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==== Benchmark assessment form for GEOS-Chem 12.5.0 BPCH vs. netCDF ====
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'''''Benchmark assessment form for GEOS-Chem 12.5.0 BPCH vs. netCDF'''''
  
 
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Revision as of 16:02, 2 July 2019

File:Page is under construction.jpg

This page includes information about all benchmark simulations for GEOS-Chem 12.5.0.

GEOS-Chem Classic 1-month benchmark

Benchmark plots

These benchmarks were primarily made with GCPy. Some benchmark plots created by GAMAP still remain because they have not been recreated in GCPy yet.

Category1 Plots Additional Information
Level Map Zonal Mean Emissions
Primary sfc 500hPa full column stratosphere sfc
Aerosols sfc 500hPa full column stratosphere sfc AOD
Bromine sfc 500hPa full column stratosphere sfc
Chlorine sfc 500hPa full column stratosphere --
Iodine sfc 500hPa full column stratosphere sfc
Nitrogen sfc 500hPa full column stratosphere sfc
Primary Organics sfc 500hPa full column stratosphere sfc
Secondary Organics sfc 500hPa full column stratosphere sfc
ROy sfc 500hPa full column stratosphere --
Sulfur sfc 500hPa full column stratosphere sfc


Emissions by HEMCO category

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

Emissions tables
J-values sfc 500hPa full column stratosphere -- --
Plots still created by GAMAP
Budget -- -- -- -- -- Ox and CO budgets

1Benchmark category definitions: benchmark_categories.json
2Lumped species definitions: lumped_species.json

NOTES:

  1. Category and lumped species definitions are simple to adjust. Updating them requires only editing the json files.
  2. All 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.

Benchmark assessment form

Description
New features added into GEOS-Chem
Feature Submitted by
Updates that will affect full-chemistry simulations
Bug fix: make sure stratospheric BrY concentrations are read properly each month Lyatt Jaeglé (U. Washington)
Retire obsolete emission inventories Eloise Marais (Leicester)
Emissions and Deposition Working Group
Fixes for GFED4 emissions, including:
  • Change the HEMCO cycling flag so that the model crashes if it doesn't find the right GFED year
  • Remove the 27% scaling of POG to POA and emit 1:1 instead
 Sidhant Pai (MIT)
Corrections for CFCs in the chemistry mechanism Xuan Wang (Harvard)
Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90 Stephen Steenrod (NASA GMAO)
Updates that will NOT affect full-chemistry simulations
Enable GEOS-Chem "Classic" netCDF (History) diagnostics to be subsetted vertically and horizontally Bob Yantosca (GCST)
Enable accurate cloud pH diagnostic calculation via post-processing Jonathan Moch (Harvard)
Updates that will only affect GCHP
Update GCHP to use MAPL v1.0.0 and ESMF v8.0.0 beta snapshot 28 Lizzie Lundgren (GCST)
Version, resolution, met fields used: GEOS-FP (72L), 4x5, July 2016
1-month benchmark finished on: Fri May 24 06:51:03 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: TBD
  • CPU time / wall time: TBD
  • % of ideal performance: TBD
  • Memory: TBD
Compared to previous benchmark: 12.4.0
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): Diagnostics
Unit test results may be viewed at: TBD
Metrics
Global mean OH from log file (% change): 12.6185673606414 x 105 molec/cm3 (TBD)
Methyl chloroform lifetime (% change): TBD (TBD)
Methane lifetime (% change): TBD years (TBD
List all SURFACE SPECIES, SURFACE J-VALUES
AND COLUMN AOD SPECIES for which
ABS(MAX(frac. diff))) > 0.1:
  • Primary: O3 CO OH NOx
  • Aerosols: NH4 NIT SO4 AERI BrSALA BrSALC ISALA ISALC NITs SO4s SOA_Simple
  • Nitrogen: NOy NOx HNO2 HNO3 HNO4 IPMN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4
  • ROy: H2O2 H HO2 O1D OH RO2
  • Sulfur: SOx DMS SO2 SO4
  • Iodine: Iy IxOy I I2 IBr ICl IO INO2 IONO2 HI HOI 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 C2H6 C3H8 PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX MAP RCHO
  • Secondary_Organics: ACET MEK MVK ALD2 CH2O HPALD MP ISOPN IEPOX ACTA EOH
  • J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CH2Cl2 CH3CCl3 HCFC123 HCFC141b N2O O2
  • Column AOD: SO4 SOA_from_Aqueous_ISOP Total
Comments on SURFACE differences: TBD
List all 500 hPa SPECIES and
500 hPA J-VALUES for which
ABS(MAX(frac. diff.) > 0.1:
  • Aerosols: NH4 NIT BrSALA BrSALC SO4s
  • Nitrogen: IPMN NIT PPN NHx NH3 NH4
  • Sulfur: DMS SO2
  • Iodine: I2 INO2 CH2I2
  • Bromine: BrOx Br Br2 BrO HOBr HBr
  • Chlorine: Cl2O2 ClNO2 HCl OClO
  • Primary_Organics: ALK4 C2H6 C3H8 PRPE TOLU XYLE ISOP MTPA LIMO GLYX MAP RCHO
  • Secondary_Organics: ACET MEK MVK ALD2 HPALD ISOPN IEPOX EOH
Comments on 500 hPa differences: TBD
List all ZONAL MEAN SPECIES
and ZONAL MEAN J-VALUES for which
ABS(MAX(frac. diff))) > 0.1:
  • Aerosols: NIT BrSALA BrSALC NITs SO4s
  • Nitrogen: NOy HNO3 IPMN NIT NO3 N2O5 MPN PPN NH3
  • Sulfur: SOx SO2
  • Iodine: I2 IBr ICl INO2 IONO2 CH2I2 OIO
  • Bromine: BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
  • Chlorine: Cly ClOx Cl Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl OClO
  • Primary_Organics: ALK4 C2H6 C3H8 PRPE ISOP MTPA LIMO GLYX RCHO
  • Secondary_Organics: MEK MVK HPALD ISOPN IEPOX
Comments on ZONAL MEAN differences: TBD
List all EMISSIONS for which
ABS(MAX(frac. diff))) > 0.1:
  • Anthro: ALD2 ALK4 C2H6 C3H8 CO MEK NH3 NO pFe PRPE SO2 SO4 SOAP
  • Ship: CO HNO3 NO2 NO O3 SO2 SOAP
  • Total: ALD2 ALK4 C2H6 C3H8 CO GLYX MEK MGLY NH3 NO pFe PRPE SO2 SO4 SOAP
Comments on EMISSIONS differences: TBD
Additional or summary comments: TBD
Approval
Requires further investigation: TBD
Approved by:
Date of approval:

GCHP 1-month benchmark

The following sections contain validation plots for GCHP 12.5.0.

Comparison of GCHP versions

This table contains plots comparing GCHP 12.3.2 (Ref) and GCHP 12.5.0 (Dev) for a 1-month simulation.

Category1 Plots2 Additional Information
Level Map Zonal Mean Emissions
Primary 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
Sulfur sfc 500hPa full column stratosphere full column
Emissions by HEMCO category

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

Emission totals

1Benchmark category definitions: benchmark_categories.json
2Lumped species definitions: lumped_species.json

Comparison of GCHP and GEOS-Chem Classic

This table contains plots comparing GEOS-Chem Classic 12.5.0 (Ref) against GCHP 12.5.0 (Dev) for a 1-month simulation.

Category1 Plots2 Additional Information
Level Map Zonal Mean Emissions
Primary 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
Sulfur sfc 500hPa full column stratosphere full column
Emissions by HEMCO category

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

Emission totals

1Benchmark category definitions: benchmark_categories.json
2Lumped species definitions: lumped_species.json


GCHP and GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 12.5.0 - GCHP 12.3.2] against the difference [GC Classic 12.5.0 - GC Classic 12.3.0], taken from 1-month benchmark simulations.

Category1 Plots2
Level Map Zonal Mean
Primary 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
Sulfur sfc 500hPa full column stratosphere

1Benchmark category definitions: benchmark_categories.json
2Lumped species definitions: lumped_species.json

NOTES:

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

Special benchmarks

In this section we list information about special (i.e. non-official) benchmark simulations that were performed. These are often necessary to validate certain model features.

GEOS-Chem Classic 12.5.0 BPCH vs. netCDF

A GEOS-Chem "Classic" 12.5.0 simulation was performed in order to compare the differences between using binary punch (aka BPCH) diagnostic output and netCDF diagnostic output. This is a necessary step before we can remove the BPCH diagnostics completely from GEOS-Chem.

Category1 Plots Additional Information
Level Map Zonal Mean Emissions
Primary sfc 500hPa full column stratosphere sfc
Aerosols sfc 500hPa full column stratosphere sfc AOD
Bromine sfc 500hPa full column stratosphere sfc
Chlorine sfc 500hPa full column stratosphere --
Iodine sfc 500hPa full column stratosphere sfc
Nitrogen sfc 500hPa full column stratosphere sfc
Primary Organics sfc 500hPa full column stratosphere sfc
Secondary Organics sfc 500hPa full column stratosphere sfc
ROy sfc 500hPa full column stratosphere --
Sulfur sfc 500hPa full column stratosphere sfc


Emissions by HEMCO category

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

Emissions tables
J-values sfc 500hPa full column stratosphere -- --
Plots still created by GAMAP
Budget -- -- -- -- -- Ox and CO budgets

1Benchmark category definitions: benchmark_categories.json
2Lumped species definitions: lumped_species.json

NOTES:

  1. Category and lumped species definitions are simple to adjust. Updating them requires only editing the json files.
  2. All 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.


Benchmark assessment form for GEOS-Chem 12.5.0 BPCH vs. netCDF

Description
New features added into GEOS-Chem
Feature Submitted by
Updates that will affect full-chemistry simulations
Bug fix: make sure stratospheric BrY concentrations are read properly each month Lyatt Jaeglé (U. Washington)
Retire obsolete emission inventories Eloise Marais (Leicester)
Emissions and Deposition Working Group
Fixes for GFED4 emissions, including:
  • Change the HEMCO cycling flag so that the model crashes if it doesn't find the right GFED year
  • Remove the 27% scaling of POG to POA and emit 1:1 instead
 Sidhant Pai (MIT)
Corrections for CFCs in the chemistry mechanism Xuan Wang (Harvard)
Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90 Stephen Steenrod (NASA GMAO)
Updates that will NOT affect full-chemistry simulations
Enable GEOS-Chem "Classic" netCDF (History) diagnostics to be subsetted vertically and horizontally Bob Yantosca (GCST)
Enable accurate cloud pH diagnostic calculation via post-processing Jonathan Moch (Harvard)
Updates that will only affect GCHP
Update GCHP to use MAPL v1.0.0 and ESMF v8.0.0 beta snapshot 28 Lizzie Lundgren (GCST)
Version, resolution, met fields used: GEOS-FP (72L), 4x5, July 2016
1-month benchmark finished on: Fri May 24 06:51:03 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: TBD
  • CPU time / wall time: TBD
  • % of ideal performance: TBD
  • Memory: TBD
Compared to previous benchmark: 12.4.0
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): Diagnostics
Unit test results may be viewed at: TBD
Metrics
Global mean OH from log file (% change): 12.6185673606414 x 105 molec/cm3 (TBD)
Methyl chloroform lifetime (% change): TBD (TBD)
Methane lifetime (% change): TBD years (TBD
List all SURFACE SPECIES, SURFACE J-VALUES
AND COLUMN AOD SPECIES for which
ABS(MAX(frac. diff))) > 0.1:
  • Primary: O3 CO OH NOx
  • Aerosols: NH4 NIT SO4 AERI BrSALA BrSALC ISALA ISALC NITs SO4s SOA_Simple
  • Nitrogen: NOy NOx HNO2 HNO3 HNO4 IPMN NIT NO NO2 NO3 N2O5 MPN PAN PPN NHx NH3 NH4
  • ROy: H2O2 H HO2 O1D OH RO2
  • Sulfur: SOx DMS SO2 SO4
  • Iodine: Iy IxOy I I2 IBr ICl IO INO2 IONO2 HI HOI 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 C2H6 C3H8 PRPE TOLU XYLE ISOP MTPA MTPO LIMO GLYX MAP RCHO
  • Secondary_Organics: ACET MEK MVK ALD2 CH2O HPALD MP ISOPN IEPOX ACTA EOH
  • J-Values: CCl4 CFC11 CFC113 CFC114 CFC115 CH2Cl2 CH3CCl3 HCFC123 HCFC141b N2O O2
  • Column AOD: SO4 SOA_from_Aqueous_ISOP Total
Comments on SURFACE differences: TBD
List all 500 hPa SPECIES and
500 hPA J-VALUES for which
ABS(MAX(frac. diff.) > 0.1:
  • Aerosols: NH4 NIT BrSALA BrSALC SO4s
  • Nitrogen: IPMN NIT PPN NHx NH3 NH4
  • Sulfur: DMS SO2
  • Iodine: I2 INO2 CH2I2
  • Bromine: BrOx Br Br2 BrO HOBr HBr
  • Chlorine: Cl2O2 ClNO2 HCl OClO
  • Primary_Organics: ALK4 C2H6 C3H8 PRPE TOLU XYLE ISOP MTPA LIMO GLYX MAP RCHO
  • Secondary_Organics: ACET MEK MVK ALD2 HPALD ISOPN IEPOX EOH
Comments on 500 hPa differences: TBD
List all ZONAL MEAN SPECIES
and ZONAL MEAN J-VALUES for which
ABS(MAX(frac. diff))) > 0.1:
  • Aerosols: NIT BrSALA BrSALC NITs SO4s
  • Nitrogen: NOy HNO3 IPMN NIT NO3 N2O5 MPN PPN NH3
  • Sulfur: SOx SO2
  • Iodine: I2 IBr ICl INO2 IONO2 CH2I2 OIO
  • Bromine: BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
  • Chlorine: Cly ClOx Cl Cl2 Cl2O2 ClOO ClNO2 ClNO3 HOCl OClO
  • Primary_Organics: ALK4 C2H6 C3H8 PRPE ISOP MTPA LIMO GLYX RCHO
  • Secondary_Organics: MEK MVK HPALD ISOPN IEPOX
Comments on ZONAL MEAN differences: TBD
List all EMISSIONS for which
ABS(MAX(frac. diff))) > 0.1:
  • Anthro: ALD2 ALK4 C2H6 C3H8 CO MEK NH3 NO pFe PRPE SO2 SO4 SOAP
  • Ship: CO HNO3 NO2 NO O3 SO2 SOAP
  • Total: ALD2 ALK4 C2H6 C3H8 CO GLYX MEK MGLY NH3 NO pFe PRPE SO2 SO4 SOAP
Comments on EMISSIONS differences: TBD
Additional or summary comments: TBD
Approval
Requires further investigation: TBD
Approved by:
Date of approval:
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