GEOS-Chem 13.0.0

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GEOS-Chem Main Page | GCHP Main Page

This page includes information about GEOS-Chem 13.0.0.

Version overview

The following items have been added to GEOS-Chem 13.0.0 since the last benchmark for GEOS-Chem 12.9.0.

Feature Submitted by Type
Updates that will affect full-chemistry simulations
Changes to benchmark setup:
  • Use MERRA-2 meteorology instead of GEOS-FP
  • Update benchmark year from 2016 to 2019
  • Use restart file that has been spun up (July 2016 restart file from GEOS-Chem 12.9.0 1-year benchmark)
GCST Structural
Update to CEDS_GBD-MAPS emission inventory (1970 - 2017), including:
  • Use CEDS GDB-MAPS total anthropogenic emissions by default; emissions by fuel type is optional
  • Make CEDS GCP-MAPS inventory the default for anthropogenic emissions and turn older regional inventories off
Erin McDuffie (Dalhousie) Science
Retire carbon-based units for VOCs Melissa Sulprizio (GCST) Science
Removal of HEMCO code from within the non-local PBL mixing modules Bob Yantosca (GCST) Structural
Use same input files for GEOS-Chem Classic and GCHP GCST Structural
Heterogeneous chem fixes, performance improvements, and clarification Chris Holmes (FSU) Bug fix
Fix handling of NOx coefficients in ucx_mod.F90 Sebastian Eastham (MIT) Bug fix
Prevent divide-by-zero errors in UCX routine UCX_NOX Bob Yantosca (GCST) Bug fix
Updates that will NOT affect full-chemistry simulations
Use GEOS-FP 5.22 data for Jan - May 2020 and store GEOS-FP 5.25 for April - May 2020 as option Jun Meng (GCST)
Melissa Sulprizio (GCST)
Data
Update QFED emissions through July 2020 Christoph Keller (NASA GMAO) Science
ODIAC fossil fuel emissions for CO2 simulations Jenny Fisher (UOW)
Yi Cao (UOW)
Science
Global Hg emissions from Streets et al. (2019) (as option) Colin Thackray (Harvard) Science
Global Hg emissions from EDGARv4.tox2 (as option) Amanda Giang (UBC) Science
Global Inventory of Methane Emissions from Fuel Exploitation Tia Scarpelli (Harvard) Science
Retire tropchem mechanism; implement new tropchem simulation using Standard mechanism below the tropopause and archived P/L rates above Melissa Sulprizio (GCST) Science
RRTMG fixes and updates Sebastian Eastham (MIT)
Lizzie Lundgren (GCST)
Bug fix
Fixes for typos: GCST Bug fix
Add global mean OH and CH4 lifetime diagnostics Bob Yantosca (GCST) Structural
Retire the GNU Make build system in both GEOS-Chem Classic and GCHP and replace with CMake Liam Bindle (WashU)
GCST
Structural
Create new GCClassic wrapper repository Lizzie Lundgren (GCST) Structural
Separate HEMCO from GEOS-Chem to use as a git submodule in GCClassic and GCHPctm Lizzie Lundgren (GCST) Structural
Retire the GEOS-Chem Unit Tester repository and move GEOS-Chem run directory creation to the GEOS-Chem repository Melissa Sulprizio (GCST) Structural
Updates to GEOS-Chem and HEMCO interface for compatibility with CESM Haipeng Lin (Harvard)
Thibaud Fritz (MIT)
Lizzie Lundgren (GCST)
Structural
Dynamically allocate diagnostic arrays based on HISTORY.rc content to minimize memory footprint Bob Yantosca (GCST) Structural
Clean up time cycle flags used in HEMCO_Config.rc Melissa Sulprizio (GCST) Structural
Update dry deposition flux diagnostic when using full PBL mixing so not all zeros Lee Murray (U. Rochester)
Lizzie Lundgren (GCST)
Bug fix
Fix sea salt diagnostics in configuration file for standard simulation so not all zeros Lizzie Lundgren (GCST) Bug fix
Features only affecting GCHP:
Retire the existing GCHP repository and replace with a new wrapper repository (GCHPctm) that uses ESMF as an external library and integrates GEOS-Chem and NASA/GMAO GEOS-ESM git repositories as git submodules Lizzie Lundgren (GCST) Structural
Enable a stretched grid capability in GCHP to run global simulations at regional high resolution Liam Bindle (WashU) Structural
Update MAPL (v2.2.7) and GMAO library dependencies Lizzie Lundgren (GCST) Structural
Enable GCHP to be compiled with RRTMG Sebastian Eastham (MIT)
Lizzie Lundgren (GCST)
Science
Avoid read problems in offline lightning by using daily rather than monthly files Lizzie Lundgren (GCST) Bug fix
Set met variable FRCLND to Olson fraction land not external met data Lizzie Lundgren (GCST) Bug fix
Enable zero diff in transport tracer simulation between single and multiple consecutive runs Lizzie Lundgren (GCST) Bug fix

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
CEDS DEFAULT
(full-chemistry simulations)
CEDS_GBD-MAPS emission inventory (1970 - 2017) HEMCO/CEDS/v2020-08/
QFED OPTIONAL Update QFED emissions through July 2020 HEMCO/QFED/v2018-07/
ODIAC CO2 DEFAULT
(CO2 simulations)
ODIAC fossil fuel emissions for CO2 simulations HEMCO/CO2/v2019-12/
MERCURY OPTIONAL
(Hg simulations)
Updated Streets Hg emissions

Updated EDGAR 4.3 Hg emissions

HEMCO/MERCURY/v2020-07/
CH4 DEFAULT
(CH4 simulations)
Global Inventory of Methane Emissions from Fuel Exploitation

Updated wetland and seep CH4 emissions

HEMCO/CH4/v2020-02/

HEMCO/CH4/v2020-04/

OFFLINE_LIGHTNING DEFAULT
(GCHP full-chemistry simulations)
Offline lightning inventory (v2020-03) saved as daily rather than monthly files HEMCO/OFFLINE_LIGHTNING/v2020-11/

1-month benchmarks

Model setup

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

Git tag(s): 13.0.0-rc.0 (same as 13.0.0-alpha.13, 13.0.0-beta.0)
Compared to previous benchmark: 12.9.0
Software environment: ifort 18.0.5
OpenMPI 4.0.1
netcdf-fortran 4.5.2
CMake 3.16.1
ESMF 8.0.1
Meteorology fields: MERRA-2
  • GEOS-Chem Classic: 4° x 5°
  • GCHP: 0.5° x 0.625°
Initial conditions: July 1, 2016 from 12.9.0 1-year benchmark
  • GEOS-Chem Classic: 4° x 5°
  • GCHP: C48 regridded from GEOS-Chem Classic 4° x 5°
Benchmark month: July 2019
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.

GEOS-Chem Classic 13.0.0 vs 12.9.0

Below are links to plots and tables comparing 1-month simulations for GEOS-Chem Classic 13.0.0 (Dev) and GEOS-Chem Classic 12.9.0 (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

sfc 500hPa full column stratosphere sfc AOD
Bromine

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

sfc 500hPa full column stratosphere sfc
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 sfc
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 sfc
Primary Organics

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

sfc 500hPa full column stratosphere sfc
Secondary Organics

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

sfc 500hPa full column stratosphere sfc
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 sfc
Sulfur

SOx, DMS, OCS, SO2, SO4

sfc 500hPa full column stratosphere sfc
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
Budgets Budgets after operations


GCHP 13.0.0 vs 12.9.0

Below are links to plots and tables comparing 1-month simulations for GCHP 13.0.0 (Dev) and GCHP 12.9.0 (Ref).

Species Category2 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

sfc 500hPa full column stratosphere sfc AOD
Bromine

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

sfc 500hPa full column stratosphere sfc
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 sfc
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 sfc
Primary Organics

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

sfc 500hPa full column stratosphere sfc
Secondary Organics

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

sfc 500hPa full column stratosphere sfc
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 sfc
Sulfur

SOx, DMS, OCS, SO2, SO4

sfc 500hPa full column stratosphere sfc
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

Budgets Budgets after operations


GCHP 13.0.0 vs GEOS-Chem 13.0.0

Below are links to plots and tables comparing 1-month simulations for GCHP 13.0.0 (Dev) and GEOS-Chem Classic 13.0.0 (Ref).

Species Category2 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

sfc 500hPa full column stratosphere sfc AOD
Bromine

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

sfc 500hPa full column stratosphere sfc
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 sfc
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 sfc
Primary Organics

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

sfc 500hPa full column stratosphere sfc
Secondary Organics

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

sfc 500hPa full column stratosphere sfc
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 sfc
Sulfur

SOx, DMS, OCS, SO2, SO4

sfc 500hPa full column stratosphere sfc
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

Budgets Budgets after operations


GCHP vs GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 13.0.0 - GCHP 12.9.0] against the difference [GC Classic 13.0.0 - GC Classic 12.9.0], taken from 1-month benchmark simulations.

Category Plots
Level Map Zonal Mean
Oxidants

O3, CO, OH, NOx

sfc 500hPa full column stratosphere
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

sfc 500hPa full column stratosphere
Bromine

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

sfc 500hPa full column stratosphere
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
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
Primary Organics

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

sfc 500hPa full column stratosphere
Secondary Organics

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

sfc 500hPa full column stratosphere
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
Sulfur

SOx, DMS, OCS, SO2, SO4

sfc 500hPa full column stratosphere
ROy

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

sfc 500hPa full column stratosphere

NOTE: At present diff-of-diffs plots are only generated for species concentrations.

Benchmark assessment form

Performance GEOS-Chem Classic GCHP
Grid resolution: 4° x 5° C48
# CPUs, nodes: 24 CPUs
1 node (Intel Cascade Lake)
48 CPUs
2 nodes (Intel Broadwell)
Wall time: 06:54:01 14:26:01
CPU time / wall time: 19.4750 47.0915
% of ideal performance: 81.15% 98.11%
Memory: 13.68 GB 71.56 GB
Global mean OH:
(% change from previous version)
11.22769648880 x 105 molec/cm3
(-8.60%)
11.24518930757 x 105 molec/cm3
(N/A)
Methyl chloroform lifetime:
(% change from previous version)
5.5460 years
(+8.20%)
5.5318 years
(N/A)
Methane lifetime:
(% change from previous version)
9.3297 years
(+8.09%)
9.3064 years
(N/A)
Details
Species, J-Values, and COLUMN AOD values that changed by 10% or more at the surface: GEOS-Chem Classic 13.0.0 vs 12.9.0 GCHP 13.0.0 vs 12.9.0

GCHP vs GEOS-Chem Classic 13.0.0

Species and J-Values that changed by 10% or more at 500 hPa: GEOS-Chem Classic 13.0.0 vs 12.9.0 GCHP 13.0.0 vs 12.9.0

GCHP vs GEOS-Chem Classic 13.0.0

Species and J-Values that changed by 10% or more in zonal mean: GEOS-Chem Classic 13.0.0 vs 12.9.0 GCHP 13.0.0 vs 12.9.0

GCHP vs GEOS-Chem Classic 13.0.0

Emissions that changed by 10% or more: GEOS-Chem Classic 13.0.0 vs 12.9.0 GCHP 13.0.0 vs 12.9.0

GCHP vs GEOS-Chem Classic 13.0.0

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. Changes to benchmark setup

Changing from GEOS-FP to MERRA-2 meteorology impacted the concentrations of most species, most notably over land and in the Tropics. Global mean OH increased by 2.11%. In addition, changing the meteorology fields impacted emissions computed by HEMCO extensions (MEGAN, soil NOx, lightning NOx, dust, etc.). Those changes are summarized below in this table of emissions by inventory created from an internal benchmark isolating just the impact of changing from GEOS-FP to MERRA-2.
The differences described above likely arise from differences in the GEOS system used to generate the two products. GEOS-FP meteorology for July 2016 are from the GEOS-5.13.1 system while MERRA-2 is frozen at GEOS-5.12.4. See NASA GMAO's website for more details on differences between GEOS versions: https://gmao.gsfc.nasa.gov/GMAO_products/NRT_products.php.
  • Update benchmark year from 2016 to 2019
Changing the benchmark year from 2016 to 2019 impacted the concentrations of most species and caused global mean OH to decrease by 1.97%. This update primarily impacted the emissions used in the benchmark simulation. For GFED and volcano emissions, changing the year meant updating to a more recent emissions year. As with changing meteorology fields, changing meteorology year also changed emissions computed by HEMCO extensions. Those changes are summarized below in this table of emissions by inventory created from an internal benchmark isolating just the impact of changing the simulation year from July 2016 to July 2019.
  • Use restart file that has been spun up
The GEOS-Chem restart file is typically updated for each major version release. This means that a restart file generated using GEOS-Chem 12.0.0 has been used for all 1-month benchmarks in the GEOS-Chem 12 series. Many science updates (e.g. updated halogen and isoprene chemistry) went into that version, so the initial conditions provided by that restart file are likely not representative of actual concentrations. In addition, any new species added since 12.0.0 are not included in that restart file so those species are initialized to default background concentrations. To address this, we have updated the restart file to use the July 2016 restart file from the last 1-year benchmark (12.9.0), which has been spun up for at least a 1.5 years (more if you include spin-up from previous 1-year benchmarks).
This update impacted concentrations of all species and global mean OH decreased by 3.45%. The exact difference in the initial concentrations from the old and new restart files can be found by viewing the log files from the 1-month benchmarks for GEOS-Chem 12.9.0 and GEOS-Chem 13.0.0. A snippet of that output is included here:
  From GC_12.9.0.log:
  ===============================================================================
  R E S T A R T   F I L E   I N P U T

  Min and Max of each species in restart file [mol/mol]:
  Species   1,     ACET: Min = 1.000000003E-30  Max = 2.716920022E-08
  Species   2,     ACTA: Min = 1.000000003E-30  Max = 7.725763085E-11
  Species   3,     AERI: Min = 1.037870635E-15  Max = 7.207419123E-12
  Species   4,     ALD2: Min = 4.684888406E-23  Max = 4.086598082E-08
  ...
  Species  88,    HONIT: Min = 1.000000003E-30  Max = 1.707073372E-11
  Species  89,    HPALD1: Use background = 9.999999683E-21
  Species  90,    HPALD2: Use background = 9.999999683E-21
  Species  91,    HPALD3: Use background = 9.999999683E-21
  Species  92,    HPALD4: Use background = 9.999999683E-21
  Species  93,   HPETHNL: Use background = 9.999999683E-21
  ...
  From GCC_13.0.0-beta.0.log:
  ===============================================================================
  R E S T A R T   F I L E   I N P U T

  Min and Max of each species in restart file [mol/mol]:
  Species   1,     ACET: Min = 1.198645368E-22  Max = 1.961477203E-08
  Species   2,     ACTA: Min = 7.944660459E-23  Max = 9.854482785E-10
  Species   3,     AERI: Min = 3.872448817E-16  Max = 1.060779242E-11
  Species   4,     ALD2: Min = 3.997531496E-23  Max = 1.028521712E-08
  ...
  Species  88,    HONIT: Min = 8.688050479E-44  Max = 4.034103954E-11
  Species  89,   HPALD1: Min = 0.000000000E+00  Max = 8.148696995E-11
  Species  90,   HPALD2: Min = 0.000000000E+00  Max = 1.696967566E-10
  Species  91,   HPALD3: Min = 0.000000000E+00  Max = 5.354099109E-11
  Species  92,   HPALD4: Min = 0.000000000E+00  Max = 1.183441123E-10
  Species  93,  HPETHNL: Min = 0.000000000E+00  Max = 1.283986667E-10
  ...

2. CEDS_GBD-MAPS emission inventory (1970 - 2017)

This benchmark now uses CEDS Global Burden of Disease - Major Air Pollution Sources (GBD-MAPS) emissions for 2017, as opposed to the prior CEDS inventory released for CMIP6 (Hoesly et al., 2018) for which 2014 was the last year. The impact of this update can be viewed in the anthropogenic emissions plots and in the emissions tables by inventories and species.
In addition, CEDS emissions are now the default anthropogenic emissions inventory, and older regional inventories (APEI, DICEAfrica, MIX, NEI2011) have been turned off in HEMCO_Config.rc. The impact of this is large changes in emissions over those regions. The species ACET, HAC, HNO2, ISOP, MACR, MVK, NO2, RCHO now have zero anthropogenic emissions because those species were included in one or more of the aforementioned regional inventories but are not included in CEDS GDB-MAPS emissions.

3. Retire carbon-based units for VOCs

The impact of retiring carbon-based units can be observed in the difference plots and tables for ACET, ALD2, ALK4, BENZ, C2H6, C3H8, EOH, ISOP, MEK, PRPE, TOLU, XYLE. Those species were traditionally treated as having a molecular weight of 12.0 g/mol which in some cases would be multiplied by the molecular ratio or number of carbon atoms in that species. Differences introduced by this update are primarily small, but arise from the difference between the actual species molecular weights compared to the molecular weight of carbon multiplied by the number of carbons (e.g. for acetone the actual molecular weight is 58.02 g/mol while it was previously treated as 12.0*3=36.0 g/mol). In addition, the GEOS-Chem and HEMCO output in 12.9.0 and earlier indicated units of v/v or kg/m2/s for many of these species when it was actually vC/v and kgC/m2/s, and this led to incorrect unit conversions in GCPy when creating benchmark plots and tables. Where possible, we have corrected that in this benchmark output for 13.0.0 so we are comparing similar units for 12.9.0 and 13.0.0 output but some species like EOH still show large differences.

4. Heterogeneous chem fixes, performance improvements, and clarification

These fixes primarily caused differences in concentrations of halogen species and other species involved in heterogeneous chemistry. Issues that have been addressed include: in-cloud condensate surface area, ice density in calculation of ice volume, cloud uptake of NO3 was double counted, and cloud uptake of NO2 was neglected. With these fixes, global mean OH decreased by 3.45%.

5. Use same input files for GEOS-Chem Classic and GCHP

  • C3H8, C2H6, NH3, and dust emissions have changed because of this update. GCHP has been using 2x2.5 files for those emissions, so we updated GEOS-Chem Classic to use those files as well (instead of the coarser 4x5 files). This change was caught by the internal benchmark denoted 13.0.0-alpha.8.

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

Additional notes:

  • Natural emissions of NH3 and emissions of ALD2 and EOH from plant decay appear to be zero in the natural emissions plots and emission tables by species. This is a diagnostic issue resulting from typos in HEMCO_Diagn.rc and has been fixed in the latest development code. The correct values can be found in the emissions table by inventory (see `GEIAnatural NH3`, `PLANTDECAY ALD2`, and `PLANTDECAY EOH`).
  • There appears to be an issue in the diagnostics for O3+hv->O(1D) and O(3P), but this is simply due to a diagnostic name change. In GEOS-Chem 12.9.0, those fields were saved to Jval_O3OP and Jval_O3O1D. In 13.0.0, they’re saved out to JvalO3OP and JvalO3O1D. Bob wrote, “This was intentional. Prior to the netCDF reduction of memory the State_Diag%JVal array had nPhotol+2 slots. The extra 2 were JVal_O1D and Jval_O3P. But we coudln't wild card O1D and O3P because they are not species names found in the species database. Rather than put in a kludgey workaround I decided to make it JvalO3O1D and JvalO3O3P. The _ implies a wild-card-able species name.” The GCPy plotting routines were only recognizing diagnostics beginning with “Jval_” so the new diagnostics were not plotted. I’ve fixed this and regenerated the J-value plots, so we can compare those fields (see pages 1-2 and 119-120). For future versions, GCPy will properly plot the differences using the new diagnostic names.
  • Many reviewers were concerned by the large change in dust emissions. These changes are primarily due to changing from 2016 GEOS-FP met fields to 2019 MERRA-2 met fields. In the DustDead extension, annual emissions are scaled to totals from a 2x2.5 GEOS-5 run for 2005. Therefore, these differences may appear large in the 1-month output, but should be less when we evaluate the annual totals in the 1-year benchmark. In addition, there are large differences in dust emissions between GCClassic and GCHP and this is due to the use of online dust emissions. To avoid this, the default recommendation for both GCClassic and GCHP is to use offline dust emissions but for the purpose of benchmarking the state-of-science code, we use online emissions in benchmarks,


Approval
Requires further investigation: No
Approved by: GCSC
Date of approval: 18 Nov 2020

1-year full-chemistry benchmarks

Model setup

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

Git tag(s): TBD
Compared to previous benchmark: 12.9.0
Software environment: ifort 18.0.5
OpenMPI 4.0.1
netcdf-fortran 4.5.2
CMake 3.16.1
ESMF 8.0.1
Meteorology fields: MERRA-2
  • GEOS-Chem Classic: 4° x 5°
  • GCHP: 0.5° x 0.625°
Spin-up initial conditions: TBD
  • GEOS-Chem Classic: 4° x 5°
  • GCHP: C48 regridded from GEOS-Chem Classic 4° x 5°
Benchmark date: Spin-up run: Jan 2018 - Dec 2018
Production run: Jan 2019 - Dec 2019

Benchmark Plots and Tables

Coming soon

1-year transport tracers benchmarks

Model setup

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

Git tag(s): TBD
Compared to previous benchmark: 12.9.0
Software environment: ifort 18.0.5
openmpi 4.0.1
netcdf-fortran 4.5.2
cmake 3.16.1
Meteorology fields: MERRA-2
  • GEOS-Chem Classic: 4° x 5°
  • GCHP: 0.5° x 0.625°
Benchmark date: Spinup run: Jan 2015 - Dec 2018
Production run: Jan 2019 - Dec 2019

Benchmark Plots and Tables

Coming soon

10-year stratospheric benchmarks

Model setup

The following table describes the GEOS-Chem setup for both GEOS-Chem Classic and GCHP 10-year benchmark simulations.

Git tag(s): TBD
Compared to previous benchmark: N/A
Software environment: ifort 18.0.5
openmpi 4.0.1
netcdf-fortran 4.5.2
cmake 3.16.1
Meteorology fields: MERRA-2
  • GEOS-Chem Classic: 4° x 5°
  • GCHP: 0.5° x 0.625°
Benchmark date: Jan 2010 - Dec 2019

Benchmark Plots and Tables

Coming soon