Difference between revisions of "GEOS-Chem 13.0.0"

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!colspan="2" bgcolor="#CCFFFF"|Updates that WILL AFFECT the full-chemistry simulation
 
!colspan="2" bgcolor="#CCFFFF"|Updates that WILL AFFECT the full-chemistry simulation
  
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/447 CEDS_GBD-MAPS emission inventory (1970 - 2017)]
 +
|Erin McDuffie (Dalhousie)
  
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/309 Retire carbon-based units for VOCs]
 +
|Melissa Sulprizio (GCST)
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/311 Removal of HEMCO code from within the non-local PBL mixing modules]
 +
|Bob Yantosca (GCST)
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/pull/396 Heterogeneous chem fixes, performance improvements, and clarification]
 +
|Chris Holmes (FSU)
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/pull/344 Fix handling of NOx coefficients in ucx_mod.F90]
 +
|Sebastian Eastham (MIT)
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/402 Prevent divide-by-zero errors in UCX routine UCX_NOX]
 +
|Bob Yantosca (GCST)
 +
 +
|-valign="top"
 +
!colspan="2" bgcolor="#CCFFFF"|Updates that will NOT affect full-chemistry simulations
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/388 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)<br>Melissa Sulprizio (GCST)
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/424 Update QFED emissions through July 2020]
 +
|Christoph Keller (NASA GMAO)
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem-unittest/pull/19 ODIAC fossil fuel emissions for CO2 simulations]
 +
|Jenny Fisher (UOW)<br>Yi Cao (UOW)
 +
 +
|-valign="top
 +
|[https://github.com/geoschem/geos-chem-unittest/pull/24 Global Hg emissions from Streets et al. (2019)] (as option)
 +
|Colin Thackray (Harvard)
 +
 +
|-valign="top
 +
|[https://github.com/geoschem/geos-chem-unittest/pull/25 Global Hg emissions from EDGARv4.tox2] (as option)
 +
|Amanda Giang (UBC)
 +
 +
|-valign="top"
 +
|[https://essd.copernicus.org/articles/12/563/2020/essd-12-563-2020.pdf Global Inventory of Methane Emissions from Fuel Exploitation]
 +
|Tia Scarpelli (Harvard)
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/332 Retire tropchem mechanism; implement new tropchem simulation using Standard mechanism below the tropopause and archived P/L rates above]
 +
|Melissa Sulprizio (GCST)
 +
 +
|-valign="top"
 +
|RRTMG fixes and updates
 +
*[https://github.com/geoschem/geos-chem/pull/347 Fix bug with stratospheric aerosol]
 +
*[https://github.com/geoschem/geos-chem/issues/350 Shift RRTMG call time sequence to begin first timestep]
 +
*[https://github.com/geoschem/geos-chem/issues/350 Fix bugs in GEOS-Chem 12 implementation of netCDF diagnostics]
 +
*[https://github.com/geoschem/geos-chem/issues/350 Complete remaining implementation of netCDF diagnostics to match binary]
 +
*[https://github.com/geoschem/geos-chem/issues/438 Fix seg fault when building RRTMG with Intel compilers]
 +
*[https://github.com/geoschem/geos-chem/pull/429 Allow turning RRTMG off when using RRTMG-enabled executable]
 +
|Sebastian Eastham (MIT)<br>Lizzie Lundgren (GCST)
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/242 Add global mean OH and CH4 lifetime diagnostics]
 +
|Bob Yantosca (GCST)
 +
 +
|-valign="top"
 +
|[http://wiki.seas.harvard.edu/geos-chem/index.php/Compiling_with_CMake Retire the GNU Make build system in both GEOS-Chem Classic and GCHP and replace with CMake]
 +
|Liam Bindle (WashU)<br>GCST
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/283 Retire the GEOS-Chem Unit Tester repository and move GEOS-Chem run directory creation to the GEOS-Chem source code repository]
 +
|Melissa Sulprizio (GCST)
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/pull/334 Updates to GEOS-Chem and HEMCO interface for compatibility with CESM]
 +
|Haipeng Lin (Harvard)<br>Thibaud Fritz (MIT)<br>Lizzie Lundgren (GCST)
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/issues/270 Dynamically allocate diagnostic arrays based on HISTORY.rc content to minimize memory footprint]
 +
|Bob Yantosca (GCST)
 +
 +
|-valign="top"
 +
|Fixes for typos:
 +
*[https://github.com/geoschem/geos-chem/issues/442 Incorrect density value used to calculate cloud ice volume]
 +
*[https://github.com/geoschem/geos-chem/issues/410 Fix stratospheric loss in CH4 simulation using 12.9.0]
 +
*[https://github.com/geoschem/geos-chem/issues/444 Update format statements in fast_jx_mod.F90 for 3 integers]
 +
*[https://github.com/geoschem/geos-chem/issues/430 Fix typo in mercury_mod.F for saving EmisHg0land]
 +
*[https://github.com/geoschem/geos-chem/issues/415 Fix for reading archived OH and Cl in CH4 simulations]
 +
*[https://github.com/geoschem/geos-chem/issues/416 Fix species name typo in Init_HetInfo subroutine]
 +
|GCST
 +
 +
|-
 +
!colspan="2" bgcolor="#CCFFFF"|Features only affecting GCHP:
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/gchp/issues/63 Retire the existing GCHP repository and replace with a new wrapper repository that uses ESMF as an external library and integrates GEOS-Chem and NASA/GMAO GEOS-ESM git repositories as git submodules]
 +
|Lizzie Lundgren (GCST)
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/pull/246 Separate HEMCO from GEOS-Chem to use as an ESMF gridded component in GCHP]
 +
|Lizzie Lundgren (GCST)
 +
 +
|-valign="top"
 +
|[https://gchp.readthedocs.io/en/latest/stretched-grid.html Enable a stretched grid capability in GCHP to run global simulations at regional high resolution]
 +
|Liam Bindle (WashU)
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/GCHPctm/commit/004ca996312028037774820c8398502561489697 Update MAPL (v2.2.7) and GMAO library dependencies]
 +
|Lizzie Lundgren (GCST)
 +
 +
|-valign="top"
 +
|[https://github.com/geoschem/geos-chem/pull/348 Enable GCHP to be compiled with RRTMG]
 +
|Sebastian Eastham (MIT)<br>Lizzie Lundgren (GCST)
  
 
|}
 
|}

Revision as of 22:29, 5 November 2020


This page includes information about all benchmark simulations for GEOS-Chem 13.0.0.

GEOS-Chem Classic 1-month benchmark

Benchmark plots

Enable PDF bookmarks1 in the files linked below to navigate between species. See the Species in GEOS-Chem wiki page for species definitions and details.

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

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


1All plots created with GCPy have PDF bookmarks. If you do not see them in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.

2Species category and lumped species definitions are simple to adjust. Updating them requires only editing the YAML files.

Benchmark assessment form

Description
New features added into GEOS-Chem
Feature Submitted by
Updates that WILL AFFECT the full-chemistry simulation
CEDS_GBD-MAPS emission inventory (1970 - 2017) Erin McDuffie (Dalhousie)
Retire carbon-based units for VOCs Melissa Sulprizio (GCST)
Removal of HEMCO code from within the non-local PBL mixing modules Bob Yantosca (GCST)
Heterogeneous chem fixes, performance improvements, and clarification Chris Holmes (FSU)
Fix handling of NOx coefficients in ucx_mod.F90 Sebastian Eastham (MIT)
Prevent divide-by-zero errors in UCX routine UCX_NOX Bob Yantosca (GCST)
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)
Update QFED emissions through July 2020 Christoph Keller (NASA GMAO)
ODIAC fossil fuel emissions for CO2 simulations Jenny Fisher (UOW)
Yi Cao (UOW)
Global Hg emissions from Streets et al. (2019) (as option) Colin Thackray (Harvard)
Global Hg emissions from EDGARv4.tox2 (as option) Amanda Giang (UBC)
Global Inventory of Methane Emissions from Fuel Exploitation Tia Scarpelli (Harvard)
Retire tropchem mechanism; implement new tropchem simulation using Standard mechanism below the tropopause and archived P/L rates above Melissa Sulprizio (GCST)
RRTMG fixes and updates Sebastian Eastham (MIT)
Lizzie Lundgren (GCST)
Add global mean OH and CH4 lifetime diagnostics Bob Yantosca (GCST)
Retire the GNU Make build system in both GEOS-Chem Classic and GCHP and replace with CMake Liam Bindle (WashU)
GCST
Retire the GEOS-Chem Unit Tester repository and move GEOS-Chem run directory creation to the GEOS-Chem source code repository Melissa Sulprizio (GCST)
Updates to GEOS-Chem and HEMCO interface for compatibility with CESM Haipeng Lin (Harvard)
Thibaud Fritz (MIT)
Lizzie Lundgren (GCST)
Dynamically allocate diagnostic arrays based on HISTORY.rc content to minimize memory footprint Bob Yantosca (GCST)
Fixes for typos: GCST
Features only affecting GCHP:
Retire the existing GCHP repository and replace with a new wrapper repository that uses ESMF as an external library and integrates GEOS-Chem and NASA/GMAO GEOS-ESM git repositories as git submodules Lizzie Lundgren (GCST)
Separate HEMCO from GEOS-Chem to use as an ESMF gridded component in GCHP Lizzie Lundgren (GCST)
Enable a stretched grid capability in GCHP to run global simulations at regional high resolution Liam Bindle (WashU)
Update MAPL (v2.2.7) and GMAO library dependencies Lizzie Lundgren (GCST)
Enable GCHP to be compiled with RRTMG Sebastian Eastham (MIT)
Lizzie Lundgren (GCST)
Version, resolution, met fields used: MERRA-2 (72L), 4x5, July 2019
1-month benchmark finished on: Mon Nov 2 03:24:27 EST 2020
Performance statistics:
  • Compiled with ifort 18.0.5
  • Ran on 24 CPUs of holy7c20304.rc.fas.harvard.edu (Intel(R) Xeon(R) Platinum 8268 CPU @ 2.90GHz)
  • Wall time: 06:54:01
  • CPU time / wall time: 19.4750
  • % of ideal performance: 81.15%
  • Memory: 13.6795 GB
Git tag 13.0.0-rc.0
Compared to previous benchmark: 12.9.0
This update will impact:
(select all that apply with boldface) 		Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Emissions, Photolysis, Chemistry, Other (please specify):
Metrics
Global mean OH from log file (% change): 11.22769648880 x 105 molec/cm3 (-8.60)
Methyl chloroform lifetime (% change): 5.5460 years (+8.20%)
Methane lifetime (% change): 9.3297 years (+8.09%)
Overview
Comments on observed differences: Below we summarize the notable changes caused by specific updates.


Details
List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:
List all 500 hPa species and J-Values that changed by 10% or more :


List all ZONAL MEAN species and J-Values that changed by 10% or more:


List all EMISSIONS that changed by 10% or more:
Approval
Requires further investigation:
Approved by:
Date of approval:

GCHP 1-month benchmark

The following sections contain validation plots for GCHP 13.0.0.

Comparison of GCHP versions

This table contains plots comparing GCHP 13.0.0 (Ref) and GCHP 12.9.0 (Dev) for a 1-month simulation.

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

Comparison of GCHP and GEOS-Chem Classic

This table contains plots comparing GEOS-Chem Classic 13.0.0 (Ref) against GCHP 13.0.0 (Dev) for a 1-month simulation.

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 sfc 500hPa full column stratosphere
Aerosols sfc 500hPa full column stratosphere
Bromine sfc 500hPa full column stratosphere
Chlorine sfc 500hPa full column stratosphere
Iodine sfc 500hPa full column stratosphere
Nitrogen sfc 500hPa full column stratosphere
Primary Organics sfc 500hPa full column stratosphere
Secondary Organics sfc 500hPa full column stratosphere
Secondary Organic Aerosols sfc 500hPa full column stratosphere
Sulfur sfc 500hPa full column stratosphere
ROy 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.

Retrieved from "https://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_13.0.0&oldid=47955"