Benchmark/GEOS-Chem 12.9.0

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This page includes information about all benchmark simulations for GEOS-Chem 12.9.0.

GEOS-Chem Classic 1-month benchmark

Benchmark plots

Enable PDF bookmarks1 in the files linked below to navigate between species. See the Species in GEOS-Chem wiki page for species definitions and details.

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

Metrics OH concentration, MCF lifetime, CH4 lifetime
Budget tables GEOS-Chem 12.7.0 (Ref)

Budget totals by vertical region

GEOS-Chem 12.9.0 (Dev)

Budget totals by vertical region

Comparison of stratosphere and troposphere budgets

1All plots created with GCPy have PDF bookmarks. If you do not see them in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.

2Species category and lumped species definitions are simple to adjust. Updating them requires only editing the YAML files.

Benchmark assessment form

Description
New features added into GEOS-Chem
Feature Submitted by
Updates that WILL AFFECT the full-chemistry simulation


Updated halogen chemistry Xuan Wang (Harvard)
Improved cloudwater pH Viral Shah (Harvard)
Jonathan Moch (Harvard)
Update offline lightning data through Dec 2019 Lee Murray (Rochester)
Convert GEOS-Chem species database to YAML format, includes: Melissa Sulprizio (GCST)
Bob Yantosca (GCST)
Update GEOS-Chem core to apply masking and scaling to HEMCO inputs Lizzie Lundgren (GCST)
Bug fix: Restore missing photolysis reatctions from 12.8.0 and add an extra error check Melissa Sulprizio (GCST)
Updates that WILL NOT AFFECT the full-chemistry simulation
Corrected issue in GEOS-Chem dry-run where some files were not being properly marked for download Bob Yantosca (GCST)
Bug fixes for the ObsPack diagnostic: Bob Yantosca (GCST)
Skip reading FLASH_DENS and CONV_DEPTH fields when lightning NOx extension is turned off Melissa Sulprizio (GCST)
Updates that affect GCHP only
Fix bug where non-advected species not updated in restart file Sebastian Eastham (MIT)


Version, resolution, met fields used: GEOS-FP (72L), 4x5, July 2016
1-month benchmark finished on: Sun Jun 28 20:55:06 EDT 2020
Performance statistics:
  • Compiled with ifort 17.0.4
  • Ran on 24 CPUs of holyjacob01.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz)
  • Wall time: 08:22:12
  • CPU time / wall time: 20.9987
  • % of ideal performance: 87.48%
  • Memory: 13.5448 GB
Git tag 12.9.0-rc.0
Compared to previous benchmark: 12.8.0
This update will impact:
(select all that apply with boldface)
Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Emissions, Photolysis, Chemistry, Other (please specify):
Unit test results may be viewed at: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.9.0/GCC/Plots/GC_12.9.0_Jun26.results.html
Metrics
Global mean OH from log file (% change): 12.3097343665254 x 105 molec/cm3 (+3.70%)
Methyl chloroform lifetime (% change): 5.0471 years (-2.82%)
Methane lifetime (% change): 8.5551 years (-2.56%)
Overview
Comments on observed differences: Below we summarize the notable changes caused by specific updates.


Details
List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:
  • Aerosols: DST1 DST2 DST3 DST4 NH4 NIT SO4 BCPI BCPO OCPI OCPO Complex_SOA Simple_SOA AER

I BrSALA BrSALC ISALA ISALC NITs SALA SALC SO4s

  • Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO CH2Br2 CHBr3 HOBr HBr
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
  • Iodine: Iy IxOy I I2 IBr ICl IO IONO IONO2 CH3I CH2I2 CH2ICl CH2IBr HI HOI OIO
  • Nitrogen: NOy NOx HNO2 HNO3 HNO4 MPAN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4 MENO3 ETNO3 IPRNO3 NPRNO3
  • Oxidants: O3 CO OH NOx
  • Primary_Organics: EOH MOH ISOP MTPA MTPO LIMO ALK4 BENZ C2H6 C3H8 PRPE TOLU XYLE
  • ROy: H2O2 H H2O HO2 O1D OH RO2
  • Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOA3 ASOA1 ASOA2 ASOA3 ASOAN TSOG0 TSOG1 TSOG2 TSOG3 ASOG1 ASOG2 ASOG3 INDIOL LVOCOA SOAIE SOAGX SOAP SOAS
  • Secondary_Organics: ACTA ALD2 CH2O HPALDs MACR IEPOX ACET MEK MVK ISOPN GLYX HCOOH MAP RCHO MP
  • Sulfur: SOx DMS SO2 SO4
  • J-Values: ACET ALD2 ATOOH Br2 BrCl BrNO2 BrNO3 BrO CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Br2 CH2Cl2 CH2I2 CH2IBr CH2ICl CH2O CH3Br CH3CCl3 CH3Cl CH3I CHBr3 Cl2 Cl2O2 ClNO2 ClNO3 ClO ClOO ETHLN ETNO3 ETP GLYC GLYX H1211 H1301 H2402 H2O2 HAC HCFC123 HCFC141b HCFC142b HCFC22 HMHP HNO2 HNO3 HNO4 HOBr HOCl HOI HONIT HPETHNL I2 I2O2 I2O3 I2O4 IBr ICN ICl IDN INO IO IONO IONO2 IPRNO3 MACR MACR1OOH MAP MCRENOL MCRHN MCRHNB MCRHP MEK MENO3 MGLY MONITS MONITU MP MPN MVK MVKHC MVKHCB MVKHP MVKN MVKPC N2O N2O5 NO NO2 NO3 NPRNO3 O2 O3O1D O3O3P OCS OClO OIO PAN PIP PP PROPNN PRPN PYAC R4N2 R4P RA3P RB3P RCHO RP
  • Column AOD: Dust BCPI OCPI SALA SALC SO4 Polar_Strat_Cloud SOA_from_Aqueous_ISOP Strat_Liquid_Aerosol Total
List all 500 hPa species and J-Values that changed by 10% or more :
  • Aerosols: DST1 DST2 DST3 DST4 NH4 NIT SO4 BCPI BCPO OCPI OCPO Complex_SOA Simple_SOA AERI BrSALA BrSALC ISALA ISALC NITs SALA SALC SO4s
  • Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO CH2Br2 CHBr3 HOBr HBr
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 CH2Cl2 CH3CCl3 CHCl3 HOCl HCl OClO
  • Iodine: Iy IxOy I I2 IBr ICl IO IONO IONO2 CH3I CH2I2 CH2ICl CH2IBr HI HOI OIO
  • Nitrogen: NOy NOx HNO2 HNO3 HNO4 MPAN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4 MENO3 ETNO3 IPRNO3 NPRNO3
  • Oxidants: O3 CO OH NOx
  • Primary_Organics: EOH MOH ISOP MTPA MTPO LIMO ALK4 BENZ C2H6 C3H8 PRPE TOLU XYLE
  • ROy: H2O2 H H2O HO2 O1D OH RO2
  • Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOA3 ASOA1 ASOA2 ASOA3 ASOAN TSOG0 TSOG1 TSOG2 TSOG3 ASOG1 ASOG2 ASOG3 INDIOL LVOCOA SOAIE SOAGX SOAP SOAS
  • Secondary_Organics: ACTA ALD2 CH2O HPALDs MACR IEPOX ACET MEK MVK ISOPN GLYX HCOOH MAP RCHO MP
  • Sulfur: SOx DMS SO2 SO4
List all ZONAL MEAN species and J-Values that changed by 10% or more:
  • Aerosols: DST1 DST2 DST3 DST4 NH4 NIT SO4 BCPI BCPO OCPI OCPO Complex_SOA Simple_SOA AERI BrSALA BrSALC ISALA ISALC NITs SALA SALC SO4s
  • Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO CH3Br CH2Br2 CHBr3 HOBr HBr
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 CCl4 CFCs CH3Cl CH2Cl2 CH3CCl3 CHCl3 HOCl HCl Halons HCFCs OClO
  • Iodine: Iy IxOy I I2 IBr ICl IO IONO IONO2 CH3I CH2I2 CH2ICl CH2IBr HI HOI OIO
  • Nitrogen: NOy NOx HNO2 HNO3 HNO4 MPAN NIT NO NO2 NO3 N2O5 MPN PAN PPN N2O NHx NH3 NH4 MENO3 ETNO3 IPRNO3 NPRNO3
  • Oxidants: O3 CO OH NOx
  • Primary_Organics: EOH MOH ISOP MTPA MTPO LIMO ALK4 BENZ CH4 C2H6 C3H8 PRPE TOLU XYLE
  • ROy: H2O2 H H2O HO2 O1D OH RO2
  • Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOA3 ASOA1 ASOA2 ASOA3 ASOAN TSOG0 TSOG1 TSOG2 TSOG3 ASOG1 ASOG2 ASOG3 INDIOL LVOCOA SOAIE SOAGX SOAP SOAS
  • Secondary_Organics: ACTA ALD2 CH2O HPALDs MACR IEPOX ACET MEK MVK ISOPN GLYX HCOOH MAP RCHO MP
  • Sulfur: SOx DMS OCS SO2 SO4
  • J-Values: ACET ALD2 ATOOH Br2 BrCl BrNO2 BrNO3 BrO CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Br2 CH2Cl2 CH2I2 CH2IBr CH2ICl CH2O CH3Br CH3CCl3 CH3Cl CH3I CHBr3 Cl2 Cl2O2 ClNO2 ClNO3 ClO ClOO ETHLN ETNO3 ETP GLYC GLYX H1211 H1301 H2402 H2O2 HAC HCFC123 HCFC141b HCFC142b HCFC22 HMHP HNO2 HNO3 HNO4 HOBr HOCl HOI HONIT HPETHNL I2 I2O2 I2O3 I2O4 IBr ICN ICl IDN INO IO IONO IONO2 IPRNO3 MACR MACR1OOH MAP MCRENOL MCRHN MCRHNB MCRHP MEK MENO3 MGLY MONITS MONITU MP MPN MVK MVKHC MVKHCB MVKHP MVKN MVKPC N2O N2O5 NO NO2 NO3 NPRNO3 O2 O3O1D O3O3P OCS OClO OIO PAN PIP PP PROPNN PRPN PYAC R4N2 R4P RA3P RB3P RCHO RP SO4
List all EMISSIONS that changed by 10% or more:
  • Biogenic: ACET ALD2 EOH ISOP LIMO MOH MTPA MTPO PRPE SOAP SOAS
  • Lightning: NO
  • Natural: DST1 DST2 DST3 DST4 SALA SALC
  • Ocean: ACET ALD2 DMS ETNO3 MENO3 MOH
  • Ship: HNO3 NO2 NO O3
  • Soil: NO
  • Total: ACET ALD2 DST1 EOH ISOP MOH MTPA NO PRPE SOAP
Approval
Requires further investigation:
Approved by:
Date of approval:

GCHP 1-month benchmark

The following sections contain validation plots for GCHP 12.9.0.

Comparison of GCHP versions

This table contains plots comparing GCHP 12.8.0 (Ref) and GCHP 12.9.0 (Dev) for a 1-month simulation.

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

Comparison of GCHP and GEOS-Chem Classic

This table contains plots comparing GEOS-Chem Classic 12.9.0 (Ref) against GCHP 12.9.0 (Dev) for a 1-month simulation.

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


GCHP and GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 12.9.0 - GCHP 12.8.0] against the difference [GC Classic 12.9.0 - GC Classic 12.8.0], taken from 1-month benchmark simulations.

Category Plots
Level Map Zonal Mean
Oxidants sfc 500hPa full column stratosphere
Aerosols sfc 500hPa full column stratosphere
Bromine sfc 500hPa full column stratosphere
Chlorine sfc 500hPa full column stratosphere
Iodine sfc 500hPa full column stratosphere
Nitrogen sfc 500hPa full column stratosphere
Primary Organics sfc 500hPa full column stratosphere
Secondary Organics sfc 500hPa full column stratosphere
Secondary Organic Aerosols sfc 500hPa full column stratosphere
Sulfur sfc 500hPa full column stratosphere
ROy sfc 500hPa full column stratosphere

NOTE: At present, we have only created the diff-of-diffs plots for species concentration. This can be extended to other categories in the future.