Difference between revisions of "GEOS-Chem 13.1.0"

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==== GCHP 13.1.0 vs GEOS-Chem Classic 13.1.0 ====
 
==== GCHP 13.1.0 vs GEOS-Chem Classic 13.1.0 ====

Revision as of 18:55, 4 June 2021

GEOS-Chem Main Page | GCHP Main Page

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 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
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
  1. Remove useless computations from reaction rate-law functions
  2. 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
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 13.1.0

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


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