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| − | ----
| + | == Objectives == |
| − | ----
| + | |
| − | <big><strong>GEOS-Chem v11-02-final</strong> '''will also carry the designation''' <strong>GEOS-Chem 12.0.0</strong>'''.''' 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 [[GEOS-Chem version numbering system|our ''GEOS-Chem version numbering system'' wiki page]].</big>
| + | |
| − | ----
| + | |
| − | ----
| + | |
| | | | |
| | + | Benchmarking supports the maintenance of GEOS-Chem as a robust state-of-the-science facility with a nimble grass-roots approach and strong version control. Benchmarking has four main objectives: |
| | + | #Document a consistent GEOS-Chem model configuration, and the expected characteristics of that configuration. |
| | + | #Support version control through traceability, and by confirming the expected behavior of model developments submitted by the community. |
| | + | #Track the evolution of the model over the years. |
| | + | #Promote scientific transparency of GEOS-Chem. |
| | | | |
| − | == Overview == | + | == Procedure == |
| | | | |
| − | The following GEOS-Chem benchmarking procedure was adopted at the 5th International GEOS-Chem Meeting (May 2011). | + | The GEOS-Chem benchmarking procedure is described below. GEOS-Chem uses [[GEOS-Chem_version_numbering_system#Numeric_versioning_system|semantic versioning (i.e. '''X.Y.Z''' version labels)]]. |
| | | | |
| − | #Any update to the GEOS-Chem source code or run directories will change the [[GEOS-Chem_version_numbering_system#Numeric_versioning_system|GEOS-Chem version number ('''X.Y.Z''')]].
| + | === 1-hour benchmarks === |
| − | #All '''Y''' versions require a dedicated [[#1-month benchmark|1-month benchmark]] with the [[GEOS-Chem_chemistry_mechanisms#Mechanisms_in_GEOS-Chem_v10-01_and_later_versions|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 [http://acmg.seas.harvard.edu/geos/geos_steering_cmte.html GEOS-Chem Steering Committee].
| + | |
| − | #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 [[GCST|GEOS-Chem Support Team]], the relevant [http://acmg.seas.harvard.edu/geos/geos_working_groups.html GEOS-Chem Working Group Chairs], and/or [http://acmg.seas.harvard.edu/people/faculty/djj/index.html Model Scientist Daniel Jacob]. GEOS-Chem Steering Committee members are also encouraged to examine and comment on the benchmark results.
| + | |
| − | #If the update is for a [[GEOS-Chem_chemistry_mechanisms#Specialty_simulations|specialty simulation]] (e.g. CO2, CH4, Hg), then a further benchmark may be conducted by the appropriate Working Group.
| + | |
| − | #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.
| + | |
| − | #[[#1-year benchmark|1-year benchmarks]] for '''Y''' versions will be conducted only if justifiably requested by the developer or by GEOS-Chem Steering Committee members.
| + | |
| − | #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 ==
| + | 1-hour benchmarks primarily serve as '''sanity checks'''. They are useful in determining if two successive updates to GEOS-Chem result in identical model output. 1-hour benchmarks are triggered when: |
| | | | |
| − | Links to information about past 1-month and 1-year benchmark simulations can be found on the [[GEOS-Chem_versions|''GEOS-Chem versions'' wiki page]]. For information about 1-year benchmark simulations for GEOS-Chem v8-02-04 and earlier, see [http://acmg.seas.harvard.edu/geos/geos_1yr_plots.html this website].
| + | #A commit is pushed to any development branch[[#Notes|<sup>1</sup>]] in the [https://github.com/geoschem/GCClassic <tt>geoschem/GCClassic</tt> "superproject" repository] |
| | + | #A commit is pushed to any development branch[[#Notes|<sup>1</sup>]] in the [https://github.com/geoschem/GCHP <tt>geoschem/GCHP</tt> "superproject" repository]. |
| | | | |
| − | == 1-month benchmark ==
| + | Evaluation tables are posted to [https://gc-dashboard.org <tt>gc-dashboard.org</tt>] upon successful completion of each 1-hour benchmark simulation. The evaluation tables include information on OH metrics, emissions totals, global mass, and a summary table. |
| | | | |
| − | === Overview === | + | === 1-month benchmarks === |
| | | | |
| − | {| border=1 cellspacing=0 cellpadding=5
| + | 1-month benchmarks (aka '''alpha benchmarks''') are primarily used to quantify the changes in model output that occur when adding a new science feature into GEOS-Chem. These benchmarks are triggered when: |
| | | | |
| − | |-valign="top" | + | #An alpha tag[[#Notes|<sup>2</sup>]] is pushed to any development branch[[#Notes|<sup>1</sup>]] in the [https://github.com/geoschem/GCClassic <tt>geoschem/GCClassic</tt> superproject repository] |
| − | !bgcolor="#cccccc"|Dates of run:
| + | #An alpha tag[[#Notes|<sup>2</sup>]] is pushed to any development branch[[#Notes|<sup>1</sup>]] in the [https://github.com/geoschem/GCHP <tt>geoschem/GCHP</tt> "superproject" repository]. |
| − | |
| + | |
| − | *July 1, 2013 – August 1, 2013 (prior to [[GEOS-Chem v11-02#v11-02e|v11-02e]])
| + | |
| − | *July 1, 2016 – August 1, 2016 ([[GEOS-Chem v11-02#v11-02e|v11-02e]] and later versions)
| + | |
| | | | |
| − | |-valign="top"
| + | Evaluation plots and tables are posted to [https://gc-dashboard.org <tt>gc-dashboard.org</tt>] upon successful completion of each 1-hour benchmark simulation. These include comparison plots of species concentrations, emissions, aerosol optical depth, J-Values, as well as the same tables produced for the [[#1-hour benchmarks|1-hour benchmarks]]. |
| − | !bgcolor="#cccccc"|[[GEOS-Chem_vertical_grids|Vertical Resolution]]:
| + | |
| − | |[[GEOS-FP]] with [[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72 hybrid sigma-pressure levels]]
| + | |
| | | | |
| − | |-valign="top"
| + | === etc === |
| − | !bgcolor="#cccccc"|[[GEOS-Chem_horizontal_grids|Horizontal Resolution]]:
| + | |
| − | |[[GEOS-Chem_horizontal_grids#GMAO_4_x_5_grid|4° latitude x 5° longitude]]
| + | |
| | | | |
| − | |-valign="top" | + | #Any update to the GEOS-Chem source code or run directories will change the [[GEOS-Chem_version_numbering_system#Numeric_versioning_system|GEOS-Chem version number ('''X.Y.Z''')]]. |
| − | !bgcolor="#cccccc"|[[Species_in_GEOS-Chem#Full-chemistry|Advected species]]:
| + | #'''Z''' versions will be released at intervals determined by the [[GCST|GEOS-Chem Support Team (GCST)]] and may include bug fixes or updates that do not impact the full-chemistry simulation. |
| − | |<u>Gas-phase species:</u> 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
| + | #Any change impacting the [[GEOS-Chem_chemistry_mechanisms#Mechanisms_in_GEOS-Chem_v10-01_and_later_versions|standard full-chemistry simulation]] will require a '''Y''' version change and a dedicated 1-month benchmark. The benchmark results will be posted on the wiki and an email will be sent to the developer(s) and the [https://geos-chem.seas.harvard.edu/geos-steering-cmte GEOS-Chem Steering Committee (GCSC)]. |
| | + | #The developer(s) and GCSC will assess the benchmark results and review a benchmark assessment form on the wiki. If there are any concerns about the benchmark results, the GCST will be notified and further investigation and/or benchmarking may be required. |
| | + | #If the update is for a [[GEOS-Chem_chemistry_mechanisms#Specialty_simulations|specialty simulation]] (e.g. CO2, CH4, Hg), then a further benchmark may be conducted by the appropriate Working Group. |
| | + | #Once the developer is satisfied with the changes in the 1-month benchmark, GEOS-Chem Model Scientist Daniel Jacob will review the results and approve the new internal version. |
| | + | #1-year full-chemistry and/or transport tracer benchmarks for '''Y''' versions will be conducted only if justifiably requested by the developer or by GEOS-Chem Steering Committee members. |
| | + | #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. |
| | | | |
| − | <u>Aerosol species:</u> 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
| + | === Notes === |
| | | | |
| − | <u>Bromine species:</u> Br2, Br, BrO, HOBr, HBr, BrNO2 BrNO3, CHBr3, CH2Br2, CH3Br
| + | # Development branches are '''dev/X.Y.Z''' and '''dev/no-diff-to-benchmark'''. |
| | + | # An alpha tag uses the format '''X.Y.Z-alpha.N''', where [[GEOS-Chem_version_numbering_system#Numeric_versioning_system|'''X.Y.Z''']] is the version number and '''N''' is a sequential index starting at 0. These are used to indicate the locations in the Git revision history where 1-month benchmarks were run. |
| | | | |
| − | <u>Stratospherically-important species:</u> 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
| + | == List of GEOS-Chem benchmarks == |
| | | | |
| − | |-valign="top"
| + | Links to past 1-month and 1-year benchmark simulations can be found on the [[GEOS-Chem_versions|''GEOS-Chem versions'']] wiki page. |
| − | !bgcolor="#cccccc"|[[GEOS-Chem_chemistry_mechanisms|Chemical Mechanism]]:
| + | |
| − | |[[FlexChem]] chemical solver<br> using the standard chemistry mechanism ([[NOx-Ox-HC-Aer-Br_chemistry_mechanism|NOx-Ox-HC-Aer-Br]] + [[UCX_chemistry_mechanism|UCX]] + [[Secondary_organic_aerosols#Complex_SOA_scheme|complex SOA]])<br>Chemistry is done in both the troposphere and the stratosphere.
| + | |
| | | | |
| − | |-valign="top"
| + | == Benchmark output archive == |
| − | !bgcolor="#cccccc"|[[FAST-JX_v7.0_photolysis_mechanism|Photolysis Mechanism]]:
| + | |
| − | |[[FAST-JX_v7.0_photolysis_mechanism|FAST-JX v7.0]] (Prather, 2012, Wild et al, 2000).
| + | |
| | | | |
| − | |-valign="top"
| + | Output files and evaluation plots for 1-month and 1-year benchmark simulations are archived at Harvard as summarized below. GEOS-Chem users may utilize these output for comparisons against their own simulations. |
| − | !bgcolor="#cccccc"|Operations:
| + | |
| − | |
| + | |
| − | *[[Advection scheme TPCORE|Advection]]
| + | |
| − | *[[ISORROPIA II|Aerosol thermodynamical equilibriium]]
| + | |
| − | *[[Boundary layer mixing]]
| + | |
| − | *[[Chemistry Issues|Chemistry]]
| + | |
| − | *[[Cloud convection]] (with updraft scavenging)
| + | |
| − | *[[Dry deposition]]
| + | |
| − | *[[Emissions overview|Emissions]]
| + | |
| − | *[[Photolysis_mechanism|Photolysis]]
| + | |
| − | *[[Wet deposition]]
| + | |
| | | | |
| − | |-valign="top" | + | {| border=1 cellpadding=5 cellspacing=0 |
| − | !bgcolor="#cccccc"|[[List_of_diagnostics_for_v11-01|Diagnostic Output]]: | + | |-bgcolor="#CCCCCC" |
| − | |The following diagnostic outputs are archived as monthly means | + | !width="550px"|Directory |
| − | *Sulfate production and loss quantities
| + | !width="300px"|Description |
| − | *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)
| + | |
| | | | |
| − | |-valign="top" | + | |-valign="top" |
| − | !bgcolor="#cccccc"|Benchmark Plots and Summaries:
| + | |<tt>https://gc-dashboard.org/search?searchString=&1Hr=1Hr&GCHP=GCHP&GCC=GCC</tt> |
| − | |The following plots, budgets, and totals are created from the oxidant-aerosol simulation: | + | |Contains the following data from the [[GEOS-Chem_benchmarking#1-hour_benchmark|1-hour benchmarks]] used to evaluate GEOS-Chem: |
| − | *Budget of Ox and CO
| + | *Evaluation plots & tables |
| − | *Mean OH concentration
| + | *Run log |
| − | *Methyl Chloroform Lifetime (w/r/t loss by tropospheric OH)
| + | *Run directory (tarball) |
| − | *Aerosol optical depth maps (this benchmark)
| + | *Diagnostic files (tarball) |
| − | *Aerosol optical depth differences (this benchmark - previous benchmark)
| + | *Restart Files (tarball) |
| − | *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
| + | |
| | | | |
| − | |} | + | |-valign="top" |
| | + | |<tt>https://gc-dashboard.org/search?searchString=&1Mon=1Mon&GCHP=GCHP&GCC=GCC</tt> |
| | + | |Contains the following data from the [[GEOS-Chem_benchmarking#1-month_benchmark|1-month benchmarks]] used to evaluate GEOS-Chem: |
| | + | *Evaluation plots & tables |
| | + | *Run log |
| | + | *Run directory (tarball) |
| | + | *Diagnostic files (tarball) |
| | + | *Restart Files (tarball) |
| | | | |
| − | === Plotting routines === | + | |-valign="top" |
| | + | |<tt>http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/</tt> |
| | + | |Contains the following data from the [[GEOS-Chem_benchmarking#1-year_benchmark|1-year benchmarks]] used to evaluate GEOS-Chem: |
| | + | *Evaluation plots |
| | + | *Restart files (tarball) |
| | + | *Model output (tarball) |
| | + | *Log files (tarball) |
| | + | *Input files (tarball) |
| | | | |
| − | ''NOTE: The 1-month benchmark plotting routines are currently written in IDL. We are planning on moving these routines to Python shortly.</span>''
| + | |-valign="top" |
| − | | + | |<tt>http://ftp.as.harvard.edu/gcgrid/geos-chem/10yr_benchmarks/</tt> |
| − | The 1-month benchmark plotting routines are included with the [http://acmg.seas.harvard.edu/gamap/doc/ GAMAP]. For more information, see the [http://acmg.seas.harvard.edu/gamap/doc/by_category/Benchmarking.html this page in the GAMAP manual].
| + | |Contains the following data from the [[GEOS-Chem_benchmarking#10-year_benchmark|10-year benchmarks]] used to evaluate GEOS-Chem: |
| − | | + | *Evaluation plots & tables |
| − | == 1-year benchmark ==
| + | *Restart files (tarball) |
| − | | + | *Model output (tarball) |
| − | === Overview ===
| + | *Log files (tarball) |
| − | | + | *Input files (tarball) |
| − | {| border=1 cellspacing=0 cellpadding=5
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | !bgcolor="#cccccc"|Spin-up:
| + | |
| − | |
| + | |
| − | *January 1, 2013 – January 1, 2014 (prior to [[GEOS-Chem v11-02#v11-02e|GEOS-Chem v11-02e]]
| + | |
| − | *January 1, 2015 – January 1, 2016 (prior to [[GEOS-Chem v11-02#v11-02e|GEOS-Chem v11-02e]]
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | !bgcolor="#cccccc"|Dates of Run:
| + | |
| − | |
| + | |
| − | *January 1, 2013 – January 1, 2014 (prior to [[GEOS-Chem v11-02#v11-02e|GEOS-Chem v11-02e]] | + | |
| − | *January 1, 2016 – January 1, 2017 (prior to [[GEOS-Chem v11-02#v11-02e|GEOS-Chem v11-02e]] | + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | !bgcolor="#cccccc"|[[GEOS-Chem_vertical_grids|Vertical Resolution]]:
| + | |
| − | |[[GEOS-FP]] with [[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72 hybrid sigma-pressure levels]]
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | !bgcolor="#cccccc"|[[GEOS-Chem_horizontal_grids|Horizontal Resolution]]:
| + | |
| − | |[[GEOS-Chem_horizontal_grids#GMAO_4_x_5_grid|4° latitude x 5° longitude]]
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | !bgcolor="#cccccc"|[[Species_in_GEOS-Chem#Full-chemistry|Advected species]]:
| + | |
| − | |<u>Gas-phase species:</u> 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
| + | |
| − | | + | |
| − | <u>Aerosol species:</u> 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
| + | |
| − | | + | |
| − | <u>Bromine species:</u> Br2, Br, BrO, HOBr, HBr, BrNO2 BrNO3, CHBr3, CH2Br2, CH3Br
| + | |
| − | | + | |
| − | <u>Stratospherically-important species:</u> 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
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | !bgcolor="#cccccc"|[[GEOS-Chem_chemistry_mechanisms|Chemical Mechanism]]:
| + | |
| − | |[[FlexChem]] chemical solver<br> using the standard chemistry mechanism ([[NOx-Ox-HC-Aer-Br_chemistry_mechanism|NOx-Ox-HC-Aer-Br]] + [[UCX_chemistry_mechanism|UCX]] + [[Secondary_organic_aerosols#Complex_SOA_scheme|complex SOA]])<br>Chemistry is done in both the troposphere and the stratosphere.
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | !bgcolor="#cccccc"|[[FAST-JX_v7.0_photolysis_mechanism|Photolysis Mechanism]]:
| + | |
| − | |[[FAST-JX_v7.0_photolysis_mechanism|FAST-JX v7.0]] (Prather, 2012, Wild et al, 2000).
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | !bgcolor="#cccccc"|Operations:
| + | |
| − | |
| + | |
| − | *[[Advection scheme TPCORE|Advection]] | + | |
| − | *[[ISORROPIA II|Aerosol thermodynamical equilibriium]]
| + | |
| − | *[[Boundary layer mixing]]
| + | |
| − | *[[Chemistry Issues|Chemistry]]
| + | |
| − | *[[Cloud convection]] (with updraft scavenging)
| + | |
| − | *[[Dry deposition]]
| + | |
| − | *[[Emissions overview|Emissions]]
| + | |
| − | *[[Photolysis_mechanism|Photolysis]]
| + | |
| − | *[[Wet deposition]]
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | !bgcolor="#cccccc"|[[List_of_diagnostics_for_v11-01|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
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | !bgcolor="#cccccc"|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: "tarball" refers to a <tt>*.tar.gz</tt> file. This is an archive of files & folders created with <tt>tar cvzf</tt> and can be extracted with <tt>tar xzvf</tt>. |
| − | | + | |
| − | ''<span style="color:darkorange">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 [[Python_code_for_GEOS-Chem#GCPy|GCPy package]].</span>''
| + | |
| − | | + | |
| − | 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 [[#Observations|below]].
| + | |
| − | | + | |
| − | === Observations ===
| + | |
| − | | + | |
| − | Here we provide an overview of the data used in the 1-year benchmark plots.
| + | |
| − | | + | |
| − | {| border=1 cellspacing=0 cellpadding=5
| + | |
| − | |-valign="top" bgcolor="#cccccc"
| + | |
| − | !Directory
| + | |
| − | !Data year
| + | |
| − | !Species
| + | |
| − | !Data source
| + | |
| − | !Provided by
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>BrO/</tt>
| + | |
| − | |2007-2008
| + | |
| − | |BrO
| + | |
| − | |[https://www.eumetsat.int/website/home/Satellites/CurrentSatellites/Metop/MetopDesign/GOME2/index.html GOME-2]
| + | |
| − | |Justin Parrella<br>(Data used to reproduce Figure 5 of [http://acmg.seas.harvard.edu/publications/2012/parrella2012.pdf Parrella et al. (2012)])
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>cmdl/</tt>
| + | |
| − | |2005, 2009<br>[[#Update 2005/2009 CMDL CO data to 2013/2014 GMD CO data|New data available]]
| + | |
| − | |CO
| + | |
| − | |[https://www.esrl.noaa.gov/gmd/ GMD] (formerly CMDL)
| + | |
| − | |Jennifer Logan and Inna Megretskaia
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>co.prof.for.gmi/</tt>
| + | |
| − | |2001-2008<br>(varies by station)
| + | |
| − | |CO
| + | |
| − | |[http://iagos.sedoo.fr/ MOZAIC]
| + | |
| − | |Jennifer Logan and Inna Megretskaia
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>eval/aircraft/</tt><br>''NOTE: Other directories in <tt>eval/</tt> aren't currently used''
| + | |
| − | |1995-2003<br>(varies by aircraft campaign)
| + | |
| − | |C2H6, C3H8, CO, H2O2, HNO3, NO, O3, PAN<br>
| + | |
| − | ''(Not currently used: ACET, ALK4, C2H2, CH2Br2, CH2BrCl, CH3Br, CH3OH, CH4, CHBr2Cl, CHBrCl2, CO2, ETHE, PRPE)''
| + | |
| − | |See [https://bitbucket.org/gcst/gc_1yr_benchmark/src/6495a17e5c0004f8290d09f141d585c30ce480ef/IDL/data/eval/aircraft/data/README.aircraft.data?at=master&fileviewer=file-view-default README]
| + | |
| − | |Jennifer Logan and Inna Megretskaia
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>netCDF/</tt>
| + | |
| − | |N/A
| + | |
| − | |C2H6, C3H8, CH3I, CO, H2O2, HNO3, NO, O3, OH, PAN, Rn
| + | |
| − | |Various<br>(contains information about station locations)
| + | |
| − | |Jennifer Logan and Inna Megretskaia
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>PAN/</tt>
| + | |
| − | |Varies
| + | |
| − | |PAN
| + | |
| − | |ARCTAS-A, ARCTAS-B, ARCPAC, INTEX-B, ITCT-2K2
| + | |
| − | |Emily Fischer<br>(Data used to reproduce Figure S1 of [https://www.atmos-chem-phys.net/14/2679/2014/acp-14-2679-2014-supplement.pdf Fischer et al. (2014) Supplement])
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>pm25_data/</tt>
| + | |
| − | |2005
| + | |
| − | |[[Particulate_matter_in_GEOS-Chem|PM2.5]]
| + | |
| − | |[http://vista.cira.colostate.edu/improve/ IMPROVE]
| + | |
| − | |Colette Heald
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>sondes.for.gmi/</tt>
| + | |
| − | |1990-2008<br>(varies by station)
| + | |
| − | |O3
| + | |
| − | |
| + | |
| − | |Jennifer Logan and Inna Megretskaia
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>strat/</tt>
| + | |
| − | |2001-2010
| + | |
| − | |NOy, O3
| + | |
| − | |[http://www.asc-csa.gc.ca/eng/satellites/odin.asp OSIRIS]
| + | |
| − | |Dylan Jones
| + | |
| − | | + | |
| − | |-valign="top"
| + | |
| − | |<tt>surface_ozone/</tt>
| + | |
| − | |
| + | |
| − | |O3
| + | |
| − | |[https://www.esrl.noaa.gov/gmd/ CMDL]
| + | |
| − | |Jennifer Logan and Inna Megretskaia
| + | |
| − | | + | |
| − | |}
| + | |
| − | | + | |
| − | --[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 14:26, 16 August 2017 (UTC)
| + | |
| − | | + | |
| − | ==== Update 2005/2009 CMDL CO data to 2013/2014 GMD CO data ====
| + | |
| − | | + | |
| − | <span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02c|v11-02c]] and approved on 21 Sep 2017.'''''</span>
| + | |
| − | | + | |
| − | '''''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:
| + | |
| − | | + | |
| − | :#Put the <tt>2013data/</tt> and <tt>2014data/</tt> in the <tt>data/cmdl/</tt> directory of the 1-year benchmark code
| + | |
| − | :#Change <span style="color:red"><tt>newdata/</tt></span> to <span style="color:green"><tt>2013data/</tt></span> in plot_cmdl_3_models_4_months.pro
| + | |
| − | :#Change <span style="color:red"><tt>Feb09/</tt></span> to <span style="color:green"><tt>2013data/</tt></span> in plot_surface_co_geos_3_models.pro
| + | |
| − | :#Change <span style="color:red"><tt>newdata/</tt></span> to <span style="color:green"><tt>2014data/</tt></span> in plot_ships_3_models_4_months.pro and plot_ships_3_models_co.pro
| + | |
| − | :#Change the line <span style="color:red"><tt>file=pre+name_sta(kk)+'.mn'</tt></span> to <span style="color:green"><tt>file=pre+name_sta(kk)+’.mn.2013'</tt></span> in plot_cmdl_3_models_4_months.pro
| + | |
| − | :#Change the line <span style="color:red"><tt>file=pre+name_sta(kk)+’.mn.2005'</tt></span> to <span style="color:green"><tt>file=pre+name_sta(kk)+’.mn.2013'</tt></span> in plot_surface_co_geos_3_models.pro
| + | |
| − | :#Change the line <span style="color:red"><tt>file=pre+name_sta(kk)+'.mn'</tt></span> to <span style="color:green"><tt>file=pre+name_sta(kk)+’.mn.2014'</tt></span> 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!
| + | == Benchmark plotting routines == |
| | | | |
| − | --[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 22:10, 15 August 2017 (UTC)
| + | The benchmark plotting routines are included with [https://github.com/geoschem/gcpy GCPy], a Python took kit available for GEOS-Chem. |
Benchmarking supports the maintenance of GEOS-Chem as a robust state-of-the-science facility with a nimble grass-roots approach and strong version control. Benchmarking has four main objectives:
Output files and evaluation plots for 1-month and 1-year benchmark simulations are archived at Harvard as summarized below. GEOS-Chem users may utilize these output for comparisons against their own simulations.
