Benchmark/GEOS-Chem 12.4.0

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This page includes information about all benchmark simulations for GEOS-Chem 12.4.0.

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
Plots still created by GAMAP
J-values maps differences ratios -- --
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
Features affecting the full-chemistry simulation:
Grid-independent dust emissions (hourly) David Ridley (CARB, formerly MIT)
Jun Meng (Dalhousie)
Grid-independent lightning NOx emissions (3-hourly) Lee Murray (Rochester)
Grid-independent biogenic emissions (hourly) Jintai Lin (PKU)
Hongjian Meng (PKU)
Grid-independent sea salt emissions (hourly) Jintai Lin (PKU)
Hongjian Meng (PKU)
Grid-independent soil NOx emissions (hourly) Jintai Lin (PKU)
Hongjian Meng (PKU)
Updated volcano emissions (1978-2019) Christoph Keller (NASA/GMAO)
Bug fix: Rebuild chemical mechanisms for FAST-JX fix added in 12.3.2 Katie Travis (NASA)
Features affecting the full-chemistry simulation:


FlexGrid Stage 2: Add capability to define custom grids Melissa Sulprizio (GCST)
Jiawei Zhuang (Harvard)
Add photolysis menu to input.geos for specifying FAST-JX directory Tomas Sherwen (York)
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: 10:50:46
  • CPU time / wall time: 19.3517
  • % of ideal performance: 80.63%
  • Memory: 13.8346 GB
Compared to previous benchmark: 12.3.0
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): Lightning NOx Emissions, Dust Emissions, Biogenic Emissions, Sea Salt Emissions, Soil NOx Emissions, Volcano Emissions
Unit test results may be viewed at: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.4.0/output/GC_12.4.0_May21.results.html
Metrics
Global mean OH from log file (% change): 12.6452510681687 x 105 molec/cm3 (0.91%)
Methyl chloroform lifetime (% change): 4.8037 years (-2.92%)
Methane lifetime (% change): 8.0807 years (-3.09%)
At the SURFACE, list all species that changed by 10% or more: NO, O3, PAN, ISOP, HNO3, H2O2, ACET, ALD2, MVK, MACR, NPMN, PPN, R4N2, PRPE, CH2O, N2O5, HNO4, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, NITs, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, NO2, NO3, HNO2, XYLE, LIMO, TSOG1, TSOA1, ISOG1, ISOG2, ISOG3, ISOA1, ISOA3, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3, SOAP, EOH, MGLY, GLYX, HPALD, DHDN, ETHLN, HCOOH, IEPOXA, IEPOXB, IEPOXD, ISN1, RIPA, RIPB, RIPD, IMAE, SOAIE, SOAME, SOAGX, SOAMG, LVOC, LVOCOA, ISN1OG, ISN1OA, MONITS, MONITU, HONIT, IONITA, MONITA, INDIOL, IPMN, HC187, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, BrSALA, BrSALC, HOI, I2, IBr, ICl, I, IO, OIO, INO, IONO, IONO2, I2O2, I2O3, I2O4, ISALA, ISALC, OH, HO2
Comments on SURFACE differences: Below we summarize the notable changes caused by specific updates.

Grid-independent dust emissions 

  ###############################################################################
  ### Emissions totals                                                        ###
  ### Ref = GC_12.3.0; Dev = GC_12.4.0                                        ###
  ###############################################################################
                                   Ref            Dev            Dev - Ref
  DST1 Natural              :      4.487948      11.225230       6.737282 Tg
  DST2 Natural              :      8.540177      23.995240      15.455063 Tg
  DST3 Natural              :     15.495716      43.538139      28.042424 Tg
  DST4 Natural              :     16.951628      47.628794      30.677167 Tg
Overall, dust emissions and concentrations increased with the introduction of the grid-independent emissions. The offline dust emissions have been scaled to match 2x2.5 online dust emissions for 2016, so further validation with a 1-year benchmark is needed to ensure these changes make sense.


Grid-independent lightning NOx emissions 

  ###############################################################################
  ### Emissions totals                                                        ###
  ### Ref = GC_12.3.0; Dev = GC_12.4.0                                        ###
  ###############################################################################
                                   Ref            Dev            Dev - Ref
  NO Lightning              :      1.603119       1.700865       0.097746 Tg
Lightning emissions increased slightly when using the grid-independent lightning NOx emissions. The pattern of the changes globally is consistent with the expected changes from caused by regridding. Some differences in the vertical distribution of NOx can be attributed to these changing emissions, with slightly lower emissions aloft and slightly higher emissions in the free troposphere.


Grid-independent biogenic emissions 

  ###############################################################################
  ### Emissions totals                                                        ###
  ### Ref = GC_12.3.0; Dev = GC_12.4.0                                        ###
  ###############################################################################
                                   Ref            Dev            Dev - Ref
  ACET Biogenic             :      3.199002       2.881931      -0.317071 Tg C
  ALD2 Biogenic             :      1.082313       0.877756      -0.204557 Tg C
  CO Monoterp               :      5.811675       5.504973      -0.306702 Tg
  EOH Biogenic              :      1.034973       0.839363      -0.195610 Tg C
  ISOP Biogenic             :     32.783415      23.495304      -9.288111 Tg C
  LIMO Biogenic             :      0.954841       1.022397       0.067556 Tg
  PRPE Biogenic             :      2.179011       1.971144      -0.207867 Tg C
  SOAP Biogenic             :      1.294232       0.086853      -1.207379 Tg
  SOAS Biogenic             :      1.294232       0.086853      -1.207379 Tg
Biogenic emissions for all species except limonene decreased when using the grid-independent biogenic emissions. This caused decreases in many of the primary and secondary organic species over land.


Grid-independent sea salt emissions 

  ###############################################################################
  ### Emissions totals                                                        ###
  ### Ref = GC_12.3.0; Dev = GC_12.4.0                                        ###
  ###############################################################################
                                   Ref            Dev            Dev - Ref
  SALA Natural              :      4.653316       5.620708       0.967392 Tg
  SALC Natural              :    281.640070     340.191067      58.550997 Tg
Sea salt emissions increased when using the grid-independent sea salt emissions, causing global increases in many of the sea-salt aerosol species (BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s) at the surface and aloft.


Grid-independent soil NOx emissions 

  ###############################################################################
  ### Emissions totals                                                        ###
  ### Ref = GC_12.3.0; Dev = GC_12.4.0                                        ###
  ###############################################################################
                                   Ref            Dev            Dev - Ref
  NO Soil                   :      1.365916       1.580800       0.214884 Tg
Soil NO emissions increased slightly when using the grid-independent soil NOx emissions. The pattern of the changes globally is consistent with the expected changes from caused by regridding.


Updated volcano emissions (1978-2019) 

  ###############################################################################
  ### Emissions totals                                                        ###
  ### Ref = GC_12.3.0; Dev = GC_12.4.0                                        ###
  ###############################################################################
                                   Ref            Dev            Dev - Ref
  SO2 VolcDegas             :      1.553769       1.509524      -0.044245 Tg
  SO2 VolcErupt             :      0.000000       0.000000       0.000000 Tg
Updating to the newer volcano inventory reduced degassing volcano SO2 emissions by 0.044 Tg. This was expected because the last year of degassing emissions in the previous volcano dataset was 2009, which was a particularly active year. The eruptive volcano SO2 emissions remained at 0.


NOTE: The bug fix to rebuild chemical mechanisms for FAST-JX fix did not impact this benchmark. The bug was introduced in 12.3.2, and would not show up in the comparisons here between 12.3.0 and 12.4.0.

At 500 hPa, list all species that changed by 10% or more: NO, O3, ALK4, ISOP, HNO3, H2O2, RCHO, MVK, MACR, NPMN, R4N2, PRPE, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NIT, NITs, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, NO2, NO3, HNO2, TOLU, XYLE, LIMO, TSOG0, ASOG1, ASOG2, ASOG3, ASOA1, ASOA3, SOAP, GLYX, HPALD, DHDN, ETHLN, IEPOXA, IEPOXB, IEPOXD, ISN1, RIPA, RIPB, RIPD, IMAE, SOAME, LVOC, ISN1OG, ISN1OA, MONITS, HONIT, IONITA, IPMN, HC187, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, BrSALA, BrSALC, CH2I2, CH2ICl, CH2IBr, HOI, I2, IBr, ICl, I, IO, HI, OIO, INO, IONO, IONO2, I2O2, I2O3, I2O4, ISALA, ISALC, OH, HO2
Comments on 500 hPa differences:
  • See comments for surface differences
In the ZONAL MEAN differences, list all species that changed by 10% or more: NO, O3, PAN, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, NPMN, PPN, R4N2, PRPE, C3H8, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, NITs, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, MAP, NO2, NO3, HNO2, BENZ, TOLU, XYLE, MTPA, LIMO, TSOG1, TSOA1, ISOG1, ISOG2, ISOG3, ISOA1, ISOA3, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3, SOAP, EOH, MGLY, GLYX, ACTA, HPALD, DHDN, ETHLN, HCOOH, IEPOXA, IEPOXB, IEPOXD, ISN1, RIPA, RIPB, RIPD, IMAE, SOAIE, SOAME, SOAGX, SOAMG, LVOC, LVOCOA, ISN1OG, ISN1OA, MONITS, MONITU, HONIT, IONITA, MONITA, INDIOL, IPMN, HC187, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, BrSALA, BrSALC, CH3I, CH2I2, CH2ICl, CH2IBr, HOI, I2, IBr, ICl, I, IO, HI, OIO, INO, IONO, IONO2, I2O2, I2O3, I2O4, ISALA, ISALC, OH, HO2
Comments on ZONAL MEAN differences:
  • See comments for surface differences
In the EMISSIONS maps, list all species that changed by 10% or more:
  • Volcano SO2
  • Lightning NO
  • Soil NO
  • Natural emissions: DST1, DST2, DST3, DST4, SALA, SALC
  • Biogenic emissions for ACET, ALD2, CO, EOH, ISOP, LIMO, PRPE, SOAP, SOAS
Comments on EMISSIONS differences:
  • See comments for surface differences
Additional or summary comments:
Approval
Requires further investigation: Will require a 1-year benchmark simulation
Approved by:
Date of approval:

GCHP 1-month benchmark

The following sections contain validation plots for GCHP 12.4.0.

Comparison of GCHP versions

This table contains plots comparing GCHP 12.3.2 (Ref) and GCHP 12.4.0 (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 12.4.0 (Ref) against GCHP 12.4.0 (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 12.4.0 - GCHP 12.3.2] against the difference [GC Classic 12.4.0 - 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.

GEOS-Chem Classic 1-year benchmark

Benchmark plots

These benchmarks plots were made using a combination of routines from GCPy and GAMAP. The 6-panel concentration, difference, and fractional difference plots were created with GCPy, while the model vs observation plots, the emissions plots and tables, and the aerosol tables were created with GAMAP because they have not been converted to Python yet.

Category1 Plots Additional Information
Level Map Zonal Mean Emissions
Primary Jan sfc

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
Plots still created by GAMAP
J-values maps differences ratios -- --
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.
 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
Plots still created by GAMAP
J-values maps differences ratios -- --
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.
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