Benchmark/GEOS-Chem 12.6.0: Difference between revisions

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|[[FAST-JX_v7.0_photolysis_mechanism#Updated_aerosol_hygroscopicity_and_optics|Updated aerosol hygroscopicity and optics]]
|[[FAST-JX_v7.0_photolysis_mechanism#Updated_aerosol_hygroscopicity_and_optics|Updated aerosol hygroscopicity and optics]]
|Robyn Latimer (Dalhousie)<br>Jun Meng (Dalhousie)
|Robyn Latimer (Dalhousie)<br>Jun Meng (Dalhousie)
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|[[DICE-Africa_anthropogenic_emissions_inventory#Add_EDGAR_BCPI_and_BCPO_emissions_for_remaining_sectors_to_DICE-Africa|Add EDGAR BCPI and BCPO emissions for remaining sectors to DICE-Africa]]
|Tomas Sherwen (York)<br>Eloise Marais (Leicester)
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!colspan="2" bgcolor="#CCFFFF"|Updates that will NOT affect full-chemistry simulations


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|[[GEOS-Chem_chemistry_mechanisms#Aerosol_nitrate_photolysis_option|Aerosol nitrate photolysis option]] (off by default)
|[[GEOS-Chem_chemistry_mechanisms#Aerosol_nitrate_photolysis_option|Aerosol nitrate photolysis option]] (off by default)
|Tomas Sherwen (York)<br>Prasad Kasibhatla (Duke)
|Tomas Sherwen (York)<br>Prasad Kasibhatla (Duke)
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!colspan="2" bgcolor="#CCFFFF"|Updates that will NOT affect full-chemistry simulations


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|List all 500 hPa species and J-Values that changed by 10% or more :
|List all 500 hPa species and J-Values that changed by 10% or more :
|
|
 
* Oxidants: None
* Aerosols: NIT BCPI BCPO AERI BrSALA BrSALC
* Nitrogen: HNO3 IPMN NIT NO NO3 N2O5 NH3
* ROy: RO2
* Sulfur: DMS SO2
* Iodine: IxOy I I2 ICl IO INO2 CH2I2 OIO
* Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
* Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
* Primary_Organics: ALK4 BENZ PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX HCOOH MAP RCHO
* Secondary_Organics: MEK MVK ALD2 HPALD MP ISOPN IEPOX ACTA EOH
* Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOG0 TSOG1 ASOG1 INDIOL ISN1OA LVOCOA SOAIE SOAGX SOAME SOAMG


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|Comments on observed differences:
|Comments on observed differences:
|'''''Below we summarize the notable changes caused by specific updates.'''''
|'''''Below we summarize the notable changes caused by specific updates.'''''
'''[[GEOS-Chem_chemistry_mechanisms#Cloud_heterogeneous_chemistry|Combined heterogeneous chemistry updates]]'''
:This update causes widespread changes in species concentrations. Global mean OH concentrations change by -4.14% due to this update alone. Notable changes at the surface include increases in NO3 and N2O5 over land and global decrease in HNO2. NOy decreases globally in the mid-to-upper troposphere.
'''[[Dry_deposition#Cold-temperature_dry_deposition_updates|HNO3 cold-temperature deposition]]'''
:With this update, HNO3 concentrations decrease slightly at the surface and aloft while NOy increases slightly at all levels.
'''[[Secondary_organic_aerosols#Removal_of_VBS_isoprene_SOA|Remove isoprene in VBS]] (leaving aqueous)'''
'''[[FAST-JX_v7.0_photolysis_mechanism#Updated_aerosol_hygroscopicity_and_optics|Updated aerosol hygroscopicity and optics]]'''


'''[[DICE-Africa_anthropogenic_emissions_inventory#Scale_DICE-Africa_emissions_to_address_errors_in_inventory|Scale DICE-Africa emissions to address errors in inventory]]'''
'''[[DICE-Africa_anthropogenic_emissions_inventory#Scale_DICE-Africa_emissions_to_address_errors_in_inventory|Scale DICE-Africa emissions to address errors in inventory]]'''
:This update contributes to changes in BC and OC concentrations over and just downwind of Africa. Slight differences can also be seen over Africa in the emission maps. The impact on the inventory emission totals are included below.
:This update contributes to changes in BC and OC concentrations over and just downwind of Africa. Slight differences can also be seen over Africa in the emission maps. The impact on the inventory emission totals are included below.


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   DICEAfrica BCPI      :          0.004153            0.006925      0.002772 Tg
   DICEAfrica BCPI      :          0.004153            0.006925      0.002772 Tg
   DICEAfrica BCPO      :          0.016612            0.027698      0.011087 Tg
   DICEAfrica BCPO      :          0.016612            0.027698      0.011087 Tg




'''The following updates produced small changes:'''
'''The following updates produced small changes:'''
*'''[[GEOS-Chem_12#Quick_fix_for_aerosol_pH_calculation_when_dry|Quick fix for aerosol pH calculation when dry]]'''


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Revision as of 14:47, 19 September 2019


This page includes information about all benchmark simulations for GEOS-Chem 12.6.0.

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

NH4, NIT, SO4, DST1, DST2, DST3, DST4, BC, OC, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, SOA_Simple, SOA_Complex

sfc 500hPa full column stratosphere sfc AOD
Bromine

Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH4Br, CH2Br2, CH2Br2, CH3Br3, HOBr, HBr

sfc 500hPa full column stratosphere sfc
Chlorine

Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH4CCl3, HOCl, HCl, Halons, HCFCs, OClO

sfc 500hPa full column stratosphere --
Iodine

Iy, IxOy, I, I2, IBr, ICl, IO, INO2, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO

sfc 500hPa full column stratosphere sfc
Nitrogen

NOy, NOx, HNO2, HNO3, HNO4, IMPN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4

sfc 500hPa full column stratosphere sfc
Primary Organics

ALK4, BENZ, CH4, C2H6, C2H4, C3H8, PRPE, TOLU, XYLE, ISOP, MTPA, MTPO, LIMO, GLYX, HCOOH, MAP, MBO, MOH, RCHO

sfc 500hPa full column stratosphere sfc
Secondary Organics

ACET, MEK, MVK, ALD2, CH2O, HPALD, MP, ISOPN, IEPOX, ACTA, EOH, MOH

sfc 500hPa full column stratosphere sfc
Secondary Organic Aerosols

SOAP, SOAS, TSOA0, TSOA1, TSOA2, TSOA3, ISOA1, ISOA2, ISOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ISOG1, ISOG2, ISOG3, ASOG1, ASOG2, ASOG3, INDIOL, ISN1OA, LVOCOA, SOAIE, SOAGX, SOAME, SOAMG

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

OH metrics OH concentration, MCF lifetime, CH4 lifetime

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 json files.

Benchmark assessment form

Description
New features added into GEOS-Chem
Feature Submitted by
Updates that will affect full-chemistry simulations
Combined heterogeneous chemistry updates, includes
  • N2O5, NO3, NO2 reactive uptake updates
  • Subgrid cloud NOy chemistry
 Chris Holmes (FSU)
Erin McDuffie (Dalhousie)
Viral Shah (UW)
Lyatt Jaegle (UW)
HNO3 cold-temperature deposition Viral Shah (Harvard)
Quick fix for aerosol pH calculation when dry Becky Alexander (UW)
Xuan Wang (Harvard)
Remove isoprene in VBS (leaving aqueous) Melissa Sulprizio (GCST)
Updated aerosol hygroscopicity and optics Robyn Latimer (Dalhousie)
Jun Meng (Dalhousie)
Add EDGAR BCPI and BCPO emissions for remaining sectors to DICE-Africa Tomas Sherwen (York)
Eloise Marais (Leicester)
Updates that will NOT affect full-chemistry simulations
Simple parameterization for CO2 dependence of stomatal resistance (off by default) Amos Tai (CUHK)
Aerosol nitrate photolysis option (off by default) Tomas Sherwen (York)
Prasad Kasibhatla (Duke)
CMake in GEOS-Chem Classic (optional) Liam Bindle (Dalhousie)
Enable GEOS-Chem "Classic" netCDF (History) diagnostics to be subsetted vertically and horizontally Bob Yantosca (GCST)
BB4CMIP historical biomass burning emissions (1750-2014)
  • NOTE: This is an optional emissions inventory.
 Pengfei Liu (Harvard)
Surface diagnostic (O3, HNO3) with user-selected height Katie Travis (MIT)
GCST
APM update and integration with GEOS-Chem 12 Gan Luo (SUNY-Albany)
Fangqun Yu (SUNY-Albany)
Version, resolution, met fields used: GEOS-FP (72L), 4x5, July 2016
1-month benchmark finished on: Sat Sep 14 03:12:29 EDT 2019
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: 07:10:48
  • CPU time / wall time: 21.4499
  • % of ideal performance: 89.37%
  • Memory: 13.0503 GB
Compared to previous benchmark: 12.5.0
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_12/12.6.0/GCC/Plots/GC_12.6.0_Sep13.results.html
Metrics
Global mean OH from log file (% change): 11.7776515135847 x 105 molec/cm3 (-5.54%)
Methyl chloroform lifetime (% change): 5.3395 (4.07%)
Methane lifetime (% change): 8.9801 years (3.83%)
List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:
  • Oxidants: NOx
  • Aerosols: NH4 NIT BCPI BCPO AERI BrSALA BrSALC ISALC NITs SO4s Complex_SOA
  • Nitrogen: NOy NOx HNO3 HNO4 IPMN NIT NO NO2 NO3 N2O5 MPN PAN PPN NH3 NH4
  • ROy: RO2
  • Sulfur: DMS SO2
  • Iodine: IxOy I I2 ICl IO INO2 IONO2 CH2I2 OIO
  • Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
  • Primary_Organics: ALK4 PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX RCHO
  • Secondary_Organics: MVK ALD2 HPALD ISOPN IEPOX EOH
  • Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOA2 TSOA3 ASOA1 ASOA2 ASOA3 TSOG0 TSOG1 TSOG2 TSOG3 ASOG1 ASOG2 ASOG3 INDIOL ISN1OA SOAIE SOAGX SOAME SOAMG
  • J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Cl2 CH3CCl3 CH3Cl HCFC123 HCFC141b HCFC142b HCFC22 N2O O2
  • Column AOD: BCPI SO4 SOA_from_Aqueous_ISOP Total
List all 500 hPa species and J-Values that changed by 10% or more :
  • Oxidants: None
  • Aerosols: NIT BCPI BCPO AERI BrSALA BrSALC
  • Nitrogen: HNO3 IPMN NIT NO NO3 N2O5 NH3
  • ROy: RO2
  • Sulfur: DMS SO2
  • Iodine: IxOy I I2 ICl IO INO2 CH2I2 OIO
  • Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
  • Primary_Organics: ALK4 BENZ PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX HCOOH MAP RCHO
  • Secondary_Organics: MEK MVK ALD2 HPALD MP ISOPN IEPOX ACTA EOH
  • Secondary_Organic_Aerosols: TSOA0 TSOA1 TSOG0 TSOG1 ASOG1 INDIOL ISN1OA LVOCOA SOAIE SOAGX SOAME SOAMG
List all ZONAL MEAN species and J-Values that changed by 10% or more:
  • Oxidants: OH NOx
  • Aerosols: NIT BCPO AERI BrSALA BrSALC SO4s
  • Nitrogen: NOx HNO3 IPMN NIT NO NO2 NO3 N2O5 MPN PPN NH3
  • ROy: H2O2 H HO2 OH RO2
  • Sulfur: DMS SO2
  • Iodine: IxOy I I2 IBr ICl IO INO2 IONO2 CH2I2 CH2ICl CH2IBr OIO
  • Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl HCl OClO
  • Primary_Organics: BENZ PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX MAP RCHO
  • Secondary_Organics: MEK MVK ALD2 HPALD MP ISOPN IEPOX ACTA EOH
  • Secondary_Organic_Aerosols: TSOA1 TSOA3 ASOA3 TSOG0 TSOG1 TSOG2 TSOG3 ASOG1 ASOG2 ASOG3 INDIOL ISN1OA LVOCOA SOAIE SOAGX SOAME SOAMG
  • J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CFC12 CH2Cl2 CH3CCl3 CH3Cl HCFC123 HCFC141b HCFC142b HCFC22 N2O O2
List all EMISSIONS that changed by 10% or more:
  • Anthro: BCPI BCPO
  • Ship: NO O3
  • Total: BCPI BCPO NO
Comments on observed differences: Below we summarize the notable changes caused by specific updates.

Combined heterogeneous chemistry updates

This update causes widespread changes in species concentrations. Global mean OH concentrations change by -4.14% due to this update alone. Notable changes at the surface include increases in NO3 and N2O5 over land and global decrease in HNO2. NOy decreases globally in the mid-to-upper troposphere.


HNO3 cold-temperature deposition

With this update, HNO3 concentrations decrease slightly at the surface and aloft while NOy increases slightly at all levels.


Remove isoprene in VBS (leaving aqueous)


Updated aerosol hygroscopicity and optics


Scale DICE-Africa emissions to address errors in inventory

This update contributes to changes in BC and OC concentrations over and just downwind of Africa. Slight differences can also be seen over Africa in the emission maps. The impact on the inventory emission totals are included below.
  ###############################################################################
  ### Inventory totals for DICEAfrica                                         ###
  ### Ref = GC_12.5.0; Dev = GC_12.6.0                                        ###
  ###############################################################################
                                   Ref            Dev            Dev - Ref
  DICEAfrica BCPI       :           0.004153            0.006925       0.002772 Tg
  DICEAfrica BCPO       :           0.016612            0.027698       0.011087 Tg


The following updates produced small changes:

Comments on additional differences in GCHP:
Approval
Requires further investigation:
Approved by:
Date of approval:

GCHP 1-month benchmark

The following sections contain validation plots for GCHP 12.6.0.

Comparison of GCHP versions

This table contains plots comparing GCHP 12.5.0 (Ref) and GCHP 12.6.0 (Dev) for a 1-month simulation.

Category Plots Additional Information
Level Map Zonal Mean Emissions
Oxidants sfc 500hPa full column stratosphere full column
Aerosols sfc 500hPa full column stratosphere full column Column AOD
Bromine sfc 500hPa full column stratosphere full column
Chlorine sfc 500hPa full column stratosphere --
Iodine sfc 500hPa full column stratosphere full column
Nitrogen sfc 500hPa full column stratosphere full column
Primary Organics sfc 500hPa full column stratosphere full column
Secondary Organics sfc 500hPa full column stratosphere full column
Secondary Organics sfc 500hPa full column stratosphere full column


Sulfur sfc 500hPa full column stratosphere full column
Emissions by HEMCO category

Aircraft, Anthro, Bioburn, Biogenic,
Lightning, Monoterp, Natural, Ocean, Seabirds, DecayingPlants,
Ship, Soil, Total, VolcDegas, VolcErupt,

Emission totals

Comparison of GCHP and GEOS-Chem Classic

This table contains plots comparing GEOS-Chem Classic 12.6.0 (Ref) against GCHP 12.6.0 (Dev) for a 1-month simulation.

Category Plots Additional Information
Level Map Zonal Mean Emissions
Oxidants sfc 500hPa full column stratosphere full column
Aerosols sfc 500hPa full column stratosphere full column Column AOD
Bromine sfc 500hPa full column stratosphere full column
Chlorine sfc 500hPa full column stratosphere --
Iodine sfc 500hPa full column stratosphere full column
Nitrogen sfc 500hPa full column stratosphere full column
Primary Organics sfc 500hPa full column stratosphere full column
Secondary Organics sfc 500hPa full column stratosphere full column
Secondary Organic Aerosols sfc 500hPa full column stratosphere full column
Sulfur sfc 500hPa full column stratosphere full column
Emissions by HEMCO category

Aircraft, Anthro, Bioburn, Biogenic,
Lightning, Monoterp, Natural, Ocean, Seabirds, DecayingPlants,
Ship, Soil, Total, VolcDegas, VolcErupt,

Emission totals

GCHP and GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 12.6.0 - GCHP 12.5.0] against the difference [GC Classic 12.6.0 - GC Classic 12.5.0], 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

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.

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