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Merge pull request ESCOMP#1093 from geoschem/feature/geoschem_14.4

cam6_4_038: GEOS-Chem 14.4 and dependencies

ESCOMP commit: 1abe4a8
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fvitt authored and Steve Goldhaber committed Oct 16, 2024
1 parent 3571609 commit c2e3896
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Showing 17 changed files with 942 additions and 393 deletions.
1 change: 1 addition & 0 deletions bld/namelist_files/geoschem_master_gas_drydep_list.xml
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ETHP
ETNO3
ETP
FURA
GLYC
GLYX
H2O2
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1 change: 1 addition & 0 deletions bld/namelist_files/geoschem_master_gas_wetdep_list.xml
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ETHN
ETHP
ETP
FURA
GLYC
GLYX
H2O2
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2 changes: 0 additions & 2 deletions bld/namelist_files/use_cases/2000_geoschem.xml
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<!-- Settings for using GEOS-Chem specifically -->

<geoschem_cheminputs>atm/cam/geoschem/ExtData/CHEM_INPUTS/</geoschem_cheminputs>

<ncdata dyn="fv" hgrid="0.9x1.25">atm/cam/geoschem/initial_conditions/f.e20.FC2010.f09_f09.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>

<ncdata dyn="fv" hgrid="1.9x2.5">atm/cam/geoschem/initial_conditions/f.e20.FC2010.f19_f19.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>
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2 changes: 0 additions & 2 deletions bld/namelist_files/use_cases/2010_geoschem.xml
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<!-- Settings in this file were adapted from 2010_trop_strat_vbs_cam6.xml -->

<geoschem_cheminputs>atm/cam/geoschem/ExtData/CHEM_INPUTS/</geoschem_cheminputs>

<ncdata dyn="fv" hgrid="0.9x1.25">atm/cam/geoschem/initial_conditions/f.e20.FC2010.f09_f09.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>

<ncdata dyn="fv" hgrid="1.9x2.5">atm/cam/geoschem/initial_conditions/f.e20.FC2010.f19_f19.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>
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4 changes: 1 addition & 3 deletions bld/namelist_files/use_cases/hist_geoschem.xml
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<!-- Settings for using GEOS-Chem -->

<geoschem_cheminputs>atm/cam/geoschem/ExtData/CHEM_INPUTS/</geoschem_cheminputs>

<ncdata dyn="fv" hgrid="0.9x1.25">atm/cam/geoschem/initial_conditions/f.e20.FC2010.f09_f09.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>

<ncdata dyn="fv" hgrid="1.9x2.5">atm/cam/geoschem/initial_conditions/f.e20.FC2010.f19_f19.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>
Expand All @@ -29,7 +27,7 @@
<gw_qbo_hdepth_scaling>0.25D0</gw_qbo_hdepth_scaling>

<flbc_type>SERIAL</flbc_type>
<flbc_file>atm/waccm/lb/LBC_1750-2014_CMIP6_0p5degLat_c170126.nc</flbc_file>
<flbc_file>atm/waccm/lb/LBC_17500116-25001216_CMIP6_SSP585_0p5degLat_c20200824.nc</flbc_file>

<prescribed_strataero_type>SERIAL</prescribed_strataero_type>

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4 changes: 1 addition & 3 deletions bld/namelist_files/use_cases/hist_geoschem_nudged.xml
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<!-- Settings for using GEOS-Chem -->

<geoschem_cheminputs>atm/cam/geoschem/ExtData/CHEM_INPUTS/</geoschem_cheminputs>

<ncdata dyn="fv" hgrid="0.9x1.25">atm/cam/geoschem/initial_conditions/f.e20.FC2010.f09_f09.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>

<ncdata dyn="fv" hgrid="1.9x2.5">atm/cam/geoschem/initial_conditions//f.e20.FC2010.f19_f19.144.GC_vbsext.001.cam.i.0007-01-01-00000.nc</ncdata>
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<gw_qbo_hdepth_scaling>0.25D0</gw_qbo_hdepth_scaling>

<flbc_type>SERIAL</flbc_type>
<flbc_file>atm/waccm/lb/LBC_1750-2014_CMIP6_0p5degLat_c170126.nc</flbc_file>
<flbc_file>atm/waccm/lb/LBC_17500116-25001216_CMIP6_SSP585_0p5degLat_c20200824.nc</flbc_file>

<prescribed_strataero_type>SERIAL</prescribed_strataero_type>

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136 changes: 134 additions & 2 deletions doc/ChangeLog
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@@ -1,3 +1,137 @@
Tag name: cam6_4_038
Originator(s): lizziel
Date: 1 Oct 2024
One-line Summary: Update to GEOS-Chem 14.4.3 and HEMCO 3.9.0, and add Cloud-J 7.7.3 and HETP 1.0
Github PR URL: https://github.com/ESCOMP/CAM/pull/1093

Purpose of changes (include the issue number and title text for each relevant GitHub issue):
Update GEOS-Chem and dependencies to newer versions. (issue #959)

Describe any changes made to build system:

Describe any changes made to the namelist:

List any changes to the defaults for the boundary datasets:

Describe any substantial timing or memory changes:

Code reviewed by: fvitt cacraigucar

List all files eliminated: N/A

List all files added and what they do: N/A

List all existing files that have been modified, and describe the changes:

M .gitmodules
- Update GEOS-Chem and HEMCO_CESM versions
- Add new dependencies cloud_j and hetp

M bld/build-namelist
- Add defaults for GEOS-Chem namelist input directories

M bld/configure
- Add MODEL_CESM and MODEL_GEOSCHEM to geoschem chem_cppdefs for use in Cloud-J
- Update hard-coded chem_nadv used for GEOS-Chem

M bld/namelist_files/geoschem_master_gas_drydep_list.xml
M bld/namelist_files/geoschem_master_gas_wetdep_list.xml
- Add new GEOS-Chem deposited species FURA
- Add SO4 which is a non-MAM aerosol species in GEOS-Chem

M bld/namelist_files/namelist_defaults_cam.xml
- Update default dep_data_file used for GEOS-Chem
- Add two input directories for GEOS-Chem

M bld/namelist_files/namelist_definition.xml
- Change GEOS-Chem chem inputs directory name
- Add new GEOS-Chem input directory used for Cloud-J

M bld/namelist_files/use_cases/2000_geoschem.xml
M bld/namelist_files/use_cases/2010_geoschem.xml
M bld/namelist_files/use_cases/hist_geoschem.xml
M bld/namelist_files/use_cases/hist_geoschem_nudged.xml
- Delete GEOS-Chem chem inputs directory since now in defaults

M cime_config/buildnml
- No-diff cleanup

M cime_config/config_component.xml
- Remove GEOS-chem from CAM40 and CAM50 options

M cime_config/config_compsets.xml
- Fix bug in FCnudged_GC where nudging incorrectly specified in compset definition

M testdefs/testlist_cam.xml
- Move GEOS-Chem tests to be grouped with similar compsets

A src/chemistry/cloud_j
- tagged version 7.7.3

M src/chemistry/geoschem/chem_mods.F90
- Update hard-coded nTracersMax, gas_pcnst, and nslvd used for
GEOS-Chem compsets

M src/chemistry/geoschem/chemistry.F90
- Updates for compatibility with GEOS-Chem 14.3.1
- Replace hard-coded photolysis inputs directory with namelist value
- Add aerosol distribution fix to deposit SO4 using Neu as gas instead of aerosol
- Update precision modifiers

M src/chemistry/geoschem/geoschem_diagnostics_mod.F90
- Update precision modifiers

M src/chemistry/geoschem/geoschem_emissions_mod.F90
- Update precision modifiers

M src/chemistry/geoschem/geoschem_src
- tagged version 14.4.3

M src/chemistry/geoschem/mo_sim_dat.F90
- Add new species to solsym: BUTDI (butendedial) and FURA (furan)

A src/chemistry/hetp
- tagged version 1.0

M src/chemistry/mozart/mo_neu_wetdep.F90
- Restrict henrys law coefficient assignment error print to masterproc
- Add GEOS-Chem bulk sulfates SO4 and SO4S

M src/hemco
- tag hemco-cesm2_0_hemco3_9_0

M test/system/TR8.sh
- Skip over GEOS-Chem and dependency modules

If there were any failures reported from running test_driver.sh on any test
platform, and checkin with these failures has been OK'd by the gatekeeper,
then copy the lines from the td.*.status files for the failed tests to the
appropriate machine below. All failed tests must be justified.

derecho/intel/aux_cam:

PEND SMS_D_Ln9_P1280x1.ne0CONUSne30x8_ne0CONUSne30x8_mt12.FCHIST.derecho_intel.cam-outfrq9s
- pre-existing failures -- need fix in CLM external

FAIL ERP_Ln9.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq9s COMPARE_base_rest
DIFF SMS_Lh12.f09_f09_mg17.FCSD_HCO.derecho_intel.cam-outfrq3h
- pre-existing failure due to HEMCO not having reproducible results issues #1018 and #856

DIFF SMS_Ld1.f09_f09_mg17.FCHIST_GC.derecho_intel.cam-outfrq1d
- expected baseline failure due to updates to GEOS-Chem

derecho/nvhpc/aux_cam: All PASS

izumi/nag/aux_cam:
FAIL DAE.f45_f45_mg37.FHS94.izumi_nag.cam-dae
- pre-existing failure - issue #670

izumi/gnu/aux_cam: ALL PASS

Summarize any changes to answers: bit-for-bit unchanged

===============================================================

Tag name: cam6_4_037
Originator(s): jimmielin
Date: Sep 30, 2024
Expand Down Expand Up @@ -144,7 +278,6 @@ izumi/gnu/aux_cam: ALL PASS

Summarize any changes to answers: bit-for-bit

===============================================================
===============================================================

Tag name: cam6_4_035
Expand Down Expand Up @@ -4964,7 +5097,6 @@ izumi/nag/aux_cam: all B4B, except:
izumi/gnu/aux_cam: all BFB

Summarize any changes to answers: bit-for-bit unchanged except GEOS-Chem and HEMCO tests described in issue #1018

===============================================================

Tag name: cam6_3_158
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1 change: 1 addition & 0 deletions src/chemistry/cloud_j
Submodule cloud_j added at d20050
12 changes: 6 additions & 6 deletions src/chemistry/geoschem/chem_mods.F90
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Expand Up @@ -7,7 +7,7 @@ module chem_mods
implicit none
save

INTEGER, PARAMETER :: nTracersMax = 267 ! Must be equal to chem_nadv
INTEGER, PARAMETER :: nTracersMax = 269 ! = chem_nadv in cam/bld/configure
INTEGER :: nTracers
REAL(r8) :: ref_MMR(pcnst)

Expand Down Expand Up @@ -62,10 +62,10 @@ module chem_mods
rxntot = 212, & ! number of total reactions
gascnt = 172, & ! number of gas phase reactions
nabscol = 2, & ! number of absorbing column densities
gas_pcnst = 269, & ! number of "gas phase" species (same as solsym length)
! Includes GC advected species (233), MAM aerosols (33),
! and CO2 (1), as well as any non-advected species added
! to solsym and mo_sim_dat.F90.
gas_pcnst = 357, & ! number of "gas phase" species (=solsym length)
! Includes GC advected species, MAM aerosols,
! and CO2, and any non-advected species added
! to solsym within mo_sim_dat.F90.
nfs = 6, & ! number of "fixed" species
relcnt = 0, & ! number of relationship species
grpcnt = 0, & ! number of group members
Expand All @@ -81,7 +81,7 @@ module chem_mods
clsze = 1, & ! loop length for implicit chemistry
rxt_tag_cnt = 0, & ! number of tagged reactions (unused in GEOS-Chem)
enthalpy_cnt = 0, &
nslvd = 86 ! number of short-lived (non-advected) species
nslvd = 88 ! number of short-lived (non-advected) species minus CO2
integer :: clscnt(5) = 0
integer :: cls_rxt_cnt(4,5) = 0
integer :: clsmap(gas_pcnst,5) = 0
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