-by: Bob Yantosca <[email protected]>

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
- Fix typo: "0 )))CEDSv2" -> ")))CEDSv2"

Signed-off-by: Bob Yantosca <[email protected]>

run/CESM/HEMCO_Config.rc
- Add the corresponding updates for emissions of new species
  to be consistent with the GCClassic and GCHP updates

Signed-off-by: Bob Yantosca <[email protected]>

run/shared/species_database.yml
- Fixed typo: "Is_Gas:true" -> "Is_Gas: true".  This causes GCPy to fail
  parsing the species_database.yml file.

Signed-off-by: Bob Yantosca <[email protected]>

run/CESM/HEMCO_Config.rc
- Trim trailing whitespace

run/CESM/geoschem_config.yml
run/GEOS/geoschem_config.yml
run/WRF/fullchem/geoschem_config.yml
- Add ACR, ALK4P, ALK7, APAN, APINP, APINN, AROMPN, BPINO, BPINN,
  BPINP, BPINOOH, BPINON, BUTN, C96O2H, C96N, C4H6, EBZ, LIMAL,
  LIMKB, LIMKET, LIMN, LIMNB, LIMO2H, MEKPN, MYRCO, PHAN, PIN,
  PINAL, PINONIC, PINO3H, PINPAN, R7N2, R7P, RCOOH, RNO3, STYR, TMB
  as advected species

run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml
- Restore ALK4P as an advected species

run/GCHP/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.fullchem
- Add Emis*Total and Emis*Bioburn entries for ACR, C4H6, HCOOH, STYR
- Add InvGFED* entries for ACR, C4H6, HCOOH, MVK, STYR

run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.fullchem
run/GCHP/geoschem_config.yml.templates/geoschem_config.yml.fullchem
- Restore ALK4P as an advected species

run/GCHP/HISTORY.rc.templates/HISTORY.rc
- Add Emis*BioBurn entries for ACR, C4H6, HCOOH, STYR,
- Add Inv*BioBurn entries for ACR, C4H6, HCOOH, STYR

run/GEOS/HEMCO_Config.rc
- Add new GFED species

run/WRF/fullchem/HEMCO_Config.rc
- Change Verbose from "0" to "false"
- Add "VerboseOnCores: root"
- Add new biomass burning species (from FURA onwards)
- Add CEDS entries for EBZ and TMB species
- Change emitted species "MACR" to "ACR" in EPA16 entries
- Update CEDS scale factors as they are in GCClassic/GCHP
- Remove .and. in ((( and ))) brackets and list them individually
- Change "$GCAPVERTRESL" to "$GCAPVERTRES" as in GCClassic/GCHP
- Add GT_Chlorine entries
- Update GFED data dir to v2023-03
- Write HEMCO_Restart file in the ./Restarts folder
- Now use Vohra timezones
- Use v2023-10 folder for NOAA_GMD_CH4
- Add scale factors as for GCClassic and GCHP

run/shared/setupConfigFiles.sh
- Now insert ASOA* and ASOG* entries after species AROMPN
  (formerly after AROMP5)

Signed-off-by: Bob Yantosca <[email protected]>

run/shared/species_database.yml
- Move the "aoa_PROP" back to the 1st column.  It was indented
  erroneously when we rebased PR #2318 atop 14.5.0-alpha.4

Signed-off-by: Bob Yantosca <[email protected]>

run/GCHP/geoschem_config.yml.templates/geoschem_config.yml.fullchem
- Added the species introduced by PR #2318 to the transported species
  list.  Somehow this was either not added or lost in a merge.

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings PR #2318 (Chemistry for RCOOH, monoterpenes, new PNs
and ANs from Travis et al. (2024), by @ktravis213) into the GEOS-Chem
14.5.0 development stream.

This PR introduces several new chemistry reactions following the
Travis et al 2024 article.

Signed-off-by: Bob Yantosca <[email protected]>

run/CESM/geoschem_config.yml
run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml
run/GCHP/geoschem_config.yml.templates/geoschem_config.yml
run/GEOS/geoschem_config.yml
run/WRF/fullchem/geoschem_config.yml
- Add transported species: ALK4N2, AROMCHO, HACTA, TLFUONE.  These
  are listed as transported in species_database.yml and need to be
  also listed here in geoschem_config.yml.  Otherwise this will cause
  a species mismatch in the budget diagnostics.

run/shared/species_database.yml
- Fix typo: "<KF2" -> "KF2"

Signed-off-by: Bob Yantosca <[email protected]>

run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem
- Removed a duplicate entry for EmisHCOOH_Total from the Emissions
  collection.  This was probably left over from the merge up to
  the dev/14.5.0 branch.  Also consolidated all HCOOH emissions
  diagnostics together in the same block.

Signed-off-by: Bob Yantosca <[email protected]>

run/GCHP/HISTORY.rc.fullchem
- Add the DryDepChm_O3 and DryDepMix_O3 fields to the DryDep colletction
  out-of-bounds error.  This is to be consistent w/ GCClassic as well.

Signed-off-by: Bob Yantosca <[email protected]>

run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem
- Only keep the fields that are necessary for fullchem benchmarks
  in the DryDep collection.  This is similar to what is being done
  in PR #2144 (which will be merged later).

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings PR #2144 (Restore dry deposition output in GCHP &
GCClassic fullchem benchmark simulations, by @yantosca) into the
GEOS-Chem 14.5.0 development stream.

This PR turns on dry deposition diagnostic output in the 1-hour, 1-month,
and 1-year fullchem benchmark simulations.  For GCHP, we now restrict the
amount of diagnostic ouptut to just what is needed to make the benchmark
plots.

Signed-off-by: Bob Yantosca <[email protected]>

update CHANGELOG

update CHANGELOG

… and read TSOIL1 when activated

A new option UseSoilTemperature has been added to the SoilNOx extension
section in HEMCO_Config.rc.

Entries for TSOIL1 have been added to HEMCO_Config.rc.gmao_fields (GCClassic)
and ExtData.rc.fullchem (GCHP). The field should only be read in GCClassic
if the option UseSoilTemperature - now renamed without spaces for use in
HEMCO logical brackets - is set to true. Additionally, a new
Input_Opt%UseSoilTemp logical is now initialized in hco_interface_mod.F90
and used in flexgrid_read_mod.F90 to only obtain TSOIL1 when UseSoilTemperature
is true in HEMCO. For GCHP, the TSOIL1 line will need to be manually edited
for now.

Signed-off-by: Melissa Sulprizio <[email protected]>

Signed-off-by: Melissa Sulprizio <[email protected]>

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.aerosol
run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
- Edit GFED4_Climatology files so that they point to the new
  climatology file for 2010-2023 generated from a HEMCO 3.10.0
  standalone simulation

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings PR #2428 (Fix mass non-conservation in VDIFF
PBL mixing, by @nicholasbalasus) into the GEOS-Chem 14.5.0 development
stream.

This PR fixes a mass conservation bug in the VDIFF PBL mixing that
especially affected long-lived species (like CH4, CO2, etc.).

Signed-off-by: Bob Yantosca <[email protected]>

These files include so4.dat etc which are read by subroutine Rd_AOD. The
new data directory is specified in the aerosol menu of geoschem_config.yml.

Signed-off-by: Lizzie Lundgren <[email protected]>

These subroutines must be called even if photolysis is off since they are
used for aerosol optical depths.

Signed-off-by: Lizzie Lundgren <[email protected]>

Signed-off-by: Lizzie Lundgren <[email protected]>

Signed-off-by: Lizzie Lundgren <[email protected]>

…tion

Fast-JX, unlike Cloud-J, uses arrays set in CALC_AOD. Since the Hg
simulation uses Fast-JX and does not trigger calling Init_Aerosol we
need to call RD_AOD and CALC_AOD during Fast-JX initialization. The Hg
simulation is the only simulation that uses Fast-JX and it will be deleted
in the future once offline aerosol wet concentration files are available
for Cloud-J.

Signed-off-by: Lizzie Lundgren <[email protected]>

Previously Init_Aerosol was initialized based on various aerosol logicals.
A more robust method is to always call Init_Aerosol for the full
chemistry and aerosol-only simulations.

Signed-off-by: Lizzie Lundgren <[email protected]>

Somehow these subroutines were not previously removed.

Signed-off-by: Lizzie Lundgren <[email protected]>

run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.Hg
- Add the the aerosols:optics:input_dir YAML tags to specify the
  location of the aerosol optics folder.  This had been omitted, and
  was causing the Hg simulation to fail with a file-not-found error.
  Now fixed.

Signed-off-by: Bob Yantosca <[email protected]>

run/GCHP/ExtData.rc.templates/ExtData.rc.fullchem
- Added missing entries for CEDS_TMB_SHP and CEDS_OTH_SHP

Signed-off-by: Bob Yantosca <[email protected]>

Headers/CMN_FJX_MOD.F90
- Change JVN from 166 to 167

KPP/fullchem/fullchem.eqn
KPP/custom/custom.eqn
- Added rxns for PPN

KPP/fullchem/CHANGELOG_fullchem.md
- Added description of updates

Signed-off-by: Bob Yantosca <[email protected]>

KPP/fullchem/gckpp*F90
- Rebuilt with KPP 3.1.1

CHANGELOG.md
KPP/fullchem/CHANGELOG_fullchem.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>

Signed-off-by: Lizzie Lundgren <[email protected]>

This merge brings PR #2371 (Adding PPN photolysis, by @bexhorner) into
the GEOS-Chem 14.5.0 development stream.

This PR adds photolysis rxns for the PPN species.

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings PR #2439 (Update run scripts and environment files for
NASA discover cluster, by @lizziel) into the GEOS-Chem 14.5.0 development
stream.

This PR updates the operational run scripts and environment files for
using GC-Classic and GCHP on the NASA discover cluster. This includes
environment files using both GNU and Intel fortran compiler on Milan
nodes. GEOS-Chem CTM users on discover can easily access these files in
GEOS-Chem run directories starting in version 14.5.0 via symlink
runScriptSamples/operational_examples/nasa_discover.

Signed-off-by: Bob Yantosca <[email protected]>

run/GCHP/ExtData.rc.templates/ExtData.rc.fullchem
- Replaced $YYYY (which is the HEMCO_Config.rc token) with %y4,
  which is the MAPL token in the OTHER_VOC_shp container.

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings PR # (Update GFED4_Climatology entries for period
2010-2023 with new species, by @yantosca) into the GEOS-Chem 14.5.0
development stream.

This is the companion PR to issue #2415. We have re-generated the GFED4
climatology and GFED4 monthly mean data files by running the HEMCO
standalone simulation for the period 2010-2023. We have also included the
new species that were introduced in PR #2318 and HEMCO PR
https://github.com/geoschem//HEMCO#285.

Signed-off-by: Bob Yantosca <[email protected]>

run/GCHP/ExtData.rc.templates/ExtData.rc.fullchem
- Fixed typo in CEDS_TMB_SHP entry, the file specified was
  HCOOH-em-anthro_CMIP_CEDS_%y4.nc but should have been
  TMB-em-anthro_CMIP_CEDS_%y4.nc.

Signed-off-by: Bob Yantosca <[email protected]>

Besides options previously in input file CJ77.dat, there is now the
option to turn off the UV absorption by water vapor.

Signed-off-by: Lizzie Lundgren <[email protected]>

The concentration is computes from species concentration is H2O is
a species. Otherwise it is computed from the specific humidity
in the input meteorology.

Signed-off-by: Lizzie Lundgren <[email protected]>

This update also moves all Cloud-J parameters set in geoschem_config.yml
to new sub-menu called cloud-j within the photolysis menu.

Signed-off-by: Lizzie Lundgren <[email protected]>

Signed-off-by: Lizzie Lundgren <[email protected]>

# Conflicts:
#	CHANGELOG.md

Signed-off-by: Lizzie Lundgren <[email protected]>

This merge brings PR #2426 (Store aerosol-specific optics files in new
Aerosol_Optics data directory, by @lizziel) into the GEOS-Chem 14.5.0\
development stream.

This PR moves the aerosol-specific optics data files (so4.dat, dust.dat, etc)
into a new data directory with path specified in the Aerosols menu in
geoschem_config.yml. Previously these files were stored in the same data
directory as photolysis input files. However, since we now have both
FAST-JX (for Hg simulation) and Cloud-J (for fullchem and aerosol sims)
we would need to store identical files in two different places.
This is not ideal. In addition it may cause confusion since these files
are no longer used for photolysis in Cloud-J. Aerosol optical properties
used in Cloud-J come from input file FJX_scat-aer.dat.

There are a few additional changes in this PR related to this data:

1. Move the calls to RD_AOD and CALC_AOD from Init_Photolysis to both
   Init_Aerosol and Init_FastJX. The former is for use in full
   chemistry and aerosol-only simulations. The latter is for use in the
   Hg simulation since it still uses Fast-JX and Fast-JX uses arrays
   computed by CALC_AOD.

2. Change the criteria to call Init_Aerosol to be based on simulation
   type rather than Input_Opt logicals for different aerosols.
   Init_Aerosol is now always called if using the full chemistry or
   aerosol-only simulation.

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings PR #2424 (Support for Cloud-J_v8.0.0, by @lizziel) into
the GEOS-Chem 14.5.0 development stream.

This pull request brings in updates for compatibility with Cloud-J
version 8.0.0. The primary change is expanding the photolysis menu in
configuration file geoschem_config.yml to allow easy run-time
configuration of Cloud-J from GEOS-Chem run directories. Previously
these settings were configured in an input file stored in external
data directories.

Also in this update is the inclusion of the option to turn off the
UV absorption by water vapor. H2O UV absorption is the main update in
Cloud-J v8 and some GEOS-Chem users may want to experiment with it.
It is turned on by default but can be toggled off in the photolysis
menu of geoschem_config.yml.

Signed-off-by: Bob Yantosca <[email protected]>

run/shared/species_database.yml
- Add "Is_Photolysis: true" YAML tag for PPN.  We had omitted
  this from PR #2371.

CHANGELOG.md
- Updated accordingly.

Signed-off-by: Bob Yantosca <[email protected]>

Signed-off-by: Melissa Sulprizio <[email protected]>

KPP/fullchem/fullchem.eqn
KPP/custom/custom.eqn
- Update comments
- Reorder the photolysis reactions to use the proper slots of the
  PHOTOL array.  This now matches the order in FJX_j2j.dat.
  - PPN     : 167
  - APINP   : 168
  - PINAL   : 169
  - PINO3H  : 170
  - PINONIC : 171
  - C96O2H  : 172
  - BPINP   : 173
  - BPINOOH : 174
  - LIMO3H  : 175
  - LIMO2H  : 176
  - LIMAL   : 177

KPP/fullchem/gckpp*.F90
- Rebuilt with KPP 3.1.1

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings PR # (Bug fix: Reorder photo rxns for PNs and ANs
(from PR #2318), by @yantosca) into the GEOS-Chem 14.5.0 development
stream.

This PR reorders the photo rxns that were added in PR #2318 so that they
now follow PPN as listed in Cloud-J config file FJX_j2j.dat.

Signed-off-by: Bob Yantosca <[email protected]>

run/shared/species_database.yml
- Added "Is_Photolysis: true" to the following entries:
    APINP, AROMCHO, BPINOOH, BPINP, C96O2H, H2O, HO2, LIMAL,
    LIMO2H, LIMO3H, PINAL, PINO3H, PINONIC, SO2
- Removed "Is_Photolysis: true" from the following entries:
    APINN, AROMPN, BPINN, BPINON, C96N, CHCl3, HC5A, LIMN,
    LIMNB, LIMPAN, MEKPN, MPAN, PHAN, PIN, PINPAN
- Moved PINO3H to be in alphabetical order.

Signed-off-by: Bob Yantosca <[email protected]>

run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem
- Updated "Jval_" entries to use only the proper photolysis species

CHANGELOG.md
- Updated accordingly

Signed-off-by: Bob Yantosca <[email protected]>

CHANGELOG.md
- Consolidate species that were added in Travis et al 2024 into
  a single note under "Added"

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings PR #2457 (Update Is_Photolysis tags in species_database.yml
to be consistent with Cloud-J file FJX_j2j.dat, by @yantosca) into the
GEOS-Chem 14.5.0 development stream.

This PR now ensures that all species that are listed as photolyzing
in the KPP fullchem.eqn file and the FJX_j2j.dat file have
"Is_Photolysis: true" tags in run/shared/species_database.yml.
The "Is_Photolysis: true" tags were also removed from species that
are not photolyzing.  Also, the JValues collection was updated in
run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem accordingly.

Signed-off-by: Bob Yantosca <[email protected]>

With the updated monoterpene/PN/AN chemistry and emissions added in
14.5.0-alpha.6 (updates on top of PR #2318), emissions for >=C6 alkanes
from CEDS were added to HEMCO_Config.rc. These were incorrectly assigned
to species ALK6 (not defined) when they should be assigned to ALK7.

Other fixes here include:

- Update HEMCO_Diagn.rc (and HISTORY.rc for GCHP) to save out ALK7 emissions
- Fix category for CEDS ship emissions of HCOOH and ALK7 in HEMCO_Config.rc (should be 10, not 1)
- Make fullchem HEMCO_Diagn.rc for WRF consistent with GCClassic version

Closes #2459

Signed-off-by: Melissa Sulprizio <[email protected]>

This merge brings PR #2430 (Updated soil NOx scheme from Yi Wang et al.
(2021) as an option, by @msulprizio) into the GEOS-Chem 14.5.0 development
stream.

This PR updates source code and configuration files to activate the new
soil NOx scheme by Yi Wang et al. 2021.  This must be merged along with
HEMCO PR #287.  This will be a zero-diff update w/r/t benchmarks,
as this option will be disabled by default until the TSOIL met
archive has been generated.

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings PR #2430 (Updated soil NOx scheme from Yi Wang et al.
(2021) as an option, by @msulprizio) into the GEOS-Chem 14.5.0 development
stream.

This PR updates source code and configuration files to activate the new
soil NOx scheme by Yi Wang et al. 2021.  This must be merged along with
HEMCO PR #287.  This will be a zero-diff update w/r/t benchmarks,
as this option will be disabled by default until the TSOIL met
archive has been generated.

Signed-off-by: Bob Yantosca <[email protected]>

This merge brings PR #2462 (Bug fix: ALK6 in HEMCO_Config.rc
should be ALK7, by @msulprizio) into the GEOS-Chem 14.5.0
development stream.

This PR fixes a bug introduced in PR #2318, where the ALK7
species was erroneously named ALK6 in HEMCO configuration files.

Signed-off-by: Bob Yantosca <[email protected]>

Previously reservoir emissions from the ResME inventory were included every
month but there should be none during the cold months. From Delwiche et al. (2022):

   Since individual reservoir modeling for stratification is beyond the scope
   of ResME, we instead provide degassing estimates for two potential
   scenarios: (a) maximum possible degassing if reservoirs were stratified
   year-round and thus T b = (0.5 + Bubdiss) x P in each month, and
   (b) reservoir is stratified for the 2 months before and after peak
   reservoir temperature (5 months total), with monthly degassing zero
   otherwise.

To apply seasonality to the ResME emissions, a monthly mask file has been
created to zero emissions above 30N and below 30S outside of the 5 warmest
months for that hemisphere.

Signed-off-by: Melissa Sulprizio <[email protected]>

This update is for full chemistry only. J-value diagnostics are only
populated with non-zero values for species in FJX_j2j.dat. Other species
that have Is_Photolysis=True have J-value diagnostics created but are
filled with all zeros.

Signed-off-by: Lizzie Lundgren <[email protected]>

Species H2O and SO2 have J-values computed which are not used in
the full chemistry simulation.

Signed-off-by: Lizzie Lundgren <[email protected]>

The data in molec/cm2/s is converted to kg/m2/s automatically if reading
data in through HEMCO. Since GCHP does not use HEMCO for data read we
need to instead specify a scaling factor in a configuration file. This
update fixes a bug in GCHP carbon simulations where CH4 emissions were
applied in the wrong units.

This commit also fixes a bug where several ExtData.rc entries for
gridded GHGI v2 Express Extension emissions were specified as monthly
when they are actually annual.

Signed-off-by: Lizzie Lundgren <[email protected]>

This commit includes two updates submitted by Yuk Chun Chan (UW) and
Becky Alexander (UW):

1. From Yuk Chun Chan: "To account for the missing Ca, Mg, and K, the Na-to-seasalt mass
   ratio was artificially increased from 0.3061 (i.e., seawater average)
   to 0.397 in previous versions. Since we are re-introducing Ca, Mg,
   and K to the model now, we should adjust the Na-to-SS mass ratio from
   0.397 back to 0.3061. Otherwise, we would get excess amount of cations
   in the model."

2. From Becky Alexander: The TNA equation needs "to be changed, which
   deals with coarse-mode sea salt aerosol. The current value is 0.378.
   I don't know why these values are different for fine and coarse mode.
   They should both be 0.3061, which is the dry mass fraction of sea salt."

Signed-off-by: Lizzie Lundgren <[email protected]>