- 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/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
- Added entries for CEDS 0.1 x 0.1 degree emissions.
  NOTE: ExtData.rc.fullchem will be updated later.

CHANGELOG.md
- Updated accordingly

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

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
- CEDS01 comment update "1750-2019" -> "1980-2019"
- Also updated header comments

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.aerosol
run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon
run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.TransportTracers
run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon
run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.TransportTracers
run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
run/GCHP/ExtData.rc.templates/ExtData.rc.carbon
run/GCHP/ExtData.rc.templates/ExtData.rc.fullchem
run/GCHP/ExtData.rc.templates/ExtData.rc.TransportTracers
- Added entries for CEDS_01x01 as the default
- Now make CEDSv2 an option

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
- For container "CEDS01_TOLU_WST", added scale factor=26, cat=1, hier=5.
  This had been omitted due to a cut-n-paste error.

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

run/GCHP/ExtData.rc.TransportTracers
- Fixed typo: "shoul'd" -> "should

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

This rebase merge brings PR #2171 (CEDS 0.1 x 0.1 emissions) atop
PR #2352 (ALK4 & R4N2 chemistry updates)

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

Updated the following configuration files to read CEDS 0.1 x 0.1
degree emissions data from the HEMCO/CEDS/v2024-06 folder:

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.aerosol
run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon
run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.tagCO
run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.TransportTracers
run/GCHP/ExtData.rc.templates/ExtData.rc.carbon
run/GCHP/ExtData.rc.templates/ExtData.rc.fullchem
run/GCHP/ExtData.rc.templates/ExtData.rc.TransportTracers

Also updated the CHANGELOG.md accordingly.

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

CHANGELOG.md
- Edited previous comment to note that the CEDS data are in v2024-06

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

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem
- Fixed mismatching brackets for CEDS_01x01_SHIP for NO emissions

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

run/GCHP/ExtData.rc.templates/ExtData.rc.carbon
- Change climatology data entries from e.g "2009 Y" to "Y Y F2009-..."
- Remove slug left over from Git merge

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