GEOS-Chem benchmarking

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GEOS-Chem v11-02-final will also carry the designation GEOS-Chem 12.0.0. We are migrating to a purely numeric versioning system in order to adhere more closely to software development best practices. For a complete description of the new versioning system, please see our GEOS-Chem version numbering system wiki page.


Overview

The following GEOS-Chem benchmarking procedure was adopted at the 5th International GEOS-Chem Meeting (May 2011).

  1. Any update to the GEOS-Chem source code or run directories will change the GEOS-Chem version number (X.Y.Z).
  2. All Y versions require a dedicated 1-month benchmark with the standard full-chemistry mechanism. The benchmark results will be posted on the wiki and an email will be sent to the developer(s) and the GEOS-Chem Steering Committee.
  3. The developer(s) will assess the benchmark results and complete a benchmark assessment form on the wiki. If the developer has any concerns about the benchmark results they will contact the GEOS-Chem Support Team, the relevant GEOS-Chem Working Group Chairs, and/or Model Scientist Daniel Jacob. GEOS-Chem Steering Committee members are also encouraged to examine and comment on the benchmark results.
  4. If the update is for a specialty simulation (e.g. CO2, CH4, Hg), then a further benchmark may be conducted by the appropriate Working Group.
  5. Once the developer is satisfied with the changes in the 1-month benchmark, GEOS-Chem Model Scientist Daniel Jacob will promptly review the results and approve the new internal version.
  6. 1-year benchmarks for Y versions will be conducted only if justifiably requested by the developer or by GEOS-Chem Steering Committee members.
  7. Each new major version release (i.e. X version) will be subject to a 1-year benchmark to be inspected by the GEOS-Chem Steering Committee before approval.

List of GEOS-Chem benchmarks

Links to information about past 1-month and 1-year benchmark simulations can be found on GEOS-Chem versions under development wiki page. For information about 1-year benchmark simulations for GEOS-Chem v8-02-04 and earlier, see this website.

1-month benchmark

Overview

Dates of run:
  • July 1, 2013 – August 1, 2013 (prior to v11-02e)
  • July 1, 2016 – August 1, 2016 (v11-02e and later versions)
Vertical Resolution: GEOS-FP with 72 hybrid sigma-pressure levels
Horizontal Resolution: 4° latitude x 5° longitude
Advected species: Gas-phase species: NO, O3, PAN, CO, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, PMN (isoprene and non-isoprene), PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, MP, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, MAP, NO2, NO3, HNO2, BENZ, TOLU, XYLE, MTPA, LIMO, MTPO, TSOG0-3, ISOG1-3, ASOG1-3, EOH, MGLY, GLYX, ACTA, HPALD, DHDN, ETHLN, HCOOH, IEPOXA, IEPOXB, IEPOXD, ISN1, RIPA, RIPB, RIPD, IMAE, LVOC, ISN1OG, MONITS, MONITU, HONIT, HC187

Aerosol species: DMS, SO2, SO4, MSA, NH3, NH4, NIT, BCPO, OCPI, BCPI, OCPI, DST1-4, SALA, SALC, SO4s, NITs, TSOA0-3, ISOA1-3, ASOAN, ASOA1-3, SOAIE, SOAME, SOAGX, SOAMG, LVOCOA, ISN1OA, IONITA, MONITA, INDIOL

Bromine species: Br2, Br, BrO, HOBr, HBr, BrNO2 BrNO3, CHBr3, CH2Br2, CH3Br

Stratospherically-important species: N2O, OCS, CH4, BrCl, HCl, CCl4, CH3Cl, CH3CCl3, CFCX, HCFCX, CFC11, CFC12, HCFC22, H1211, H2402, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl202, H2O

Chemical Mechanism: FlexChem chemical solver
using the standard chemistry mechanism (NOx-Ox-HC-Aer-Br + UCX + complex SOA)
Chemistry is done in both the troposphere and the stratosphere.
Photolysis Mechanism: FAST-JX v7.0 (Prather, 2012, Wild et al, 2000).
Operations:
Diagnostic Output: The following diagnostic outputs are archived as monthly means
  • Sulfate production and loss quantities
  • Dust aerosol sources
  • Carbon aerosol sources
  • Sea salt aerosol sources
  • Acetone sources
  • Sulfur sources
  • Optical Depths
  • Noontime J-values
  • Biomass burning emission fluxes
  • CO sources
  • Surface Pressure
  • NOx sources
  • Biofuel emission fluxes
  • Anthropogenic emission fluxes
  • Scavenging loss from moist convection
  • Scavenging loss from wet deposition
  • Concentrations of chemically produced OH and HO2
  • Dry deposition fluxes and velocities
  • Tracer concentrations
  • Biogenic emission fluxes
  • Tropopause height
  • DAO 3-D met fields
  • DAO 2-D met fields
  • Air masses and grid box heights
  • Surface area
  • Lifetime of Methylchloroform (CH3CCl3)
Benchmark Plots and Summaries: The following plots, budgets, and totals are created from the oxidant-aerosol simulation:
  • Budget of Ox and CO
  • Mean OH concentration
  • Methyl Chloroform Lifetime (w/r/t loss by tropospheric OH)
  • Aerosol optical depth maps (this benchmark)
  • Aerosol optical depth differences (this benchmark - previous benchmark)
  • Concentration maps (this benchmark) of tracers + OH + HO2 at the surface and at 500 hPa
  • Difference maps (this benchmark - previous benchmark) of tracers + OH + HO2 at the surface and at 500 hPa
  • Summary of emission totals (this benchmark vs. previous benchmark)
  • Emissions maps (this benchmark) for all emitting tracers
  • Emissions difference maps (this benchmark - previous benchmark) for all emitting tracers
  • Emissions ratio maps (this benchmark / previous benchmark) for all emitting tracers
  • Frequency distribution histogram of ratios (this benchmark vs previous benchmark) for tracers, OH, and optical depths
  • J-value maps (this benchmark)
  • J-value difference maps (this benchmark - previous benchmark)
  • J-value ratio maps (this benchmark / previous benchmark)
  • Ratio maps (this benchmark / previous benchmark) of tracers + OH + HO2 at the surface and at 500 hPa
  • Zonal mean concentration maps (this benchmark) of tracers + OH + HO2
  • Zonal mean difference maps (this benchmark - previous benchmark) of tracers + OH + HO2

Plotting routines

NOTE: The 1-month benchmark plotting routines are currently written in IDL. We are planning on moving these routines to Python shortly.

The 1-month benchmark plotting routines are included with the GAMAP. For more information, see the this page in the GAMAP manual.

1-year benchmark

Overview

Spin-up:
Dates of Run:
Vertical Resolution: GEOS-FP with 72 hybrid sigma-pressure levels
Horizontal Resolution: 4° latitude x 5° longitude
Advected species: Gas-phase species: NO, O3, PAN, CO, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, PMN (isoprene and non-isoprene), PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, MP, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, MAP, NO2, NO3, HNO2, BENZ, TOLU, XYLE, MTPA, LIMO, MTPO, TSOG0-3, ISOG1-3, ASOG1-3, EOH, MGLY, GLYX, ACTA, HPALD, DHDN, ETHLN, HCOOH, IEPOXA, IEPOXB, IEPOXD, ISN1, RIPA, RIPB, RIPD, IMAE, LVOC, ISN1OG, MONITS, MONITU, HONIT, HC187

Aerosol species: DMS, SO2, SO4, MSA, NH3, NH4, NIT, BCPO, OCPI, BCPI, OCPI, DST1-4, SALA, SALC, SO4s, NITs, TSOA0-3, ISOA1-3, ASOAN, ASOA1-3, SOAIE, SOAME, SOAGX, SOAMG, LVOCOA, ISN1OA, IONITA, MONITA, INDIOL

Bromine species: Br2, Br, BrO, HOBr, HBr, BrNO2 BrNO3, CHBr3, CH2Br2, CH3Br

Stratospherically-important species: N2O, OCS, CH4, BrCl, HCl, CCl4, CH3Cl, CH3CCl3, CFCX, HCFCX, CFC11, CFC12, HCFC22, H1211, H2402, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl202, H2O

Chemical Mechanism: FlexChem chemical solver
using the standard chemistry mechanism (NOx-Ox-HC-Aer-Br + UCX + complex SOA)
Chemistry is done in both the troposphere and the stratosphere.
Photolysis Mechanism: FAST-JX v7.0 (Prather, 2012, Wild et al, 2000).
Operations:
Diagnostic Output: All diagnostics above are saved as monthly means.
  • Sulfate production and loss quantities
  • Dust aerosol sources
  • Carbon aerosol sources
  • Sea salt aerosol sources
  • Acetone sources
  • Sulfur sources
  • Optical Depths
  • Noontime J-values
  • Transport fluxes (N/S, E/W, up/down)
  • Biomass burning emission fluxes
  • CO sources
  • Surface Pressure
  • NOx sources
  • Biofuel emission fluxes
  • Anthropogenic emission fluxes
  • Scavenging loss from moist convection
  • Scavenging loss from wet deposition
  • Concentrations of chemically produced OH and HO2
  • Dry deposition fluxes and velocities
  • Tracer concentrations
  • Biogenic emission fluxes
  • Tropopause height
  • DAO 3-D met fields
  • DAO 2-D met fields
  • Air masses and grid box heights
  • Surface area
  • Lifetime of Methylchloroform (CH3CCl3)
  • Satellite timeseries of BrO, cloud fraction, and cloud top height
Benchmark Plots: The following plots compare advected species from 3 different benchmark simulations (versions 1-3, where version 3 is the current benchmark version). Plots are created for January, April, July, and October.
  • Aerosol optical depth maps (version 1, version 2, and version 3)
  • Emission maps (version 1, version 2, and version 3)
  • Emisison difference maps (version 3 - version 1, version 3 - version 2)
  • Emission ratio maps (version 3 / version 1, version 3 / version 2)
  • J-value maps (version 1, version 2, and version 3)
  • J-value difference maps (version 3 - version 1, version 3 - version 2)
  • J-value ratio maps (version 3 / version 1, version 3 / version 2)
  • Tracer difference maps at the surface and 500 hPa (version 3 - version 1, version 3 - version 2)
  • Tracer ratio maps at the surface and 500 hPa (version 3 / version 1, version 3 / version 2)
  • Tracer difference profiles along longitude slices (15S, 42N) (version 3 - version 1, version 3 - version 2)

The following plots show data from 3 benchmark simulations side-by-side with observations. GEOS-Chem output is plotted in red for version 1, in green for version 2, and in blue for version 3 (current benchmark version)

  • BrO seasonal columns vs. observations
  • C2H6 vertical profiles vs. observations from various aircraft campaigns
  • C3H8 vertical profiles vs. observations from various aircraft campaigns
  • CO seasonal cycle at the surface vs. MOZAIC observations
  • CO vertical profiles vs. MOZAIC observations
  • CO vertical profiles vs. various sonde observations
  • H2O2 vertical profiles vs. observations from various aircraft campaigns
  • IMPROVE difference maps (benchmark simulation output vs. surface sites)
  • IMPROVE scatter plots (benchmark simulation output vs. surface sites)
  • HNO3 vertical profiles vs. observations from various aircraft campaigns
  • NO vertical profiles vs. observations from various aircraft campaigns
  • O3 seasonal cycle @ the surface vs. MOZAIC observations
  • O3 seasonal cycle @ 300, 500, and 800 hPa vs. MOZAIC observations
  • O3 seasonal cycle @ 300, 500, and 800 hPa vs. sonde observations
  • O3 seasonal cycle @ 150, 300, 500,and 800 hPa vs. sonde observations
  • O3 vertical profiles vs. observations from various aircraft campaigns
  • O3 vertical profiles vs. observations from various aircraft campaigns
  • O3 vertical profiles vs. various sonde observations
  • O3 vertical profiles vs. MOZAIC observations
  • PAN vertical profiles vs. observations from various aircraft campaigns
  • PM2.5 difference maps (benchmark simulation output vs. surface sites)
  • PM2.5 scatter plots (benchmark simulation output vs. surface sites)

Plotting routines

NOTE: The 1-month benchmark plotting routines are currently written in IDL. We are planning on moving these routines to Python for the GEOS-Chem v11-02 release as part of the GCPy package.

The 1-year benchmark plotting routines can be downloaded from Bitbucket via Git using: 

 git clone https://bitbucket.org/gcst/gc_1yr_benchmark

The data files needed for the plots are included in the repository and are discussed in more detail below.

Observations

Here we provide an overview of the data used in the 1-year benchmark plots.

Directory Data year Species Data source Provided by
BrO/ 2007-2008 BrO GOME-2 Justin Parrella
(Data used to reproduce Figure 5 of Parrella et al. (2012))
cmdl/ 2005, 2009
New data available 		CO GMD (formerly CMDL) Jennifer Logan and Inna Megretskaia
co.prof.for.gmi/ 2001-2008
(varies by station) 		CO MOZAIC Jennifer Logan and Inna Megretskaia
eval/aircraft/
NOTE: Other directories in eval/ aren't currently used 		1995-2003
(varies by aircraft campaign) 		C2H6, C3H8, CO, H2O2, HNO3, NO, O3, PAN

(Not currently used: ACET, ALK4, C2H2, CH2Br2, CH2BrCl, CH3Br, CH3OH, CH4, CHBr2Cl, CHBrCl2, CO2, ETHE, PRPE)

See README Jennifer Logan and Inna Megretskaia
netCDF/ N/A C2H6, C3H8, CH3I, CO, H2O2, HNO3, NO, O3, OH, PAN, Rn Various
(contains information about station locations) 		Jennifer Logan and Inna Megretskaia
PAN/ Varies PAN ARCTAS-A, ARCTAS-B, ARCPAC, INTEX-B, ITCT-2K2 Emily Fischer
(Data used to reproduce Figure S1 of Fischer et al. (2014) Supplement)
pm25_data/ 2005 PM2.5 IMPROVE Colette Heald
sondes.for.gmi/ 1990-2008
(varies by station) 		O3 Jennifer Logan and Inna Megretskaia
strat/ 2001-2010 NOy, O3 OSIRIS Dylan Jones
surface_ozone/ O3 CMDL Jennifer Logan and Inna Megretskaia

--Melissa Sulprizio (talk) 14:26, 16 August 2017 (UTC)

Update 2005/2009 CMDL CO data to 2013/2014 GMD CO data

This update was included in v11-02c and approved on 21 Sep 2017.

Jenny Fisher wrote:

Attached is a zip file containing routines to process the GMD (previously CMDL) CO data for use in the benchmarking scripts, as well as the 2013 and 2014 data. I added the 2014 data because there was no ships data for 2013 (or 2012), so this seemed like the best approximation.
To replace the existing benchmark data with these, you will want to do the following in the 1-year benchmark code:
  1. Put the 2013data/ and 2014data/ in the data/cmdl/ directory of the 1-year benchmark code
  2. Change newdata/ to 2013data/ in plot_cmdl_3_models_4_months.pro
  3. Change Feb09/ to 2013data/ in plot_surface_co_geos_3_models.pro
  4. Change newdata/ to 2014data/ in plot_ships_3_models_4_months.pro and plot_ships_3_models_co.pro
  5. Change the line file=pre+name_sta(kk)+'.mn' to file=pre+name_sta(kk)+’.mn.2013' in plot_cmdl_3_models_4_months.pro
  6. Change the line file=pre+name_sta(kk)+’.mn.2005' to file=pre+name_sta(kk)+’.mn.2013' in plot_surface_co_geos_3_models.pro
  7. Change the line file=pre+name_sta(kk)+'.mn' to file=pre+name_sta(kk)+’.mn.2014' in plot_ships_3_models_4_months.pro and plot_ships_3_models_co.pro
As I said before, I think this would be a useful improvement to our benchmarks, rather than using data >10 years old!

--Melissa Sulprizio (talk) 22:10, 15 August 2017 (UTC)

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