GEOS-Chem 13.0.0: Difference between revisions

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|colspan="3"|'''''Below we summarize the notable changes caused by specific updates.'''''
|colspan="3"|'''''Below we summarize the notable changes caused by specific updates. Supplementary plots may be viewed at http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/.'''''


'''Changes to benchmark setup'''
'''Changes to benchmark setup'''
*Use [[MERRA-2]] meteorology instead of [[GEOS-FP]]
*'''Use [[MERRA-2]] meteorology instead of [[GEOS-FP]]'''
*Update benchmark year from 2016 to 2019
:Changing from GEOS-FP  to MERRA-2 meteorology impacted the [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.0.0-alpha.5+MERRA2/BenchmarkResults/Tables/GlobalMass_Trop.txt concentrations of most species], most notably over land and in the Tropics. Global mean OH increased by 2.11%. In addition, changing the meteorology fields impacted emissions computed by HEMCO extensions (MEGAN, soil NOx, lightning NOx, dust, etc.). Those changes are summarized below in [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.0.0-alpha.5+MERRA2/BenchmarkResults/Emissions/Inventory_totals.txt this table of emissions by inventory] created from an internal benchmark isolating just the impact of changing from GEOS-FP to MERRA-2.
*Use restart file that has been spun up (July 2016 restart file from GEOS-Chem 12.9.0 1-year benchmark)
:The differences described above likely arise from differences in the GEOS system used to generate the two products. GEOS-FP meteorology for July 2016 are from the GEOS-5.13.1 system while MERRA-2 is frozen at GEOS-5.12.4. See NASA GMAO's website for more details on differences between GEOS versions: https://gmao.gsfc.nasa.gov/GMAO_products/NRT_products.php.
 
*'''Update benchmark year from 2016 to 2019'''
:Changing the benchmark year from 2016 to 2019 impacted the [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.0.0-alpha.5+MERRA2+2019/BenchmarkResults/Tables/GlobalMass_Trop.txt concentrations of most species] and caused global mean OH to decrease by 1.97%. This update primarily impacted the emissions used in the benchmark simulation. For GFED and volcano emissions, changing the year meant updating to a more recent emissions year. As with changing meteorology fields, changing meteorology year also changed emissions computed by HEMCO extensions. Those changes are summarized below in [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.0.0-alpha.5+MERRA2+2019/BenchmarkResults/Emissions/Inventory_totals.txt this table of emissions by inventory] created from an internal benchmark isolating just the impact of changing the simulation year from July 2016 to July 2019.
 
 
*''Use restart file that has been spun up '''
:The GEOS-Chem restart file is typically updated for each major version release. This means that a restart file generated using GEOS-Chem 12.0.0 has been used for all 1-month benchmarks in the GEOS-Chem 12 series. Many science updates (e.g. updated halogen and isoprene chemistry) went into that version, so the initial conditions provided by that restart file are likely not representative of actual concentrations. In addition, any new species added since 12.0.0 are not included in that restart file so those species are initialized to default background concentrations. To address this, we have updated the restart file to use the July 2016 restart file from the last 1-year benchmark (12.9.0), which has been spun up for at least a 1.5 years (more if you include spin-up from previous 1-year benchmarks).
:This update impacted [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.0.0-alpha.5+MERRA2+2019+newRst/BenchmarkResults/Tables/GlobalMass_Trop.txt concentrations of all species] and global mean OH decreased by 3.45%. The exact difference in the initial concentrations from the old and new restart files can be found by viewing the log files from the 1-month benchmarks for [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.9.0/GCC/GC_12.9.0.log GEOS-Chem 12.9.0] and [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.0.0-beta.0/GCClassic/GCC_13.0.0-beta.0.log GEOS-Chem 13.0.0]. A snippet of that output is included here:
 
  From GC_12.9.0.log:
  ===============================================================================
  R E S T A R T  F I L E  I N P U T
  Min and Max of each species in restart file [mol/mol]:
  Species  1,    ACET: Min = 1.000000003E-30  Max = 2.716920022E-08
  Species  2,    ACTA: Min = 1.000000003E-30  Max = 7.725763085E-11
  Species  3,    AERI: Min = 1.037870635E-15  Max = 7.207419123E-12
  Species  4,    ALD2: Min = 4.684888406E-23  Max = 4.086598082E-08
  ...
  Species  88,    HONIT: Min = 1.000000003E-30  Max = 1.707073372E-11
  Species  89,    HPALD1: Use background = 9.999999683E-21
  Species  90,    HPALD2: Use background = 9.999999683E-21
  Species  91,    HPALD3: Use background = 9.999999683E-21
  Species  92,    HPALD4: Use background = 9.999999683E-21
  Species  93,  HPETHNL: Use background = 9.999999683E-21
  ...
 
  From GCC_13.0.0-beta.0.log:
  ===============================================================================
  R E S T A R T  F I L E  I N P U T
  Min and Max of each species in restart file [mol/mol]:
  Species  1,    ACET: Min = 1.198645368E-22  Max = 1.961477203E-08
  Species  2,    ACTA: Min = 7.944660459E-23  Max = 9.854482785E-10
  Species  3,    AERI: Min = 3.872448817E-16  Max = 1.060779242E-11
  Species  4,    ALD2: Min = 3.997531496E-23  Max = 1.028521712E-08
  ...
  Species  88,    HONIT: Min = 8.688050479E-44  Max = 4.034103954E-11
  Species  89,  HPALD1: Min = 0.000000000E+00  Max = 8.148696995E-11
  Species  90,  HPALD2: Min = 0.000000000E+00  Max = 1.696967566E-10
  Species  91,  HPALD3: Min = 0.000000000E+00  Max = 5.354099109E-11
  Species  92,  HPALD4: Min = 0.000000000E+00  Max = 1.183441123E-10
  Species  93,  HPETHNL: Min = 0.000000000E+00  Max = 1.283986667E-10
  ...
 


'''[https://github.com/geoschem/geos-chem/issues/447 CEDS_GBD-MAPS emission inventory (1970 - 2017)]'''
'''[https://github.com/geoschem/geos-chem/issues/447 CEDS_GBD-MAPS emission inventory (1970 - 2017)]'''
Line 995: Line 1,040:
:This benchmark now uses CEDS Global Burden of Disease - Major Air Pollution Sources (GBD-MAPS) emissions for 2017, as opposed to the prior CEDS inventory released for CMIP6 (Hoesly et al., 2018) for which 2014 was the last year. The impact on emission totals is summarized below:
:This benchmark now uses CEDS Global Burden of Disease - Major Air Pollution Sources (GBD-MAPS) emissions for 2017, as opposed to the prior CEDS inventory released for CMIP6 (Hoesly et al., 2018) for which 2014 was the last year. The impact on emission totals is summarized below:


###############################################################################
  ###############################################################################
### Emissions totals for inventory CEDS                                    ###
  ### Emissions totals for inventory CEDS                                    ###
### Ref = GCC_12.9.0; Dev = GCC_13.0.0-beta.0                              ###
  ### Ref = GCC_12.9.0; Dev = GCC_13.0.0-beta.0                              ###
###############################################################################
  ###############################################################################
                                         Ref                Dev      Dev - Ref
                                         Ref                Dev      Dev - Ref
CEDS ALD2            :          0.154944            0.154553      -0.000391 Tg
  CEDS ALD2            :          0.154944            0.154553      -0.000391 Tg
CEDS ALK4            :          5.366765            6.199071      0.832306 Tg
  CEDS ALK4            :          5.366765            6.199071      0.832306 Tg
CEDS BCPI            :          0.124817            0.091399      -0.033419 Tg
  CEDS BCPI            :          0.124817            0.091399      -0.033419 Tg
CEDS BCPO            :          0.499270            0.365595      -0.133675 Tg
  CEDS BCPO            :          0.499270            0.365595      -0.133675 Tg
CEDS BENZ            :          0.538499            0.540498      0.002000 Tg
  CEDS BENZ            :          0.538499            0.540498      0.002000 Tg
CEDS C2H6            :          0.000000            0.000000      0.000000 Tg
  CEDS C2H6            :          0.000000            0.000000      0.000000 Tg
CEDS C3H8            :          0.000000            0.000000      0.000000 Tg
  CEDS C3H8            :          0.000000            0.000000      0.000000 Tg
CEDS CH2O            :          0.207237            0.188655      -0.018582 Tg
  CEDS CH2O            :          0.207237            0.188655      -0.018582 Tg
CEDS CH4              :          0.000000                nan            nan Tg
  CEDS CH4              :          0.000000                nan            nan Tg
CEDS CO              :          48.242726          43.334313      -4.908413 Tg
  CEDS CO              :          48.242726          43.334313      -4.908413 Tg
CEDS EOH              :          0.338720            0.192327      -0.146393 Tg
  CEDS EOH              :          0.338720            0.192327      -0.146393 Tg
CEDS HCOOH            :          0.790157            0.787156      -0.003002 Tg
  CEDS HCOOH            :          0.790157            0.787156      -0.003002 Tg
CEDS MEK              :          0.259010            0.317764      0.058754 Tg
  CEDS MEK              :          0.259010            0.317764      0.058754 Tg
CEDS MOH              :          0.235222            0.256436      0.021214 Tg
  CEDS MOH              :          0.235222            0.256436      0.021214 Tg
CEDS NH3              :          4.601724            4.532344      -0.069381 Tg
  CEDS NH3              :          4.601724            4.532344      -0.069381 Tg
CEDS NO              :          6.332088            5.357930      -0.974158 Tg
  CEDS NO              :          6.332088            5.357930      -0.974158 Tg
CEDS OCPI            :          0.775254            0.517257      -0.257997 Tg
  CEDS OCPI            :          0.775254            0.517257      -0.257997 Tg
CEDS OCPO            :          0.775254            0.517257      -0.257997 Tg
  CEDS OCPO            :          0.775254            0.517257      -0.257997 Tg
CEDS PRPE            :          0.273593            0.278035      0.004443 Tg
  CEDS PRPE            :          0.273593            0.278035      0.004443 Tg
CEDS SO2              :          8.222032            5.677984      -2.544048 Tg
  CEDS SO2              :          8.222032            5.677984      -2.544048 Tg
CEDS SO4              :          0.254883            0.176018      -0.078865 Tg
  CEDS SO4              :          0.254883            0.176018      -0.078865 Tg
CEDS SOAP            :          3.328738            2.990056      -0.338683 Tg
  CEDS SOAP            :          3.328738            2.990056      -0.338683 Tg
CEDS TOLU            :          0.641471            0.694438      0.052966 Tg
  CEDS TOLU            :          0.641471            0.694438      0.052966 Tg
CEDS XYLE            :          0.627999            0.653520      0.025521 Tg
  CEDS XYLE            :          0.627999            0.653520      0.025521 Tg
CEDS pFe              :          0.008222            0.005678      -0.002544 Tg
  CEDS pFe              :          0.008222            0.005678      -0.002544 Tg




'''[https://github.com/geoschem/geos-chem/issues/309 Retire carbon-based units for VOCs]'''
'''[https://github.com/geoschem/geos-chem/issues/309 Retire carbon-based units for VOCs]'''


:The impact of retiring carbon-based units can be observed in the difference plots and tables for ACET, ALD2, ALK4,  
:The impact of retiring carbon-based units can be observed in the difference plots and tables for ACET, ALD2, ALK4, BENZ, C2H6, C3H8, EOH, ISOP, MEK, PRPE, TOLU, XYLE. Those species were traditionally treated as having a molecular weight of 12.0 g/mol which in some cases would be multiplied by the molecular ratio or number of carbon atoms in that species. Differences introduced by this update are primarily small, but arise from the difference between the actual species molecular weights compared to the molecular weight of carbon multiplied by the number of carbons (e.g. for acetone the actual molecular weight is 58.02 g/mol while it was previously treated as 12.0*3=36.0 g/mol). In addition, the GEOS-Chem and HEMCO output in 12.9.0 and earlier indicated units of v/v or kg/m2/s for many of these species when it was actually vC/v and kgC/m2/s, and this led to incorrect unit conversions in GCPy when creating benchmark plots and tables. Where possible, we have corrected that in this benchmark output for 13.0.0 so we are comparing similar units for 12.9.0 and 13.0.0 output but some species like EOH still show large differences.
BENZ, C2H6, C3H8, EOH, ISOP, MEK, PRPE, TOLU, XYLE. Those species were traditionally treated as having a molecular weight of 12.0 g/mol which in some cases would be multiplied by the molecular ratio or number of carbon atoms in that species. Differences introduced by this update are primarily small, but arise from the difference between the actual species molecular weights compared to the molecular weight of carbon multiplied by the number of carbons (e.g. for acetone the actual molecular weight is 58.02 g/mol while it was previously treated as 12.0*3=36.0 g/mol). In addition, the GEOS-Chem and HEMCO output in 12.9.0 and earlier indicated units of v/v or kg/m2/s for many of these species when it was actually vC/v and kgC/m2/s, and this led to incorrect unit conversions in GCPy when creating benchmark plots and tables. Where possible, we have corrected that in this benchmark output for 13.0.0 so we are comparing similar units for 12.9.0 and 13.0.0 output but some species like EOH still show large differences.
 


'''[https://github.com/geoschem/geos-chem/pull/396 Heterogeneous chem fixes, performance improvements, and clarification]'''
'''[https://github.com/geoschem/geos-chem/pull/396 Heterogeneous chem fixes, performance improvements, and clarification]'''


'''[https://github.com/geoschem/geos-chem/pull/344 Fix handling of NOx coefficients in ucx_mod.F90]'''


'''The following updates introduced differences on the order of numerical noise:'''
'''The following updates introduced differences on the order of numerical noise:'''
*[https://github.com/geoschem/geos-chem/pull/344 Fix handling of NOx coefficients in ucx_mod.F90]
*[https://github.com/geoschem/geos-chem/issues/311 Removal of HEMCO code from within the non-local PBL mixing modules]
*[https://github.com/geoschem/geos-chem/issues/311 Removal of HEMCO code from within the non-local PBL mixing modules]
*[https://github.com/geoschem/geos-chem/issues/402 Prevent divide-by-zero errors in UCX routine UCX_NOX]
*[https://github.com/geoschem/geos-chem/issues/402 Prevent divide-by-zero errors in UCX routine UCX_NOX]

Revision as of 06:09, 10 November 2020

GEOS-Chem Main Page | GCHP Main Page

This page includes information about GEOS-Chem 13.0.0.

Version overview

The following items have been added to GEOS-Chem 13.0.0 since the last benchmark for GEOS-Chem 12.9.0.

Feature Submitted by Type
Updates that will affect full-chemistry simulations
Changes to benchmark setup:
  • Use MERRA-2 meteorology instead of GEOS-FP
  • Update benchmark year from 2016 to 2019
  • Use restart file that has been spun up (July 2016 restart file from GEOS-Chem 12.9.0 1-year benchmark)
 GCST Structural
CEDS_GBD-MAPS emission inventory (1970 - 2017) Erin McDuffie (Dalhousie) Science
Retire carbon-based units for VOCs Melissa Sulprizio (GCST) Science
Removal of HEMCO code from within the non-local PBL mixing modules Bob Yantosca (GCST) Structural
Heterogeneous chem fixes, performance improvements, and clarification Chris Holmes (FSU) Bug fix
Fix handling of NOx coefficients in ucx_mod.F90 Sebastian Eastham (MIT) Bug fix
Prevent divide-by-zero errors in UCX routine UCX_NOX Bob Yantosca (GCST) Bug fix
Updates that will NOT affect full-chemistry simulations
Use GEOS-FP 5.22 data for Jan - May 2020 and store GEOS-FP 5.25 for April - May 2020 as option Jun Meng (GCST)
Melissa Sulprizio (GCST) 		Data
Update QFED emissions through July 2020 Christoph Keller (NASA GMAO) Science
ODIAC fossil fuel emissions for CO2 simulations Jenny Fisher (UOW)
Yi Cao (UOW) 		Science
Global Hg emissions from Streets et al. (2019) (as option) Colin Thackray (Harvard) Science
Global Hg emissions from EDGARv4.tox2 (as option) Amanda Giang (UBC) Science
Global Inventory of Methane Emissions from Fuel Exploitation Tia Scarpelli (Harvard) Science
Retire tropchem mechanism; implement new tropchem simulation using Standard mechanism below the tropopause and archived P/L rates above Melissa Sulprizio (GCST) Science
RRTMG fixes and updates Sebastian Eastham (MIT)
Lizzie Lundgren (GCST) 		Bug fix
Add global mean OH and CH4 lifetime diagnostics Bob Yantosca (GCST) Structural
Retire the GNU Make build system in both GEOS-Chem Classic and GCHP and replace with CMake Liam Bindle (WashU)
GCST 		Structural
Create new GCClassic wrapper repository Lizzie Lundgren (GCST) Structural
Separate HEMCO from GEOS-Chem to use as a git submodule in GCClassic in GCHPctm Lizzie Lundgren (GCST) Structural
Retire the GEOS-Chem Unit Tester repository and move GEOS-Chem run directory creation to the GEOS-Chem repository Melissa Sulprizio (GCST) Structural
Updates to GEOS-Chem and HEMCO interface for compatibility with CESM Haipeng Lin (Harvard)
Thibaud Fritz (MIT)
Lizzie Lundgren (GCST) 		Structural
Dynamically allocate diagnostic arrays based on HISTORY.rc content to minimize memory footprint Bob Yantosca (GCST) Structural
Fixes for typos: GCST Bug fix
Features only affecting GCHP:
Retire the existing GCHP repository and replace with a new wrapper repository (GCHPctm) that uses ESMF as an external library and integrates GEOS-Chem and NASA/GMAO GEOS-ESM git repositories as git submodules Lizzie Lundgren (GCST) Structural
Enable a stretched grid capability in GCHP to run global simulations at regional high resolution Liam Bindle (WashU) Structural
Update MAPL (v2.2.7) and GMAO library dependencies Lizzie Lundgren (GCST) Structural
Enable GCHP to be compiled with RRTMG Sebastian Eastham (MIT)
Lizzie Lundgren (GCST) 		Science

New data directories

The following data directories have been added or updated in this version. You will have to download the directories relevant to your simulation.

Inventory Type What was added? Directory
CEDS DEFAULT
(full-chemistry simulations) 		CEDS_GBD-MAPS emission inventory (1970 - 2017) HEMCO/CEDS/v2020-08/
QFED OPTIONAL Update QFED emissions through July 2020 HEMCO/QFED/v2018-07/
ODIAC CO2 DEFAULT
(CO2 simulations) 		ODIAC fossil fuel emissions for CO2 simulations HEMCO/CO2/v2019-12/
MERCURY OPTIONAL
(Hg simulations) 		Updated Streets Hg emissions

Updated EDGAR 4.3 Hg emissions

HEMCO/MERCURY/v2020-07/
CH4 DEFAULT
(CH4 simulations) 		Global Inventory of Methane Emissions from Fuel Exploitation

Updated wetland and seep CH4 emissions

HEMCO/CH4/v2020-02/

HEMCO/CH4/v2020-04/

1-month benchmarks

Model setup

The following table describes the GEOS-Chem setup for both GEOS-Chem Classic and GCHP 1-month benchmark simulations.

Git tag(s): 13.0.0-rc.0
Compared to previous benchmark: 12.9.0
Software environment: ifort 18.0.5
openmpi 4.0.1
netcdf-fortran 4.5.2
cmake 3.16.1
Meteorology fields: MERRA-2
Benchmark month: July 2019
This version will impact:
(select all that apply with boldface)
  • Advection
  • BL Mixing
  • Convection
  • Meteorology Fields
  • Dry Deposition*
  • Wet Deposition
  • Emissions
  • Photolysis
  • Chemistry
  • Other (please specify):

Benchmark Plots and Tables

NOTES:

  • Enable PDF bookmarks in the files linked above to navigate between species. See the Species in GEOS-Chem wiki page for species definitions and details. If you do not see bookmarks in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.
  • Species categories and lumped species definitions are simple to adjust. Updating them requires only editing the YAML files.

GCClassic version comparison

Below are links to plots and tables comparing 1-month simulations for GEOS-Chem Classic 12.9.0 (Ref) and GEOS-Chem Classic 13.0.0 (Dev).

Species Category Plots Additional Information
Level Map Zonal Mean Emissions
Oxidants

O3, CO, OH, NOx

sfc 500hPa full column stratosphere sfc
Aerosols

DST1, DST2, DST3, DST4, NH4, NIT, SO4, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA

sfc 500hPa full column stratosphere sfc AOD
Bromine

Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr

sfc 500hPa full column stratosphere sfc
Chlorine

Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, CHCl3, HOCl, HCl, Halons, HCFCs, OClO

sfc 500hPa full column stratosphere --
Iodine

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

sfc 500hPa full column stratosphere sfc
Nitrogen

NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3

sfc 500hPa full column stratosphere sfc
Primary Organics

EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H6, C3H8, PRPE, TOLU, XYLE

sfc 500hPa full column stratosphere sfc
Secondary Organics

ACTA, ALD2, CH2O, HPALDs, MACR, IEPOX, ACET, MEK, MVK, ISOPN, GLYX, HCOOH, MAP, RCHO, MP

sfc 500hPa full column stratosphere sfc
Secondary Organic Aerosols

TSOA0, TSOA1, TSOA2, TSOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ASOG1, ASOG2, ASOG3, INDIOL, LVOCOA, SOAIE, SOAGX, SOAP, SOAS

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

Metrics OH concentration, MCF lifetime, CH4 lifetime
Budgets Budgets after operations



GCHP version comparison

Below are links to plots and tables comparing 1-month simulations for GCHP 12.9.0 (Ref) and GCHP 13.0.0 (Dev).

Species Category2 Plots Additional Information
Level Map Zonal Mean Emissions
Oxidants

O3, CO, OH, NOx

sfc 500hPa full column stratosphere sfc
Aerosols

DST1, DST2, DST3, DST4, NH4, NIT, SO4, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA

sfc 500hPa full column stratosphere sfc AOD
Bromine

Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr

sfc 500hPa full column stratosphere sfc
Chlorine

Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, CHCl3, HOCl, HCl, Halons, HCFCs, OClO

sfc 500hPa full column stratosphere --
Iodine

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

sfc 500hPa full column stratosphere sfc
Nitrogen

NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3

sfc 500hPa full column stratosphere sfc
Primary Organics

EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H6, C3H8, PRPE, TOLU, XYLE

sfc 500hPa full column stratosphere sfc
Secondary Organics

ACTA, ALD2, CH2O, HPALDs, MACR, IEPOX, ACET, MEK, MVK, ISOPN, GLYX, HCOOH, MAP, RCHO, MP

sfc 500hPa full column stratosphere sfc
Secondary Organic Aerosols

TSOA0, TSOA1, TSOA2, TSOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ASOG1, ASOG2, ASOG3, INDIOL, LVOCOA, SOAIE, SOAGX, SOAP, SOAS

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

Budgets Budgets after operations


GCHP and GEOS-Chem Classic comparison

Below are links to plots and tables comparing 1-month simulations for GEOS-Chem Classic 13.0.0 (Ref) and GCHP 13.0.0 (Dev).

Species Category2 Plots Additional Information
Level Map Zonal Mean Emissions
Oxidants

O3, CO, OH, NOx

sfc 500hPa full column stratosphere sfc
Aerosols

DST1, DST2, DST3, DST4, NH4, NIT, SO4, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA

sfc 500hPa full column stratosphere sfc AOD
Bromine

Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr

sfc 500hPa full column stratosphere sfc
Chlorine

Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, CHCl3, HOCl, HCl, Halons, HCFCs, OClO

sfc 500hPa full column stratosphere --
Iodine

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

sfc 500hPa full column stratosphere sfc
Nitrogen

NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3

sfc 500hPa full column stratosphere sfc
Primary Organics

EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H6, C3H8, PRPE, TOLU, XYLE

sfc 500hPa full column stratosphere sfc
Secondary Organics

ACTA, ALD2, CH2O, HPALDs, MACR, IEPOX, ACET, MEK, MVK, ISOPN, GLYX, HCOOH, MAP, RCHO, MP

sfc 500hPa full column stratosphere sfc
Secondary Organic Aerosols

TSOA0, TSOA1, TSOA2, TSOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ASOG1, ASOG2, ASOG3, INDIOL, LVOCOA, SOAIE, SOAGX, SOAP, SOAS

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

Budgets Budgets after operations


GCHP and GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 13.0.0 - GCHP 12.9.0] against the difference [GC Classic 13.0.0 - GC Classic 12.9.0], taken from 1-month benchmark simulations.

Category Plots
Level Map Zonal Mean
Oxidants

O3, CO, OH, NOx

sfc 500hPa full column stratosphere
Aerosols

DST1, DST2, DST3, DST4, NH4, NIT, SO4, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA

sfc 500hPa full column stratosphere
Bromine

Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH3Br, CH2Br2, CHBr3, HOBr, HBr

sfc 500hPa full column stratosphere
Chlorine

Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, CHCl3, HOCl, HCl, Halons, HCFCs, OClO

sfc 500hPa full column stratosphere
Iodine

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

sfc 500hPa full column stratosphere
Nitrogen

NOy, NOx, HNO2, HNO3, HNO4, MPAN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4, MENO3, ETNO3, IPRNO3, NPRNO3

sfc 500hPa full column stratosphere
Primary Organics

EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H6, C3H8, PRPE, TOLU, XYLE

sfc 500hPa full column stratosphere
Secondary Organics

ACTA, ALD2, CH2O, HPALDs, MACR, IEPOX, ACET, MEK, MVK, ISOPN, GLYX, HCOOH, MAP, RCHO, MP

sfc 500hPa full column stratosphere
Secondary Organic Aerosols

TSOA0, TSOA1, TSOA2, TSOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ASOG1, ASOG2, ASOG3, INDIOL, LVOCOA, SOAIE, SOAGX, SOAP, SOAS

sfc 500hPa full column stratosphere
Sulfur

SOx, DMS, OCS, SO2, SO4

sfc 500hPa full column stratosphere
ROy

H2O2, H, H2, H2O, HO2, O1D, OH, RO2

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.


Benchmark assessment form

Performance GCClassic GCHP
# CPUs, nodes: 24 CPUs
1 node (Intel Cascade Lake) 		48 CPUs
2 nodes (Intel Broadwell)
Wall time: 06:54:01 14:26:01
CPU time / wall time: 19.4750 47.0915
% of ideal performance: 81.15% 98.11%
Memory: 13.6795 GB 133.28 GB
Global mean OH:
(% change from previous version) 		11.22769648880 x 105 molec/cm3
(-8.60%) 		11.24518930757 x 105 molec/cm3
(N/A)
Methyl chloroform lifetime:
(% change from previous version) 		5.5460 years
(+8.20%) 		5.5318 years
(N/A)
Methane lifetime:
(% change from previous version) 		9.3297 years
(+8.09%) 		9.3064 years
(N/A)
Details
Species, J-Values, and COLUMN AOD values that changed by 10% or more at the surface: GCClassic version comparison GCHP version comparison

GCClassic vs GCHP

Species and J-Values that changed by 10% or more at 500 hPa: GCClassic version comparison GCHP version comparison

GCClassic vs GCHP

Species and J-Values that changed by 10% or more in zonal mean: GCClassic version comparison GCHP version comparison

GCClassic vs GCHP

Emissions that changed by 10% or more: GCClassic version comparison GCHP version comparison

GCClassic vs GCHP

Overview
Below we summarize the notable changes caused by specific updates. Supplementary plots may be viewed at http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/.

Changes to benchmark setup

Changing from GEOS-FP to MERRA-2 meteorology impacted the concentrations of most species, most notably over land and in the Tropics. Global mean OH increased by 2.11%. In addition, changing the meteorology fields impacted emissions computed by HEMCO extensions (MEGAN, soil NOx, lightning NOx, dust, etc.). Those changes are summarized below in this table of emissions by inventory created from an internal benchmark isolating just the impact of changing from GEOS-FP to MERRA-2.
The differences described above likely arise from differences in the GEOS system used to generate the two products. GEOS-FP meteorology for July 2016 are from the GEOS-5.13.1 system while MERRA-2 is frozen at GEOS-5.12.4. See NASA GMAO's website for more details on differences between GEOS versions: https://gmao.gsfc.nasa.gov/GMAO_products/NRT_products.php.
  • Update benchmark year from 2016 to 2019
Changing the benchmark year from 2016 to 2019 impacted the concentrations of most species and caused global mean OH to decrease by 1.97%. This update primarily impacted the emissions used in the benchmark simulation. For GFED and volcano emissions, changing the year meant updating to a more recent emissions year. As with changing meteorology fields, changing meteorology year also changed emissions computed by HEMCO extensions. Those changes are summarized below in this table of emissions by inventory created from an internal benchmark isolating just the impact of changing the simulation year from July 2016 to July 2019.


  • Use restart file that has been spun up '
The GEOS-Chem restart file is typically updated for each major version release. This means that a restart file generated using GEOS-Chem 12.0.0 has been used for all 1-month benchmarks in the GEOS-Chem 12 series. Many science updates (e.g. updated halogen and isoprene chemistry) went into that version, so the initial conditions provided by that restart file are likely not representative of actual concentrations. In addition, any new species added since 12.0.0 are not included in that restart file so those species are initialized to default background concentrations. To address this, we have updated the restart file to use the July 2016 restart file from the last 1-year benchmark (12.9.0), which has been spun up for at least a 1.5 years (more if you include spin-up from previous 1-year benchmarks).
This update impacted concentrations of all species and global mean OH decreased by 3.45%. The exact difference in the initial concentrations from the old and new restart files can be found by viewing the log files from the 1-month benchmarks for GEOS-Chem 12.9.0 and GEOS-Chem 13.0.0. A snippet of that output is included here:
  From GC_12.9.0.log:
  ===============================================================================
  R E S T A R T   F I L E   I N P U T

  Min and Max of each species in restart file [mol/mol]:
  Species   1,     ACET: Min = 1.000000003E-30  Max = 2.716920022E-08
  Species   2,     ACTA: Min = 1.000000003E-30  Max = 7.725763085E-11
  Species   3,     AERI: Min = 1.037870635E-15  Max = 7.207419123E-12
  Species   4,     ALD2: Min = 4.684888406E-23  Max = 4.086598082E-08
  ...
  Species  88,    HONIT: Min = 1.000000003E-30  Max = 1.707073372E-11
  Species  89,    HPALD1: Use background = 9.999999683E-21
  Species  90,    HPALD2: Use background = 9.999999683E-21
  Species  91,    HPALD3: Use background = 9.999999683E-21
  Species  92,    HPALD4: Use background = 9.999999683E-21
  Species  93,   HPETHNL: Use background = 9.999999683E-21
  ...

  From GCC_13.0.0-beta.0.log:
  ===============================================================================
  R E S T A R T   F I L E   I N P U T

  Min and Max of each species in restart file [mol/mol]:
  Species   1,     ACET: Min = 1.198645368E-22  Max = 1.961477203E-08
  Species   2,     ACTA: Min = 7.944660459E-23  Max = 9.854482785E-10
  Species   3,     AERI: Min = 3.872448817E-16  Max = 1.060779242E-11
  Species   4,     ALD2: Min = 3.997531496E-23  Max = 1.028521712E-08
  ...
  Species  88,    HONIT: Min = 8.688050479E-44  Max = 4.034103954E-11
  Species  89,   HPALD1: Min = 0.000000000E+00  Max = 8.148696995E-11
  Species  90,   HPALD2: Min = 0.000000000E+00  Max = 1.696967566E-10
  Species  91,   HPALD3: Min = 0.000000000E+00  Max = 5.354099109E-11
  Species  92,   HPALD4: Min = 0.000000000E+00  Max = 1.183441123E-10
  Species  93,  HPETHNL: Min = 0.000000000E+00  Max = 1.283986667E-10
  ...


CEDS_GBD-MAPS emission inventory (1970 - 2017)

This benchmark now uses CEDS Global Burden of Disease - Major Air Pollution Sources (GBD-MAPS) emissions for 2017, as opposed to the prior CEDS inventory released for CMIP6 (Hoesly et al., 2018) for which 2014 was the last year. The impact on emission totals is summarized below:
  ###############################################################################
  ### Emissions totals for inventory CEDS                                     ###
  ### Ref = GCC_12.9.0; Dev = GCC_13.0.0-beta.0                               ###
  ###############################################################################
                                       Ref                 Dev      Dev - Ref
  CEDS ALD2             :           0.154944            0.154553      -0.000391 Tg
  CEDS ALK4             :           5.366765            6.199071       0.832306 Tg
  CEDS BCPI             :           0.124817            0.091399      -0.033419 Tg
  CEDS BCPO             :           0.499270            0.365595      -0.133675 Tg
  CEDS BENZ             :           0.538499            0.540498       0.002000 Tg
  CEDS C2H6             :           0.000000            0.000000       0.000000 Tg
  CEDS C3H8             :           0.000000            0.000000       0.000000 Tg
  CEDS CH2O             :           0.207237            0.188655      -0.018582 Tg
  CEDS CH4              :           0.000000                 nan            nan Tg
  CEDS CO               :          48.242726           43.334313      -4.908413 Tg
  CEDS EOH              :           0.338720            0.192327      -0.146393 Tg
  CEDS HCOOH            :           0.790157            0.787156      -0.003002 Tg
  CEDS MEK              :           0.259010            0.317764       0.058754 Tg
  CEDS MOH              :           0.235222            0.256436       0.021214 Tg
  CEDS NH3              :           4.601724            4.532344      -0.069381 Tg
  CEDS NO               :           6.332088            5.357930      -0.974158 Tg
  CEDS OCPI             :           0.775254            0.517257      -0.257997 Tg
  CEDS OCPO             :           0.775254            0.517257      -0.257997 Tg
  CEDS PRPE             :           0.273593            0.278035       0.004443 Tg
  CEDS SO2              :           8.222032            5.677984      -2.544048 Tg
  CEDS SO4              :           0.254883            0.176018      -0.078865 Tg
  CEDS SOAP             :           3.328738            2.990056      -0.338683 Tg
  CEDS TOLU             :           0.641471            0.694438       0.052966 Tg
  CEDS XYLE             :           0.627999            0.653520       0.025521 Tg
  CEDS pFe              :           0.008222            0.005678      -0.002544 Tg


Retire carbon-based units for VOCs

The impact of retiring carbon-based units can be observed in the difference plots and tables for ACET, ALD2, ALK4, BENZ, C2H6, C3H8, EOH, ISOP, MEK, PRPE, TOLU, XYLE. Those species were traditionally treated as having a molecular weight of 12.0 g/mol which in some cases would be multiplied by the molecular ratio or number of carbon atoms in that species. Differences introduced by this update are primarily small, but arise from the difference between the actual species molecular weights compared to the molecular weight of carbon multiplied by the number of carbons (e.g. for acetone the actual molecular weight is 58.02 g/mol while it was previously treated as 12.0*3=36.0 g/mol). In addition, the GEOS-Chem and HEMCO output in 12.9.0 and earlier indicated units of v/v or kg/m2/s for many of these species when it was actually vC/v and kgC/m2/s, and this led to incorrect unit conversions in GCPy when creating benchmark plots and tables. Where possible, we have corrected that in this benchmark output for 13.0.0 so we are comparing similar units for 12.9.0 and 13.0.0 output but some species like EOH still show large differences.


Heterogeneous chem fixes, performance improvements, and clarification


The following updates introduced differences on the order of numerical noise:


Approval
Requires further investigation:
Approved by:
Date of approval:

1-year full-chemistry benchmarks

Model setup

The following table describes the GEOS-Chem setup for both GEOS-Chem Classic and GCHP 1-year benchmark simulations.

Git tag(s): TBD
Compared to previous benchmark: 12.9.0
Software environment: ifort 18.0.5
openmpi 4.0.1
netcdf-fortran 4.5.2
cmake 3.16.1
Meteorology fields: MERRA-2
Benchmark date: Spin-up run: Jan 2018 - Dec 2018
Production run: Jan 2019 - Dec 2019

Benchmark Plots and Tables

Coming soon

1-year transport tracers benchmarks

Model setup

The following table describes the GEOS-Chem setup for both GEOS-Chem Classic and GCHP 1-year benchmark simulations.

Git tag(s): TBD
Compared to previous benchmark: 12.9.0
Software environment: ifort 18.0.5
openmpi 4.0.1
netcdf-fortran 4.5.2
cmake 3.16.1
Meteorology fields: MERRA-2
Benchmark date: Spinup run: Jan 2015 - Dec 2018
Production run: Jan 2019 - Dec 2019

Benchmark Plots and Tables

Coming soon

10-year stratospheric benchmarks

Model setup

The following table describes the GEOS-Chem setup for both GEOS-Chem Classic and GCHP 10-year benchmark simulations.

Git tag(s): TBD
Compared to previous benchmark: N/A
Software environment: ifort 18.0.5
openmpi 4.0.1
netcdf-fortran 4.5.2
cmake 3.16.1
Meteorology fields: MERRA-2
Benchmark date: Jan 2010 - Dec 2019

Benchmark Plots and Tables

Coming soon

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