Difference between revisions of "GEOS-Chem 13.4.0"

From Geos-chem
Jump to: navigation, search
(1-month fullchem: GEOS-Chem Classic 13.4.0-rc.0 vs 13.3.0)
(Benchmark assessment form)
Line 484: Line 484:
 
|'''Metrics'''
 
|'''Metrics'''
 
|colspan="6"|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.4.0-rc.0/GCClassic/BenchmarkResults/Tables/OH_metrics.txt OH concentration, MCF lifetime, CH4 lifetime]
 
|colspan="6"|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.4.0-rc.0/GCClassic/BenchmarkResults/Tables/OH_metrics.txt OH concentration, MCF lifetime, CH4 lifetime]
 
|}
 
 
=== Benchmark assessment form ===
 
 
{| border=1 cellspacing=0 cellpadding=5
 
|-bgcolor="#CCCCCC"
 
!width="325px"|Performance
 
!width="250px"|GEOS-Chem Classic (rc.0)
 
!width="250px"|GCHP (rc.0)
 
 
|-valign="top"
 
|Grid resolution:
 
|4° x 5°
 
|C48
 
 
|-valign="top"
 
|# CPUs, nodes:
 
|48 CPUs<br>1 node (Intel Cascade Lake)
 
|48 CPUs<br>2 nodes (Intel Cascade Lake)
 
 
|-valign="top"
 
|Wall time:
 
|03:37:13
 
|06:20:26
 
 
|-valign="top"
 
|[[Scalability|CPU time / wall time]]:
 
|31.79
 
|95.0732
 
 
|-valign="top"
 
|% of ideal performance:
 
|66.23%
 
|99.03%
 
 
|-valign="top"
 
|Memory:
 
|11.4128 GB
 
|108.5 GB
 
 
|-valign="top"
 
|Global mean OH:<br>(% change from previous version)
 
|11.70790814279 x 10<sup>5</sup> molec/cm3 <br>(-0.329%)
 
|TBD
 
 
|-valign="top"
 
|Methyl chloroform lifetime:<br>(% change from previous version)
 
|5.294530 years<br>(+0.557%)
 
|TBD
 
 
|-valign="top"
 
|Methane lifetime:<br>(% change from previous version)
 
|8.923431 years<br>(+0.581%)
 
|TBD
 
 
|-valign="top" bgcolor="#cccccc"
 
!colspan="4"|Details
 
 
|-valign="top"
 
|Species, J-Values, and COLUMN AOD values that changed by 10% or more at the '''surface''':
 
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.4.0-rc.0/GCClassic/BenchmarkResults/SigDiffs_sfc.txt GEOS-Chem Classic<br>13.4.0-rc.1 vs. 13.3.0-rc.0]
 
|TBD
 
 
|-valign="top"
 
|Species and J-Values that changed by 10% or more at '''500 hPa''':
 
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.4.0-rc.0/GCClassic/BenchmarkResults/SigDiffs_500hpa.txt GEOS-Chem Classic<br>13.4.0-rc.1 vs. 13.3.0-rc.0]
 
|TBD
 
 
|-valign="top"
 
|Species and J-Values that changed by 10% or more in '''zonal mean''':
 
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.4.0-rc.0/GCClassic/BenchmarkResults/SigDiffs_zonalmean.txt GEOS-Chem Classic<br>13.4.0-rc.1 vs. 13.3.0-rc.0]
 
|TBD
 
 
|-valign="top"
 
|'''Emissions''' that changed by 10% or more:
 
|[http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.4.0-rc.0/GCClassic/BenchmarkResults/SigDiffs_emissions.txt GEOS-Chem Classic<br>13.4.0-rc.1 vs. 13.3.0-rc.0]
 
|TBD
 
 
|-valign="top" bgcolor="#cccccc"
 
!colspan="4"|Overview
 
 
|-valign="top"
 
|colspan="4"|'''''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/13.4.0/.'''''
 
 
'''''1. [https://github.com/geoschem/geos-chem/pull/1054 Migrating sulfate chemistry into KPP]'''''
 
 
<blockquote>An error in GEOS-Chem 13.3.0 meant that HMS chemistry was not properly implemented. This has now been fixed in 13.4.0-rc.0 ([http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_13/13.4.0-rc.0/GCClassic/BenchmarkResults/Sulfur/Sulfur_Surface.pdf see this plot]).
 
 
Other changes in benchmark output related to this update are:
 
*Very small changes in OH Metrics (mean OH +0.0004%)
 
*Small changes in Oxidants concentrations.
 
*SO2 at surface decreases by ~10%.
 
*Large SO4 decreases (~50%) in the boreal forest regions of Canada & Russia.
 
</blockquote>
 
 
'''''2. [https://github.com/geoschem/geos-chem/issues/1001 Fix bug in Henry law CALC_HEFF routine in hetchem computations]'''''
 
 
<blockquote>Changes in benchmark output related to this update are:
 
*Very small changes in the OH metrics (mean OH -0.0698%, MCF lifetime +0.10%; CH4 lifetime +0.05%)
 
*Small changes in Trop+Strat masses for most species.
 
*Cl/Br species concentrations have significant changes primarily in the extratropics.
 
</blockquote>
 
 
'''''3. [https://github.com/geoschem/geos-chem/pull/1067 Fix scale factors applied to VOC aircraft emissions in AEIC inventory]'''''
 
 
<blockquote>The updated scale factors, which corrected the conversion from atoms C to kg species, resulted in significant decreases in emissions for VOC species. This was observed mostly in the northern hemisphere and up to the lower stratosphere (where most aircraft emissions occur).</blockquote>
 
 
    ###################################################################################
 
    ### Emissions totals for inventory AEIC [Tg]                                    ###
 
    ### Ref = GCC_13.3.0-rc.1; Dev = GCC_13.4.0-rc.0                                ###
 
    ###################################################################################
 
                                    Ref                Dev          Dev - Ref    % diff
 
    AEIC ACET          :          0.000139            0.000086    -0.000053  -38.027
 
    AEIC ALD2          :          0.001829            0.000996    -0.000833  -45.529
 
    AEIC ALK4          :          0.005617            0.004274    -0.001343  -23.912
 
    AEIC C2H6          :          0.000152            0.000122    -0.000031  -20.213
 
    AEIC C3H8          :          0.000022            0.000018    -0.000004  -18.386
 
    AEIC MACR          :          0.001827            0.000100    -0.001727  -94.522
 
    AEIC PRPE          :          0.004855            0.003779    -0.001076  -22.168
 
    AEIC RCHO          :          0.001384            0.003358      0.001974  142.621
 
 
<blockquote>However, this update resulted in minimal changes to global quantities, as VOC aircraft emissions are typically less than 1Gg for the simulation month. 
 
 
Other changes in benchmark output related to this update are:
 
* Very small changes in oxidants (too small to show up in ratio plots). 
 
* Slight change in most primary organics, but % differences are of order 1e-4 or 1e-5.
 
* Some zonal mean plots show diffs at top of atm where conc's are already low.
 
* Mean OH decreased by -0.005%, CH4 and MCF increasd by +0.006%.
 
* Very small changes in mass for most species. 
 
</blockquote>
 
 
'''''4. [https://github.com/geoschem/geos-chem/issues/1034 Bug fix: Remove double-counting of HCl uptake on acidic sea salt]'''''
 
 
<blockquote>Changes in benchmark output related to this update are:
 
 
*As expected, chlorine species concentrations decrease in the southern latitudes (esp. at about 40S), where there is more sea salt (and now less removal of HCl due to the bug fix).
 
*Some increase of Cl species concentrations at northern latitudes are observed.
 
*Cly concentrations generally increase.
 
*Very small chagnes in OH metrics as well (mean OH -0.03% change).
 
</blockquote>
 
 
'''''5. [https://github.com/geoschem/geos-chem/issues/997 Update surface resistance for ozone deposition to ice/snow]'''''
 
 
<blockquote>Barten et.al 2021 (https://doi.org/10.5194/acp-21-10229-2021) increased the surface resistance of ozone dry deposition to snow and ice to 1E4 s m−1, this results in a reduction of ozone deposition velocity to ice of <= 0.01 cm s−1 (~ 66% reduction) which has better agreement with observations and results in improved comparison between Ozone observations in the arctic.
 
 
Changes in benchmark output related to this update are:
 
*Increase in O3 concentration at the summer polar latitudes (i.e. deposition to ice/snow is suppressed);
 
*Minor change in other oxidants;
 
*Neglible effect on OH metrics;
 
*Neglible change in species mass (O3 only increases by 0.01%).
 
</blockquote>
 
 
'''''6. [https://github.com/geoschem/HEMCO/pull/121 HEMCO bug fix: restore archiving via manual diagnostics (which had been inadvertently disabled in a prior update)]'''''
 
 
<blockquote>This update causes very slight changes in NOx soil and fertilizer emissions, as shown below.  The HEMCO soil NOx extension uses an manual diagnostic to keep track of NOx from fertilizers.</blockquote>
 
 
      ###################################################################################
 
      ### Emissions totals for species NO [Tg]                                        ###
 
      ### Ref = GCC_13.3.0-rc.1; Dev = GCC_13.4.0-rc.0                                ###
 
      ###################################################################################
 
                                          Ref                Dev    Dev - Ref    % diff
 
      NO Aircraft        :          0.156922            0.156922      0.000000    0.000
 
      NO Anthro          :          5.327773            5.327773      0.000000    0.000
 
      NO BioBurn        :          1.882279            1.882279      0.000000    0.000
 
      <span style="color:red">NO Fert            :          0.359627            0.359458    -0.000169    -0.047</span>
 
      NO Lightning      :          1.664984            1.664984      0.000000    0.000
 
      NO Ship            :          0.073301            0.074878      0.001577    2.152
 
      <span style="color:red">NO Soil            :          1.745616            1.745500    -0.000115    -0.007</span>
 
      -----------------------------------------------------------------------------------
 
      <span style="color:red">NO Total          :          10.850869          10.852331      0.001462    0.013<span style="color:red">
 
 
'''''7. [https://github.com/geoschem/geos-chem/issues/1005 Use degassing-only volcano emissions in GEOS-Chem benchmark simulations]'''''
 
 
<blockquote>Removing eruptive volcanoes from the benchmark simulations reduces the amount of SO2 emitted by 1%:</blockquote>
 
 
      ###################################################################################
 
      ### Emissions totals for species SO2 [Tg]                                      ###
 
      ### Ref = GCC_13.3.0-rc.1; Dev = GCC_13.4.0-rc.0                                ###
 
      ###################################################################################
 
                                    Ref                Dev          Dev - Ref    % diff
 
      SO2 Aircraft      :          0.019036            0.019036      0.000000    0.000
 
      SO2 Anthro        :          5.872509            5.872509      0.000000    0.000
 
      SO2 BioBurn        :          0.555350            0.555350      0.000000    0.000
 
      SO2 Ship          :          0.951114            0.951114      0.000000    0.000
 
      SO2 VolcDegas      :          1.826465            1.826465      0.000000    0.000
 
      <span style="color:red">SO2 VolcErupt      :          0.101063            0.000000    -0.101063  -100.000</span>
 
      -----------------------------------------------------------------------------------
 
      <span style="color:red">SO2 Total          :          9.325534            9.224471    -0.101063    -1.084</span>
 
 
<blockquote>Other changes in benchmark output related to this update are:
 
*OH metrics show very small change;
 
*SO2 mass changes by -9%, SO4 by -4.6%, NIT by +4.3%, NH3 by +1.5%, NH4 by -1.1%.
 
*Some gas phase species show corresponding mass changes (e.g.ITCN & ITHN, +1.3%, KO2, -0.49%, MCHRN ; 5 S+0.8; *Other species mass change typically by +/- 0.5%;
 
*Minor decreases in SOx concentration at surface observed over SA, Africa, Indonesia, Australia.
 
</blockquote>
 
 
'''''8. [https://github.com/geoschem/geos-chem/pull/945 Add option for driving GEOS-Chem & GCHP with native GEOS meteorological files]'''''
 
 
<blockquote>
 
Changes in benchmark output related to this update are:
 
*Very small changes in OH metrics (mean OH -0.007%, MCF lifetime +0.011%, CH4 lifetime +0.011%)
 
*Mostly small changes in species mass (typically less than +/- 1%), except for a few species such as ACET, ATO2, BrSALA, which are larger;
 
*Minor differences in species concentration in the polar regions due to the removal of ALBEDO as a proxy for snow/ice.
 
</blockquote>
 
 
----
 
 
'''The following updates introduced differences on the order of numerical noise:'''
 
 
TBD
 
 
----
 
 
'''The following were zero-difference updates:'''
 
 
#GCHP-specific updates:
 
#*[https://github.com/geoschem/geos-chem/pull/1008 Define a GCHP "Default" collection that will archive a small number of commonly-requested diagnostic fields]
 
#*Add capability to use mass fluxes in advection
 
#CH4 simulation updates:
 
#*[https://github.com/geoschem/HEMCO/issues/122 Retire HEMCO extension for CH4 wetland emissions (now use WETCHARTS emissions instead)]
 
#*[https://doi.org/10.5194/acp-2021-911 Updated Global Inventory of Methane Emissions from Oil/Gas/Coal (GFEI v2)]
 
#*[https://doi.org/10.1088/1748-9326/ac40b1 Anthropogenic Methane Emission Inventory for Canada]
 
#*[https://edgar.jrc.ec.europa.eu/dataset_ghg60 Use EDGARv6 global anthro emissions for CH4 simulation]
 
#Hg simulation updates:
 
#*[https://pubs-acs-org.ezp-prod1.hul.harvard.edu/doi/10.1021/acs.est.1c03160 Updated Hg chemistry (implemented as a KPP mechanism)]
 
#TransportTracers simulation updates:
 
#*[https://acp.copernicus.org/articles/21/1861/2021/ Updated Rn-222 emissions for TransportTracers simulations]
 
#Diagnostic updates:
 
#*[https://github.com/geoschem/geos-chem/issues/1020 Bug fix: Allow GEOS-Chem Classic History to archive irregular intervals (e.g. a month and a day)]
 
#*[https://github.com/geoschem/geos-chem/pull/992 Use updated definition of PM2.5; Add PM10 diagnostic]
 
#Other updates:
 
#*[https://github.com/geoschem/geos-chem/pull/459 Updates to enable automated run directory creation]
 
#*[https://github.com/geoschem/geos-chem/issues/951 Bug fix: Use REAL*8 precision in for CH3O2 + OH reaction definition in fullchem.eqn]
 
 
 
|-bgcolor="#cccccc"
 
!colspan="4"|Approval
 
 
|-valign="top"
 
|Requires further investigation:
 
|colspan="4"|
 
 
|-valign="top"
 
|Approved by:
 
|colspan="4"|
 
 
|-valign="top"
 
|Date of approval:
 
|colspan="4"|
 
  
 
|}
 
|}

Revision as of 22:39, 25 January 2022

GEOS-Chem Versions Page

This page includes information about GEOS-Chem 13.4.0 (currently under development)

Version overview

The following items have been added to GEOS-Chem 13.4.0 since the last GEOS-Chem version GEOS-Chem 13.3.4. Also see the following Github pages:

Feature Contributor(s) Model scope Notes and references
Updates that will affect full-chemistry benchmark simulations
Migrating sulfate chemistry into KPP Mike Long (GCST)
Viral Shah (Harvard)
Bob Yantosca (GCST)
Chemistry &
Structural
Fix bug in Henry law CALC_HEFF routine in hetchem computations Viral Shah (Harvard) Chemistry
Bug fix: Remove double-counting of HCl uptake on acidic sea salt Viral Shah (Harvard) Chemistry
Update surface resistance for ozone deposition to ice/snow Ryan Pound (York)
Shuting Zhai (UW)
Drydep
Use updated definition of PM2.5; Add PM10 diagnostic Bob Yantosca (GCST) Diagnostics &
Benchmarking
Fix scale factors applied to VOC aircraft emissions in AEIC inventory Flavio Quadros (TU Delft)
Seb Eastham (GCST)
Emissions &
Bug Fix
HEMCO bug fix: restore archiving via manual diagnostics (which had been inadvertently disabled in a prior update) Melissa Sulprizio (GCST)
Bob Yantosca (GCST)
Emissions
Use degassing-only volcano emissions in GEOS-Chem benchmark simulations Christoph Keller (GMAO)
Daniel Jacob (Harvard)
Emissions &
Benchmarking
Add option for driving GEOS-Chem with native GEOS meteorological files Liam Bindle (GCST) Structural
Updates that will NOT affect full-chemistry benchmark simulations
Updated Hg chemistry in KPP Viral Shah (Harvard)
Colin Thackray (Harvard)
Mike Long (GCST)
Bob Yantosca (GCST)
Chemistry
Bug fix: Use REAL*8 precision in for CH3O2 + OH reaction definition in fullchem.eqn Bob Yantosca (GCST) Chemistry
Updated Global Inventory of Methane Emissions from Oil/Gas/Coal (GFEI v2) Tia Scarpelli (U. Edinburgh) Emissions
Anthropogenic Methane Emission Inventory for Canada Tia Scarpelli (U. Edinburgh) Emissions
Use EDGARv6 global anthro emissions for CH4 simulation Melissa Sulprizio (GCST) Emissions
Updated Rn-222 emissions for TransportTracers simulations Bo Zhang (NIA) Emissions
Retire HEMCO extension for CH4 wetland emissions Melissa Sulprizio (GCST) Emissions
Updates to enable automated run directory creation Liam Bindle (GCST)
Melissa Sulprizio (GCST)
Run directory
Bug fix: Allow GEOS-Chem Classic History to archive irregular intervals (e.g. a month and a day) Bob Yantosca (GCST) Diagnostics
Updates for running GEOS-Chem within GEOS Christoph Keller (GMAO)
Lizzie Lundgren (GCST)
GEOS
Updates that will only affect GCHP
Add capability to use mass fluxes in advection Sebastian Eastham (MIT)
Liam Bindle (GCST)
Advection
Define a GCHP "Default" diagnostic collection that will archive a small number of commonly-requested diagnostic fields Liam Bindle (GCST) Structural
Add capability to read native meteorological data files Liam Bindle (GCST)
Bob Yantosca (GCST)
Structural

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 Needed for What was added? Directory
ZHANG_Rn222 TransportTracers simulations only Updated Rn222 emissions for TransportTracers simulations. See Bo Zhang et al (2021) HEMCO/ZHANG_Rn222/v2021-11
Updated Hg simulation restart file Hg simulations only Sample restart file for the updated Hg mechanism. See Viral Shah et al (2021) ExtData/GEOSCHEM_RESTARTS/v2021-12
Updated TOMAS simulation restart files TOMAS simulations only Added HSO3m and SO3mm species to TOMAS restart files ExtData/GEOSCHEM_RESTARTS/v2021-12

1-month benchmarks

Model setup for 1-month benchmarks

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

Git tag(s):
Compared to previous benchmark: 13.3.0
Software environment: gcc 10.2.0
OpenMPI 4.1.0
netcdf-fortran 4.5.3
CMake 3.17.3
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
  • NOTE: GCHP c48 restart file regridded from GEOS-Chem Classic 4° x 5°
Benchmark month: July 2019
Emissions setup: TBD
Chemistry mechanism: TBD
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):
    • Diagnostics
    • CH4 simulation
    • TransportTracers simulation
    • Run directory creation scripts

1-month fullchem: GEOS-Chem Classic 13.4.0-rc.0 vs 13.3.0

NOTES:

  • Enable PDF bookmarks in the file links to navigate between species. If you do not see bookmarks in your browser try using a different browser (not Safari) or installing an Adobe Acrobat plug-in.
  • See the species database for species definitions and details.
  • Species categories and lumped species are defined in YAML files within the GEOS-Chem post-processing software GCPy.

1-month fullchem: GEOS-Chem Classic 13.4.0-rc.0 vs 13.4.0-rc.0

Below are links to plots and tables comparing 1-month simulations for GEOS-Chem Classic 13.4.0-rc.0 (Dev) and GEOS-Chem Classic 13.4.0-rc.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, HMS, BCPI, BCPO, OCPI, OCPO, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, Simple_SOA, Complex_SOA, pFe

sfc 500hPa full column stratosphere column total AOD
Bromine

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

sfc 500hPa full column stratosphere column total
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 column total
Nitrogen

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

sfc 500hPa full column stratosphere column total
Primary Organics

EOH, MOH, ISOP, MTPA, MTPO, LIMO, ALK4, BENZ, CH4, C2H2, C2H4, C2H6, C3H8, PRPE, TOLU, XYLE

sfc 500hPa full column stratosphere column total
Secondary Organics

ACTA, ALD2, BALD, CH2O, HPALDs, MACR, IEPOX, ACET, HAC, MEK, MVK, ISOPN, GLYC, GLYX, HCOOH, MAP, PHEN, RCHO, ETHP, MP

sfc 500hPa full column stratosphere column total
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 column total
Sulfur

SOx, DMS, HMS, OCS, SO2, SO4

sfc 500hPa full column stratosphere column total
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