…atalyzed SO2 oxidation (ref: Shao et al., 2019, ACP)

…s (ref: Moch et al., 2020, JGR)

This brings the HMS chemistry according to J. Moch et al into
GEOS-Chem.  See geoschem/geos-chem PR #456.

Resolved conflicts in:
- GeosCore/isorropiaII_mod.F90
- GeosCore/sulfate_mod.F90
- Headers/state_diag_mod.F90
- run/shared/species_database.yml

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

This commit adds the hetchem rate law function updates into
the development branch with HMS chemistry.

Resolved conflicts in:
- GeosCore/aerosol_mod.F90

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

GeosCore/sulfate_mod.F90:
- Add missing comma in !$OMP PRIVATE statement in CHEM_SO2

Headers/state_diag_mod.F90
- Add HMS-related fields to TYPE(DgnState)
- Add Init_and_Register calls for HMS-related fields of TYPE(DgnState)
- Add Finalize calls for HMS-related fields of TYPE(DgnState)
- Trimmed trailing whitespace

run/GCClassic/input.geos.templates/input.geos.fullchem
- Added HMS to list of advected species

run/shared/species_database.yml
- Added Background_VV = 1.0e-15 for HMS.  This should be a better
  initial concentration than 1e-20 or 1e-30, and should not cause
  chemistry to exit with error.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

The README.md file says that KPP/aciduptake will be used in
future GC development, but is being ignored for now.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

Change requested time from 16h to 5h.  Most integration tests finish
in about 3 to 3.5 hours.

Change requested memory from 60000 to 75000.  This is needed for the
nested-grid NA simulation at 0.25 degree resolution.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

run/GCClassic/createRunDir.sh
- For fullchem and aerosol simulations, point to the restart files
  in ExtData/GEOSCHEM_RESTARTS/v2021-09.  This has the same concentrations
  as the restart files in GC_13.0.0, plus HMS, SO3mm, and HSO3m.
  (will add C2H2 and C2H4 later)

run/shared/species_database.yml
- Add chemical formula for HMS

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

The HMS chemistry modifications in sulfate_mod.F90 and aerosol_mod.F90
assume HMS is an advected species.  We have now added HMS to the
run/GCClassic/input.geos.templates/input.geos.aerosol template file
that is used in run directory creation.  This should allow integration
tests to pass.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

…-09/

We have added extra species (such as HMS) for new chemistry in 13.3.0
and later versions into the restart files in the
ExtData/GEOSCHEM_RESTARTS/v2021-09 folder.  When creating GEOS-Chem
"Classic" run directories for fullchem or TOMAS simulations, these
restart files must be placed in the run directory or else there will
be a species not found error due to the HEMCO_Config.rc "EFYO"
time cycle flag.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

Prior to this commit, HMS0 was set to zero for aerosol-only simulations.
Now it is set to Spc(I,J,L,id_HMS). This had caused aerosol-only
integration tests to fail.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

(1) Make sure that HOBr, HOCl, HCHO, HMS, and OH are only referenced
    from state_chm%species if it is a fullchem simulation.

(2) Removed some ELSE statements (i.e. zero variables before IF).

(3) Expanded IS_FULLCHEM to Input_Opt%ITS_A_FULLCHEM_SIM

(4) Trimmed trailing whitespace.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

HMS is only needed for the fullchem simulation.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

Modified the sequence fed to createRunDir.sh in script
test/GCClassic/intTestCreate.sh to create TOMAS15 and TOMAS40
integration test rundirs with 47 levels instead of 72.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

GeosCore/aerosol_mod.F90:
- Only include HMS in SO4_NH4_NIT if id_HMS > 0
- Set the HMS array to 0 if id_HMS < 0

GeosCore/isorropia_mod.F90
- Add an IS_HMS flag to denote when id_HMS > 0
- If id_HMS = 0 and it's an aerosol-only sim, let run proceed
- Only add HMS to TSO4 if IS_HMS = TRUE
- Only add HMS to DEN_SAV if IS_HMS = TRUE

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>