GEOS-Chem 13.1.0

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This page includes information about GEOS-Chem 13.1.0.

Version overview

The following items have been added to GEOS-Chem 13.1.0 since the last benchmark for GEOS-Chem 13.0.0. See also the 13.1.0 milestone on Github.

Feature	Submitted by	Type	Notes
Updates that will affect full-chemistry simulations
Distribute CEDS emissions vertically in the boundary layer	Barron Henderson (EPA) GCST	Science
Diurnal scale factors of power plants emissions in China	Hongjian Weng (PKU) Jintai Lin (PKU)	Science	See geoschem/geos-chem #548 Scale factors are applied to CEDS energy sector emissions over China
Fix H2O boundary conditions at tropopause	Sebastian Eastham (MIT)	Bug fix
Initial modifications for HEMCO internal grid	Haipeng Lin (Harvard)	Structural
Updates to speed up the chemical solver Remove useless computations from reaction rate-law functions Use !$OMP COLLAPSE(3) to vectorize the parallel loop in DO_FLEXCHEM	Bob Yantosca (GCST) Chris Holmes (FSU)	Structural
Update PM2.5 definition	Randall Martin (WashU)	Diagnostic
Fix parallelization issues in ISORRPOIA and get_ndep_mod.F90	Bob Yantosca (GCST)	Bug fix
Updates that will NOT affect full-chemistry simulations
GCAP 2.0	Lee Murray (Rochester)	Science	See geoschem/geos-chem #670 and geoschem/HEMCO #77
Updated CH4 emissions, including: Emissions through 2019 for GFED4 and JPL WetCharts inventories Anthropogenic emissions over Mexico from Scarpelli et al. (2020)	Xiao Lu (Harvard) Tia Scarpelli (Harvard)	Science
Restore J-values for the planeflight diagnostic	Tomas Sherwen (York)	Diagnostics
Retire RRTMG binary diagnostics	Lizzie Lundgren (GCST)	Diagnostics
Bug fix for nested grid simulations to read boundary conditions continuously	Melissa Sulprizio (GCST)	Bug fix
Features only affecting GCHP:
Initial modifications for GCHP adjoint - CO2 simulation	Colin Lee (CUBoulder)	Structural
Update GMAO submodules in GCHP	Lizzie Lundgren (GCST)	Structural	MAPL updated from v2.2.7 to v2.6.3 Library updates exclude ESMA_cmake
Use logging.yml for MAPL ExtData debug prints	Sebastian Eastham (MIT) Tom Clune (GMAO)	Config files
Add monthly diagnostic capability to History	Atanas Trayanov (GMAO)	Diagnostics	Monthly diagnostics no longer require breaking up runs into 1-month jobs
Change GCHP diagnostic filenames to be same as GEOS-Chem Classic	Lizzie Lundgren (GCST) Atanas Trayanov (GMAO)	Diagnostics	Time-averaged file timestamp changed from averaging period mid-point to start Filename prefix changed from GCHP to GEOSChem
Retire support for ifort18 fortran compiler	GCST	Environment

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
VerticalScaleFactors	DEFAULT	Scale factors for vertically distributing CEDS energy, industry, and ship emissions	HEMCO/VerticalScaleFactors/v2020-05
GCAP 2.0	OPTIONAL	GCAP 2.0 meteorology	GCAP2
Restart files for GCAP2	OPTIONAL	GCAP 2.0 restart files	ExtData/GCAP2_RESTARTS/
GCAP2	OPTIONAL	Oxidant fields and prod/loss rates for GCAP 2.0 simulations	HEMCO/GCAP2/
CMIP6	OPTIONAL	CEDS (historical) or Shared Socioeconomic Pathways (future) emissions, consistent with the CMIP6 simulation experimental design. Includes BB4MIPs biomass burning emissions.	HEMCO/CMIP6/v2021-01/

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):	13.1.0-beta.0
Compared to previous benchmark:	13.0.0-rc.2
Software environment:	ifort 19.0.5 OpenMPI 4.0.1 netcdf-fortran 4.5.2 CMake 3.16.1 ESMF 8.0.1
Model resolution:	GEOS-Chem Classic: 4° x 5° GCHP: c48
Meteorology fields:	MERRA-2 GEOS-Chem Classic: 4° x 5° GCHP: 0.5° x 0.625°
Initial conditions:	July 1, 2019 from 13.0.0 10-year benchmark NOTE: GCHP c48 restart file regridded from GEOS-Chem Classic 4° x 5°
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 file links 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 are defined in YAML files within the GEOS-Chem post-processing software GCPy.

GEOS-Chem Classic 13.1.0 vs 13.0.0

Below are links to plots and tables comparing 1-month simulations for GEOS-Chem Classic 13.1.0 (Dev) and GEOS-Chem Classic 13.0.0 (Ref).

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 13.1.0 vs 13.0.0

Below are links to plots and tables comparing 1-month simulations for GCHP 13.1.0 (Dev) and GCHP 13.0.0 (Ref).

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 13.1.0 vs GEOS-Chem Classic 13.1.0

Below are links to plots and tables comparing 1-month simulations for GCHP 13.1.0 (Dev) and GEOS-Chem Classic 13.1.0 (Ref).

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 vs GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 13.1.0 - GCHP 13.0.0] against the difference [GC Classic 13.1.0 - GC Classic 13.0.0], 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 diff-of-diffs plots are only generated for species concentrations.

Benchmark assessment form

Performance	GEOS-Chem Classic	GCHP
Grid resolution:	4° x 5°	C48
# CPUs, nodes:	48 CPUs 1 node (Intel Cascade Lake)	48 CPUs 2 nodes (Intel Cascade Lake)
Wall time:	04:31:10	10:50:40
CPU time / wall time:	39.5229	47.6711
% of ideal performance:	82.34%	99.31%
Memory:	14.22 GB	69.00 GB
Global mean OH: (% change from previous version)	11.19414388492 x 105 molec/cm3 (+1.02%)	11.24264752821 x 105 molec/cm3 (+0.94%)
Methyl chloroform lifetime: (% change from previous version)	5.5285 years (-1.23%)	5.5088 years (-1.11%)
Methane lifetime: (% change from previous version)	9.3034 years (-1.28%)	9.2718 years (-1.15%)
Details
Species, J-Values, and COLUMN AOD values that changed by 10% or more at the surface:	GEOS-Chem Classic 13.1.0 vs 13.0.0	GCHP 13.1.0 vs 3.0.0 GCHP vs GEOS-Chem Classic 13.1.0
Species and J-Values that changed by 10% or more at 500 hPa:	GEOS-Chem Classic 13.1.0 vs 13.0.0	GCHP 13.1.0 vs 13.0.0 GCHP vs GEOS-Chem Classic 13.1.0
Species and J-Values that changed by 10% or more in zonal mean:	GEOS-Chem Classic 13.1.0 vs 13.0.0	GCHP 13.1.0 vs 13.0.0 GCHP vs GEOS-Chem Classic 13.1.0
Emissions that changed by 10% or more:	GEOS-Chem Classic 13.1.0 vs 13.0.0	GCHP 13.1.0 vs 13.0.0 GCHP vs GEOS-Chem Classic 13.1.0
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/. 1. Distribute CEDS emissions vertically in the boundary layer This update modified 2D CEDS energy, industry, and ship emissions and vertically distributes them based on scale factors provided by Barron Henderson. All species with CEDS emissions were impacted, including NO, CO, SOAP, SO2, SO4, pFe, NH3, BCPI, BCPO, OCPI, OCPO, MOH, EOH, C2H6, C3H8, ALK4, C2H4, PRPE, C2H2, BENZ, TOLU, XYLE, CH2O, ALD2, MEK, and HCOOH. Differences caused by this update are small. 2. Diurnal scale factors of power plants emissions in China This update impacted CEDS emissions for the energy sector for species NO, CO, SOAP, SO2, SO4, pFe, NH3, BCPI, BCPO, OCPI, OCPO, MOH, EOH, C2H6, C3H8, ALK4, C2H4, PRPE, C2H2, BENZ, TOLU, XYLE, CH2O, ALD2, MEK, and HCOOH. To apply this update, the default diurnal scale factors from EDGAR are removed before the diurnal scale factors from PKU are applied to CEDS emissions over China only. Differences were very small due to distributing emissions differently across the 24 hours, as summarized below: ################################################################################### ### Emissions totals for inventory CEDS [Tg] ### ### Ref = GCC_13.1.0-alpha.6; Dev = GCC_13.1.0-alpha.7 ### ################################################################################### Ref Dev Dev - Ref  % diff CEDS ALD2  : 0.154553 0.154553 -0.000000 -0.000 CEDS ALK4  : 6.199071 6.199071 -0.000000 -0.000 CEDS BCPI  : 0.091399 0.091399 0.000000 0.000 CEDS BCPO  : 0.365595 0.365595 0.000000 0.000 CEDS BENZ  : 0.540498 0.540499 0.000000 0.000 CEDS C2H6  : 0.000000 0.000000 0.000000 nan CEDS C3H8  : 0.000000 0.000000 0.000000 nan CEDS CH2O  : 0.188655 0.188655 0.000000 0.000 CEDS CO  : 43.334313 43.334313 -0.000000 -0.000 CEDS EOH  : 0.192327 0.192327 -0.000000 -0.000 CEDS HCOOH  : 0.787156 0.787155 -0.000000 -0.000 CEDS MEK  : 0.317764 0.317764 -0.000000 -0.000 CEDS MOH  : 0.256436 0.256436 -0.000000 -0.000 CEDS NH3  : 4.532344 4.532344 0.000000 0.000 CEDS NO  : 5.357930 5.358063 0.000133 0.002 CEDS OCPI  : 0.517257 0.517257 -0.000000 -0.000 CEDS OCPO  : 0.517257 0.517257 -0.000000 -0.000 CEDS PRPE  : 0.278035 0.278035 -0.000000 -0.000 CEDS SO2  : 5.677984 5.678095 0.000111 0.002 CEDS SO4  : 0.176018 0.176021 0.000003 0.002 CEDS SOAP  : 2.990056 2.990060 0.000004 0.000 CEDS TOLU  : 0.694438 0.694438 0.000000 0.000 CEDS XYLE  : 0.653520 0.653520 0.000000 0.000 CEDS pFe  : 0.005678 0.005678 0.000000 0.002 3. Fix H2O boundary conditions at tropopause 4. Update PM2.5 definition This update impacted the PM2.5 diagnostic, but did not cause differences to species concentrations. 5. The following updates introduced differences on the order of numerical noise: Initial modifications for HEMCO internal grid Remove useless computations from reaction rate-law functions Fix parallelization issues in ISORRPOIA and get_ndep_mod.F90
Approval
Requires further investigation:
Approved by:
Date of approval: