GEOS-Chem 13.3.0: Difference between revisions

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'''4. [https://github.com/geoschem/geos-chem/issues/907 Revise gamma(N2O5) computation; cap A at 3.2e-8]'''
'''4. [https://github.com/geoschem/geos-chem/issues/907 Revise gamma(N2O5) computation; cap A at 3.2e-8]'''


:This update has a relatively small (<10%) impact on [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.5/Tables/GlobalMass_Trop.txt most species], but causes a large decrease in ClNO2. This is to be expected, because prior to this fix, the reaction probability (gamma) for ClNO2 het chem reactions was too high over the oceans.  This update now fixes the gamma computation. See [https://github.com/geoschem/geos-chem/issues/907 this Github issue] for further discussion on the changes from this update.
:This update has a relatively small (<10%) impact on [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.3.0-alpha.5/Tables/GlobalMass_Trop.txt most species], but causes a large decrease in ClNO2. This is to be expected, because prior to this fix, the reaction probability (gamma) for ClNO2 het chem reactions was too high over the oceans.  This update now caps gamma(ClNO2) at ~0.036, which is consistent with lab results. See [https://github.com/geoschem/geos-chem/issues/907 this Github issue] for further discussion on the changes from this update.


'''5. [https://doi.org/10.5194/acp-2021-441 Updates to IONO2 hydrolysis from Wang et al. (2021)]'''
'''5. [https://doi.org/10.5194/acp-2021-441 Updates to IONO2 hydrolysis from Wang et al. (2021)]'''

Revision as of 19:57, 14 October 2021

GEOS-Chem Versions Page

This page includes information about GEOS-Chem 13.3.0 which is currently in development.

Version overview

The items listed below have been added to GEOS-Chem 13.3.0 since GEOS-Chem 13.2.0. See also the following Github pages:

Feature Contributor(s) Model scope Notes
Updates that will affect full-chemistry benchmark simulations
Aromatic VOC chemistry Kelvin Bates (Harvard)
Ke Li (Harvard)
Mike Long (Harvard) 		Chemistry
C2H2 and C2H4 chemistry Kelvin Bates (Harvard)
Ke Li (Harvard)
Mike Long (GCST) 		Chemistry
CH3O2 + OH reaction Kelvin Bates (Harvard) Chemistry
HMS chemistry (via sulfate_mod.F90) Jonathan Moch (Harvard)
Mike Long (GCST) 		Chemistry
Updates to IONO2 hydrolysis from Wang et al. (2021) Tomas Sherwen (York) Chemistry
Revise gamma(N2O5) computation; cap A at 3.2e-8 Viral Shah (Harvard) Chemistry
Bug fixes in heterogeneous chemistry: Viral Shah (Harvard)
Chris Holmes(FSU) 		Chemistry
Cleaning up heterogeneous chemistry reaction rate computations Bob Yantosca (GCST) Chemistry &
Structural
Updated aerosol dry deposition Jeff Pierce (CSU) Dry deposition
Avoid double counting of acetone source from monoterpenes when using online MEGAN Dylan Millet (UMN) Emissions
Update volcano emissions to May 2020 and add climatology Christoph Keller (NASA/GMAO) Emissions
Updates that will NOT affect full-chemistry benchmark simulations
Updated offline dust emissions from Meng et al. (2021) Jun Meng (WUStL)
Yanshun Li (WUStL) 		Emissions
Update US emissions to NEI2016 (as option) Barron Henderson (EPA)
Lyssa Freese (MIT)
Melissa Sulprizio (GCST) 		Emissions
Send all HEMCO error messages to GEOS-Chem log Lizzie Lundgren (GCST) HEMCO
The ObsPack diagnostic can now use the ?ADV? wildcard Jessica Haskins (MIT) Diagnostics
Features only affecting GCHP:
Include thread number in GEOS-Chem and HEMCO error messages Lizzie Lundgren (GCST) GCHP/GEOS


GCHP Adjoint updates Colin Lee (CU Boulder) GCHP

New data directories

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory Type What was added? Directory
GEOS-Chem Restart Files Default Updated full-chemistry and TOMAS restart files with new species for 13.3.0 added. ExtData/GEOSCHEM_RESTARTS/v2021-09/
Boundary conditions Default
(nested-grid simulations only) 		Updated sample nested-grid boundary conditions with new species for 13.3.0 added. ExtData/HEMCO/SAMPLE_BCs/v2021-09/
OFFLINE_DUST Default Offline dust emissions from Meng et al. (2021) HEMCO/OFFLINE_DUST/v2021-08
VOLCANO Default Update offline dust emissions to May 2020 and add climatology HEMCO/VOLCANO/v2021-09
NEI2016 Optional EPA NEI2016 emissions (2002-2020) HEMCO/NEI2016/v2021-06

1-month benchmarks

1-month fullchem: Model setup

The following table describes the GEOS-Chem setup for both GEOS-Chem Classic and GCHP 1-month benchmark simulations.

Git tag(s):
Compared to previous benchmark: 13.2.0
Software environment: gcc 10.2.0
OpenMPI 4.1.0
netcdf-fortran 4.5.3
CMake 3.17.3
ESMF 8.0.1
Model resolution:
  • GEOS-Chem Classic: 4° x 5°
  • GCHP: c48
Meteorology fields: MERRA-2
  • GEOS-Chem Classic: 4° x 5°
  • GCHP: 0.5° x 0.625°
Initial conditions: July 1, 2019
  • NOTE: GCHP c48 restart file regridded from GEOS-Chem Classic 4° x 5°
Benchmark month: July 2019
Emissions setup: HEMCO_Config.rc
Chemistry mechanism: fullchem.eqn
This version will impact:
(select all that apply with boldface)
  • Advection
  • BL Mixing
  • Convection
  • Meteorology Fields
  • Dry Deposition
  • Wet Deposition
  • Emissions
  • Photolysis
  • Chemistry
  • Other (please specify):

Benchmark Plots and Tables

NOTES:

  • Enable PDF bookmarks in the file links to navigate between species. See the Species in GEOS-Chem wiki page for species definitions and details. If you do not see bookmarks in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.
  • Species categories and lumped species are defined in YAML files within the GEOS-Chem post-processing software GCPy.

1-month fullchem: GEOS-Chem Classic 13.3.0 vs 13.2.0

Below are links to plots and tables comparing 1-month simulations for GEOS-Chem Classic 13.3.0 (Dev) and GEOS-Chem Classic 13.2.0 (Ref).

Species Category Plots Additional Information
Level Map Zonal Mean Emissions
Oxidants

O3, CO, OH, NOx

sfc 500hPa full column stratosphere sfc
Aerosols

DST1, DST2, DST3, DST4, NH4, NIT, SO4, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA. pFe

sfc 500hPa full column stratosphere column total AOD
Bromine

Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr

sfc 500hPa full column stratosphere column total
Chlorine

Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, CHCl3, HOCl, HCl, Halons, HCFCs, OClO

sfc 500hPa full column stratosphere --
Iodine

Iy, IxOy, I, I2, IBr, ICl, IO, IONO, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO

sfc 500hPa full column stratosphere column total
Nitrogen

NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3

sfc 500hPa full column stratosphere column total
Primary Organics

EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H6, C3H8, PRPE, TOLU, XYLE

sfc 500hPa full column stratosphere column total
Secondary Organics

ACTA, ALD2, CH2O, HPALDs, MACR, IEPOX, ACET, HAC, MEK, MVK, ISOPN, GLYC, GLYX, HCOOH, MAP, RCHO, MP

sfc 500hPa full column stratosphere column total
Secondary Organic Aerosols

TSOA0, TSOA1, TSOA2, TSOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ASOG1, ASOG2, ASOG3, INDIOL, LVOCOA, SOAIE, SOAGX, SOAP, SOAS

sfc 500hPa full column stratosphere column total
Sulfur

SOx, DMS, OCS, SO2, SO4

sfc 500hPa full column stratosphere column total
ROy

H2O2, H, H2, H2O, HO2, O1D, OH, RO2

sfc 500hPa full column stratosphere --
J-values sfc 500hPa full column stratosphere -- --
 
Emissions by HEMCO category Total

Aircraft, Anthropogenic, Biomass Burning, Biogenic, Lightning, Natural, Ocean, Seabirds, Decaying Plants, Ship, Soil, Degassing Volcanoes, Erupting Volcanoes

Emission totals Tables by species

Tables by inventory

Global mass Entire atmosphere

Troposphere only

Metrics OH concentration, MCF lifetime, CH4 lifetime

Benchmark assessment form

Performance GEOS-Chem Classic GCHP
Grid resolution: 4° x 5° C48
# CPUs, nodes: 48 CPUs
1 node (Intel Cascade Lake) 		48 CPUs
2 nodes (Intel Cascade Lake)
Wall time: 03:30:53 TBD
CPU time / wall time: 31.5510 TBD
% of ideal performance: 65.73% TBD
Memory: 12.097 GB TBD
Global mean OH:
(% change from previous version) 		11.74989868895 x 105 molec/cm3
(+4.68) 		TBD
Methyl chloroform lifetime:
(% change from previous version) 		5.263415 years
(-4.47%) 		TBD
Methane lifetime:
(% change from previous version) 		8.868914 years
(-4.34%) 		TBD
Details
Species, J-Values, and COLUMN AOD values that changed by 10% or more at the surface: GEOS-Chem Classic 13.3.0 vs 13.1.0 TBD
Species and J-Values that changed by 10% or more at 500 hPa: GEOS-Chem Classic 13.3.0 vs 13.1.0 TBD
Species and J-Values that changed by 10% or more in zonal mean: GEOS-Chem Classic 13.3.0 vs 13.1.0 TBD
Emissions that changed by 10% or more: GEOS-Chem Classic 13.3.0 vs 13.1.0 TBD
Overview
Below we summarize the notable changes caused by specific updates. Supplementary plots may be viewed at http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/.

1. HMS chemistry (via sulfate_mod.F90)

This update introduces new advected species hydroxymethanesulfonate (HMS) in GEOS-Chem. This new chemistry has a relatively small impact on other species' concentrations and on global mean OH. Complete results from a 1-month benchmark evaluating the impact of this chemistry update may be viewed at this link.

2. C2H2 and C2H4 chemistry

This update introduces new advected species C2H2, C2H4, ETHN, and ETHP and adds one photolysis reaction. The new chemistry has a large (>10% impact) on GLYC, GLYX, H2O2, HCOOH, HMHP, MO2, MOH, MP, SOAGX (see this table). Global mean OH is reduced by -1.49%. Complete results from a 1-month benchmark evaluating the impact of this chemistry update may be viewed at this link.

3. Fixed typo in CloudHet

This fix has a large impact on many halogen species and changed global mean OH by +6.65%. These large changes are expected, because this bug was in the CloudHet routine (which is used to adjust heterogeneous reaction rates based on the amount of cloud in the grid box). See this Github issue for further discussion on the changes from this fix.

4. Revise gamma(N2O5) computation; cap A at 3.2e-8

This update has a relatively small (<10%) impact on most species, but causes a large decrease in ClNO2. This is to be expected, because prior to this fix, the reaction probability (gamma) for ClNO2 het chem reactions was too high over the oceans. This update now caps gamma(ClNO2) at ~0.036, which is consistent with lab results. See this Github issue for further discussion on the changes from this update.

5. Updates to IONO2 hydrolysis from Wang et al. (2021)

This update has a large (>10%) impact on IONO2 and HOI, but a relatively small impact on other species (see this table). Global mean OH changed by -0.11%. See the original pull request on Github for more details of this update and its impact on model output.

6. Aromatic VOC chemistry

This update added new advected species AONITA, AROMP4, AROMP5, BALD, BENZP, BZCO3H, BZPAN, CSL, MCT, NPHEN, PHEN and four photolysis reactions. The impact on other species is summarized in this table, and global mean OH changed by -0.36%. Complete results from a 1-month benchmark evaluating the impact of this chemistry update may be viewed at this link.

7. Updated aerosol dry deposition

This feature brings aerosol dry deposition in line with https://www.pnas.org/content/117/42/26076 Emerson et al 2020]. The code modifications were minimal, and involved ly involves changing the values of certain aerosol parameters within the drydep_mod.F90. See this Github feature request for details on the expected impact of this update. Global mean OH increased by 0.024%. Most gas-phase species show small changes in mass (except for Br2 and ClNO2, which decreased by more than 5%). On the other hand, aerosol species such as AERI, ASOA1-4, DST1-4, show large decreases. On the other hand, the mass of MSA increased by 7.7%. Complete results from a 1-month benchmark evaluating the impact of this chemistry update may be viewed at this link.

8. Update volcano emissions to May 2020 and add climatology

The volcano emissions inventory from GMAO has been updated from v20180523 to v202005. Plots for a 1-month benchmark evaluating the impact of this fix may be viewed at this link. The impact on SO2 emissions from volcanoes is:
    ###################################################################################
    ### Emissions totals for inventory VOLCANOdegas [Tg]                            ###
    ### Ref = GCC_13.3.0-alpha.7; Dev = GCC_13.3.0-alpha.8                          ###
    ###################################################################################
                                        Ref                 Dev     Dev - Ref    % diff
    VOLCANOdegas SO2   :           1.953161            1.826465     -0.126697    -6.487
  
    ###################################################################################
    ### Emissions totals for inventory VOLCANOerupt [Tg]                            ###
    ### Ref = GCC_13.3.0-alpha.7; Dev = GCC_13.3.0-alpha.8                          ###
    ###################################################################################
                                        Ref                 Dev     Dev - Ref    % diff
    VOLCANOerupt SO2   :           0.000000            0.101063      0.101063       nan

9. Avoid double counting of acetone source from monoterpenes when using online MEGAN

This update reduced ACET emissions in the MEGAN extension. Plots for a 1-month benchmark evaluating the impact of this fix may be viewed at this link. The impact on total ACET emissions from MEGAN is:
    ###################################################################################
    ### Emissions totals for inventory MEGAN [Tg]                                   ###
    ### Ref = GCC_13.2.1; Dev = GCC_13.3.0-alpha.0                                  ###
    ###################################################################################
                                        Ref                 Dev     Dev - Ref    % diff
    MEGAN ACET         :           4.967504            4.374804     -0.592700   -11.932

The following updates introduced differences on the order of numerical noise:

Approval
Requires further investigation:
Approved by:
Date of approval:

1-year benchmarks

TBD

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