Benchmark/GEOS-Chem 12.9.0

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 PBL Troposphere Full atmosphere			GEOS-Chem 12.9.0 (Dev) Budget totals by vertical region PBL Troposphere Full atmosphere 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: Defining all species properties in the species database, not just advected species Initializing the species database with values read from the YAML file 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: Change units of ObsPack specific humidity (Q) field to g/kg Restore missing code due to Git merge that caused the OBSPACK MENU of input.geos not to be read 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:	Wed Jun 17 02:09:24 EDT 2020
Performance statistics:	Compiled with ifort 17.0.4 Ran on 48 CPUs of holy7c22103.rc.fas.harvard.edu Wall time: 08:21:40 CPU time / wall time: 20.8233 % of ideal performance: 43.38% Memory: 13.5429 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_Jun18.results.html
Metrics
Global mean OH from log file (% change):	12.2776500175971 x 105 molec/cm3 (+3.54%)
Methyl chloroform lifetime (% change):	5.1261 years (-1.90%)
Methane lifetime (% change):	8.6318 years (-1.68%)
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: NH4 NIT SO4 Complex_SOA AERI BrSALA BrSALC ISALA ISALC NITs SO4s Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO 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 CH2I2 HI HOI OIO Nitrogen: NOy NOx HNO2 HNO3 HNO4 MPAN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4 MENO3 ETNO3 Oxidants: O3 OH NOx Primary_Organics: EOH MOH ISOP MTPA MTPO LIMO TOLU XYLE ROy: H2O2 H HO2 O1D OH RO2 Secondary_Organic_Aerosols: ASOA3 ASOAN ASOG3 INDIOL LVOCOA SOAIE SOAGX Secondary_Organics: ACTA CH2O HPALDs MACR IEPOX MVK ISOPN GLYX MAP RCHO MP Sulfur: SOx DMS SO2 SO4 J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Br2 CH2Cl2 CH3CCl3 CH3Cl H1301 HCFC123 HCFC141b HCFC142b HCFC22 N2O O2 Column AOD: BCPI OCPI SALA SALC SO4 SOA_from_Aqueous_ISOP
List all 500 hPa species and J-Values that changed by 10% or more :	Aerosols: NH4 NIT BrSALA BrSALC ISALA ISALC NITs SO4s Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO 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 CH2I2 HI HOI OIO Nitrogen: NOy NOx HNO2 HNO3 HNO4 MPAN NIT NO NO2 NO3 N2O5 MPN PAN NHx NH3 NH4 MENO3 Oxidants: O3 OH NOx Primary_Organics: EOH ISOP MTPA MTPO LIMO ALK4 C2H6 C3H8 TOLU ROy: H2O2 H HO2 O1D OH RO2 Secondary_Organic_Aerosols: ASOA1 ASOA3 ASOG1 ASOG3 SOAGX Secondary_Organics: CH2O HPALDs MACR IEPOX MVK ISOPN GLYX Sulfur: DMS SO2
List all ZONAL MEAN species and J-Values that changed by 10% or more:	Aerosols: NH4 NIT SO4 BrSALA BrSALC ISALA ISALC NITs SO4s Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO 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 CH2I2 CH2ICl CH2IBr HI HOI OIO Nitrogen: NOx HNO2 HNO4 MPAN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4 MENO3 Oxidants: O3 OH NOx Primary_Organics: ISOP MTPA MTPO LIMO ALK4 C2H6 C3H8 PRPE TOLU XYLE ROy: H2O2 H HO2 O1D OH RO2 Secondary_Organic_Aerosols: ASOA1 ASOA3 ASOG1 ASOG3 SOAGX Secondary_Organics: ACTA ALD2 CH2O MACR IEPOX MEK MVK ISOPN GLYX HCOOH MAP RCHO MP Sulfur: SOx DMS SO2 SO4
List all EMISSIONS that changed by 10% or more:	Lightning: NO Ship: NO2 NO O3 Total: NO
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.