GEOS-Chem 13.0.0: Difference between revisions

Revision as of 06:15, 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 Fix bug with stratospheric aerosol Shift RRTMG call time sequence to begin first timestep Fix bugs in GEOS-Chem 12 implementation of netCDF diagnostics Complete remaining implementation of netCDF diagnostics to match binary Fix seg fault when building RRTMG with Intel compilers Allow turning RRTMG off when using RRTMG-enabled executable	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: Incorrect density value used to calculate cloud ice volume Fix stratospheric loss in CH4 simulation using 12.9.0 Update format statements in fast_jx_mod.F90 for 3 integers Fix typo in mercury_mod.F for saving EmisHg0land Fix for reading archived OH and Cl in CH4 simulations Fix species name typo in Init_HetInfo subroutine	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 Use MERRA-2 meteorology instead of GEOS-FP 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 12.03=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* These fixes primarily caused differences in concentrations of halogen species and other species involved in heterogeneous chemistry. Global mean OH decreased by 3.45%. The following updates introduced differences on the order of numerical noise: Fix handling of NOx coefficients in ucx_mod.F90 Removal of HEMCO code from within the non-local PBL mixing modules Prevent divide-by-zero errors in UCX routine UCX_NOX
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

@@ Line 994: / Line 994: @@
 :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 '''
-*''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:
     ===============================================================================
@@ Line 1,037: / Line 1,035: @@
 '''[https://github.com/geoschem/geos-chem/issues/447 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                                     ###
@@ Line 1,073: / Line 1,069: @@
 '''[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, 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]'''
+:These fixes primarily caused differences in [http://ftp.as.harvard.edu/gcgrid/geos-chem/validation/InternalBenchmarks/GCC_13.0.0-alpha.7/BenchmarkResults/Tables/GlobalMass_Trop.txt concentrations of halogen species] and other species involved in heterogeneous chemistry. Global mean OH decreased by 3.45%.

GEOS-Chem 13.0.0: Difference between revisions

Revision as of 06:15, 10 November 2020

Contents

Version overview

New data directories

1-month benchmarks

Model setup

Benchmark Plots and Tables

GCClassic version comparison

GCHP version comparison

GCHP and GEOS-Chem Classic comparison

GCHP and GEOS-Chem Classic difference of differences

Benchmark assessment form

1-year full-chemistry benchmarks

Model setup

Benchmark Plots and Tables

1-year transport tracers benchmarks

Model setup

Benchmark Plots and Tables

10-year stratospheric benchmarks

Model setup

Benchmark Plots and Tables

Navigation menu

GEOS-Chem 13.0.0: Difference between revisions

Revision as of 06:15, 10 November 2020

Version overview

New data directories

1-month benchmarks

Model setup

Benchmark Plots and Tables

GCClassic version comparison

GCHP version comparison

GCHP and GEOS-Chem Classic comparison

GCHP and GEOS-Chem Classic difference of differences

Benchmark assessment form

1-year full-chemistry benchmarks

Model setup

Benchmark Plots and Tables

1-year transport tracers benchmarks

Model setup

Benchmark Plots and Tables

10-year stratospheric benchmarks

Model setup

Benchmark Plots and Tables

Navigation menu

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