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Updates from GMAO #125

Merged
merged 24 commits into from
Jan 21, 2022
Merged

Updates from GMAO #125

merged 24 commits into from
Jan 21, 2022

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lizziel
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@lizziel lizziel commented Jan 11, 2022 •
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This PR brings in changes made to HEMCO for use in GEOSgcm with GEOS-Chem 13.3.4.

Changes include:

  1. Skip check for PBLHEIGHT field if not running GEOS. There are HEMCO applications in GEOS that don't require PBLHEIGHT to be defined.
  2. Change criteria for assuming restart field is all fill values. The new criteria is max value is negative. Previously it was global sum equal to zero.
  3. Force the soil NOx code to grab the restart fields from the internal state on each call if using GEOS, rather than rely on whatever is in local memory.
  4. Rework how to determine when to read volcano table. The new method is to keep track of the emissions data day that is in memory (new variable YmdOnFile) and then compare the current simulation day against that.
  5. Edits to prevent undefined variable when calculating vertical scale factor. This updates adds handling for when HcoState%Grid%BXHEIGHT_M%Val is associated and HcoState%Options%VertWeight is false.

Christoph Keller and others added 19 commits April 19, 2021 10:05
HEMCO structural updates, including header name changes, build update…
8f2a4e8 
…s, and updates to precision settings.
@mathomp4
Remove redundant files in src/Shared
8810076 
We now have two copies of files in `src/Shared`. This PR removes the
older versions (without `hco_` prefix)
@mathomp4
Merge pull request #6 from GEOS-ESM/bugfix/mathomp4/remove-redundant-…
5365483 
…files

Remove redundant files in src/Shared
@lizziel
Merge branch 'geoschem/3.0' into feature/elundgren/update_to_3.0
6bd123e 
# Conflicts:
#	CMakeLists.txt
#	run/createRunDir.sh
#	src/Core/CMakeLists.txt
#	src/Core/hco_config_mod.F90
#	src/Core/hcoio_read_std_mod.F90
#	src/Core/hcoio_util_mod.F90
#	src/Extensions/hcox_gc_POPs_mod.F90
#	src/Extensions/hcox_seasalt_mod.F90
#	src/Interfaces/GCHPctm/HEMCO_GridCompMod.F90
#	src/Shared/GeosUtil/hco_julday_mod.F90
#	src/Shared/NcdfUtil/hco_ncdf_mod.F90

Signed-off-by: Lizzie Lundgren <[email protected]>
prevent undefined variable when calculating vertical scale factor
7ede721
Fast-track bug fix for biogenic acetone double-counting (geoschem#93)
27ce8e8
Make sure that HEMCO level unit is always defined
fd0222b
@wmputman
Updates in support of 3km GEOSchem run
a6a5e76
Don't require PBLHEIGHT as a defined variable when running HEMCO in E…
ede00e5 
…SMF. For many HEMCO applications within GEOS, the PBL height is not needed and the code works without that information. There is an explicit check for PBL height fields if it is indeed needed.
Merge branch 'geos/develop' of https://github.com/GEOS-ESM/HEMCO into…
03c7b00 
… geos/develop
Add VFEI biomass burning extension
0b211cf
Add description and make PBL fraction and max. emission height a conf…
e96c130 
…igurable parameter
Use internal day tracker instead of HEMCO clock for updating volcano …
6a58b8f 
…emissions
Declare HEMCO restart field as missing if all values are negative, ra…
53ab3f7 
…ther than all zeros
Get soil NOx restart files on every run call rather than just at the …
28e5393 
…beginning
Add SO4 to VFEI
3f76bd0
remove VFEI code since not yet operational
141a414
@aoloso
Few lines added to hco_types_mod.F90 and mom6_cmake/CMakeLists.txt fo…
4ee0bd7 
…r succesful build
@lizziel
Merge remote-tracking branch 'upstream/main' into feature/ewlundgr/he…
cd41222 
…mco_3.2.2

# Conflicts:
#	src/Core/hco_calc_mod.F90
#	src/Extensions/hcox_megan_mod.F90

Signed-off-by: Lizzie Lundgren <[email protected]>
@lizziel lizziel added the category: Feature Request New feature or request label Jan 11, 2022
@lizziel lizziel self-assigned this Jan 11, 2022
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lizziel commented Jan 12, 2022

This new line in CMakeLists.txt, added for 3km GEOS-Chem runs, is problematic:

# Enable OpenMP
target_link_libraries(${this} PRIVATE OpenMP::OpenMP_Fortran)

@lizziel
Remove CMake command to enable OpenMP by default
1377d0a 
Enabling OpenMP in HEMCO by default was added for using GEOS with
3 km runs. Rather than explicitly set OpenMP in HEMCO CMakeLists.txt, the
OMP setting should be used higher up in the model. If set to true then
HEMCO will build with OpenMP enabled.

Signed-off-by: Lizzie Lundgren <[email protected]>
@christophkeller
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No need to include the new line in CMakeLists.txt that was added for the 3km test runs.

christophkeller
christophkeller suggested changes Jan 19, 2022
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There was a merge error in hco_calc_mod.F90, see my comment there. Everything looks good otherwise.

src/Core/hco_calc_mod.F90 Outdated Show resolved Hide resolved
@lizziel lizziel changed the title [WIP] Updates for HEMCO in GEOSgcm Updates for HEMCO in GEOSgcm Jan 19, 2022
@lizziel lizziel changed the title Updates for HEMCO in GEOSgcm Updates from GMAO Jan 19, 2022
@lizziel lizziel added this to the 3.4.0 milestone Jan 19, 2022
@lizziel lizziel marked this pull request as ready for review January 19, 2022 17:44
lizziel
lizziel commented Jan 19, 2022
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src/Core/hco_calc_mod.F90 Outdated Show resolved Hide resolved
src/Extensions/hcox_soilnox_mod.F90 Show resolved Hide resolved
src/Extensions/hcox_volcano_mod.F90 Show resolved Hide resolved
christophkeller
christophkeller approved these changes Jan 19, 2022
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Looks good now.

@lizziel
Prevent undefined variable when calculating vertical scale factor
5a98989 
This update was originally added by C. Keller for GEOS only. With this
updatet is now standard handling when calculating dilution factor. It is
only executed when HcoState%Grid%BXHEIGHT_M%Val is associated and
HcoState%Options%VertWeight is false.

Signed-off-by: Lizzie Lundgren <[email protected]>
@lizziel
Use standard solution not GEOS solution for ensuring LevDct_Unit is d…
570eb98 
…efined

Signed-off-by: Lizzie Lundgren <[email protected]>
@lizziel lizziel force-pushed the feature/ewlundgr/hemco_3.2.2_in_geos branch from 89f4f9e to 570eb98 Compare January 19, 2022 20:00
@lizziel
Final cleanup
f31ffd6 
Signed-off-by: Lizzie Lundgren <[email protected]>
@yantosca yantosca merged commit f31ffd6 into geoschem:dev Jan 21, 2022
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FYI, this fix has been tagged in GC-Classic and GCHP as 13.4.0-rc.2. I have a GCHP benchmark pending on Cannon and an GC-Classic benchmark running on the AWS cloud.

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@lizziel @christophkeller @yantosca @mathomp4 @wmputman @aoloso