Benchmark/GEOS-Chem 12.7.0: Difference between revisions

From Geos-chem
Jump to navigation Jump to search
Line 308: Line 308:
*Compiled with ifort 17.0.4
*Compiled with ifort 17.0.4
*Ran on 24 CPUs of holyjacob01.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz)
*Ran on 24 CPUs of holyjacob01.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz)
*Wall time:  
*Wall time: 08:40:40
*[[Scalability|CPU time / wall time]]:  
*[[Scalability|CPU time / wall time]]: 21.1277
*% of ideal performance: %
*% of ideal performance: 88.03%
*Memory:  GB
*Memory:  12.1784 GB


|-valign="top"
|-valign="top"
Line 331: Line 331:
|-valign="top"
|-valign="top"
|Global mean OH from log file (% change):
|Global mean OH from log file (% change):
|11.7991194063953 x 10<sup>5</sup> molec/cm<sup>3</sup> (0.3268%)
|11.7991194063953 x 10<sup>5</sup> molec/cm<sup>3</sup> (+0.33%)


|-valign="top"
|-valign="top"
Line 348: Line 348:
|Comments on observed differences:
|Comments on observed differences:
|'''''Below we summarize the notable changes caused by specific updates.'''''
|'''''Below we summarize the notable changes caused by specific updates.'''''
'''[https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2018JD029046 Small alkyl nitrate chemistry]'''
:This update introduced four new advected species: MENO3, ETNO3, IPRNO3, and NPRNO3. These species have been added to the [http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.7.0/GCC/Plots/Nitrogen/ Nitrogen] benchmark category. The global mean OH concentrations increase of +0.17% as a result of this chemistry update.
'''[https://www.atmos-chem-phys.net/19/9097/2019/acp-19-9097-2019.html Methanol as part of standard chemical mechanism]'''
:With this update, methanol is now a chemically active species as well as a transported species. The overall impact of this update is small, contributing to a global mean OH change of +0.0083%.
'''[[Leaf_area_indices_in_GEOS-Chem#Yuan_processed_MODIS_LAI|Update to Yuan processed MODIS LAI product (covering years 2005-2016)]]
:This update contributed to a global mean OH change of +0.21% and primarily impacts the biogenic emissions. The Yuan-processed MODIS LAI product is used as input in the MEGAN extension (off by default) and in this version we have switched to the [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/OFFLINE_BIOVOC/v2019-10/README updated offline biogenic VOC files] generated with that MODIS LAI product. The impact on biogenic emissions is summarized below:
  ###############################################################################
  ### Emissions totals                                                  ###
  ### Ref = GC_12.7.0_Ref; Dev = GC_12.7.0_YuanXLAI                        ###
  ###############################################################################
                                          Ref                Dev      Dev - Ref
  ACET Biogenic        :          2.982478            2.734815      -0.247663 Tg C
  ALD2 Biogenic        :          1.037183            0.971226      -0.065957 Tg C
  EOH Biogenic          :          0.991817            0.928745      -0.063072 Tg C
  ISOP Biogenic        :          33.723910          33.565337      -0.158573 Tg C
  LIMO Biogenic        :          0.976173            0.930596      -0.045576 Tg
  MTPA Biogenic        :          8.644930            8.089232      -0.555698 Tg
  MTPO Biogenic        :          4.000710            3.756286      -0.244424 Tg
  PRPE Biogenic        :          2.030293            1.855930      -0.174363 Tg C
  SOAP Biogenic        :          1.467334            1.405632      -0.061702 Tg
  SOAS Biogenic        :          1.467334            1.405632      -0.061702 Tg
'''[https://github.com/geoschem/geos-chem/pull/78 Latitudinally and monthly resolved fixed surface concentrations for long-lived organohalogen species (1750-2014) and methane (prior to 1979)]'''
:This update changes surface concentrations of CH3Br, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, Halons, HCFCs, and as a result it also impacts concentrations of several other halogen species. Global mean OH changes by -0.12%.
'''[https://github.com/geoschem/geos-chem/issues/123 Fix incorrect uptake coefficient for N2O5 in heterogeneous chemistry]'''
:This fix causes small changes in N2O5 and in some halogen species. The impact on global mean OH is -0.015%.
'''[https://github.com/geoschem/geos-chem/issues/121 Fix offline dust scale factors]'''
:This update corrects the scale factor used for offline emissions of DST1 so that the species uses the same factor used for DST2, DST3, and DST4. The impact on emissions is summarized below:
  ###############################################################################
  ### Emissions totals for species DST1                                      ###
  ### Ref = GC_12.7.0_YuanXLAI; Dev = GC_12.7.0_DustSF                        ###
  ###############################################################################
                                          Ref                Dev      Dev - Ref
  DST1 Natural          :          11.225230            9.550223      -1.675007 Tg




Revision as of 06:06, 22 January 2020


This page includes information about all benchmark simulations for GEOS-Chem 12.7.0.

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

NH4, NIT, SO4, DST1, DST2, DST3, DST4, BC, OC, AERI, BrSALA, BrSALC, ISALA, ISALC, NITs, SALA, SALC, SO4s, SOA_Simple, SOA_Complex

sfc 500hPa full column stratosphere sfc AOD
Bromine

Bry, BrOx, Br, Br2, BrCl, BrNO2, BrNO3, BrO, CH4Br, CH2Br2, CH2Br2, CH3Br3, HOBr, HBr

sfc 500hPa full column stratosphere sfc
Chlorine

Cly, ClOx, Cl, ClO, Cl2, Cl2O2, ClOO, ClNO2, ClNO3, CCl4, CFCs, CH3Cl, CH2Cl2, CH4CCl3, HOCl, HCl, Halons, HCFCs, OClO

sfc 500hPa full column stratosphere --
Iodine

Iy, IxOy, I, I2, IBr, ICl, IO, INO2, IONO2, CH3I, CH2I2, CH2ICl, CH2IBr, HI, HOI, OIO

sfc 500hPa full column stratosphere sfc
Nitrogen

NOy, NOx, HNO2, HNO3, HNO4, IMPN, NIT, NO, NO2, NO3, N2O5, MPN, PAN, PPN, N2O, NHx, NH3, NH4

sfc 500hPa full column stratosphere sfc
Primary Organics

ALK4, BENZ, CH4, C2H6, C2H4, C3H8, PRPE, TOLU, XYLE, ISOP, MTPA, MTPO, LIMO, GLYX, HCOOH, MAP, MBO, MOH, RCHO

sfc 500hPa full column stratosphere sfc
Secondary Organics

ACET, MEK, MVK, ALD2, CH2O, HPALD, MP, ISOPN, IEPOX, ACTA, EOH, MOH

sfc 500hPa full column stratosphere sfc
Secondary Organic Aerosols

SOAP, SOAS, TSOA0, TSOA1, TSOA2, TSOA3, ISOA1, ISOA2, ISOA3, ASOA1, ASOA2, ASOA3, ASOAN, TSOG0, TSOG1, TSOG2, TSOG3, ISOG1, ISOG2, ISOG3, ASOG1, ASOG2, ASOG3, INDIOL, ISN1OA, LVOCOA, SOAIE, SOAGX, SOAME, SOAMG

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

OH metrics OH concentration, MCF lifetime, CH4 lifetime

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 json files.

Benchmark assessment form

Description
New features added into GEOS-Chem
Feature Submitted by
Updates that will affect full-chemistry simulations
Small alkyl nitrate chemistry Jenny Fisher (Wollongong)
Methanol as part of standard chemical mechanism Xin Chen (UMN)
Dylan Millet (UMN)
Katie Travis (NASA)
Update to Yuan processed MODIS LAI product (covering years 2005-2016) GCST
Latitudinally and monthly resolved fixed surface concentrations for long-lived organohalogen species (1750-2014) and methane (prior to 1979) Tomás Sherwen (York)
Lee Murray (Rochester)
Bug fix: Prevent differences in chemistry caused by toggling the ND65 bpch diagnostics off or on Bob Yantosca (GCST)
Fix incorrect uptake coefficient for N2O5 in heterogeneous chemistry Hyeonmin Kim (Seoul Nat'l U.)
Chris Holmes (FSU)
Fix offline dust scale factors Jun Meng (GCST)
Melissa Sulprizio (GCST)
Features NOT affecting the full-chemistry simulation:
Add GEOS-Chem "dry-run" option to obtain a list of required input files Haipeng Lin (Harvard)
Jiawei Zhuang (Harvard)
Bob Yantosca (GCST)
HEMCO 2.2.0: Updates and fixes to improve file I/O Melissa Sulprizio (GCST)
Implement Gan Luo et al wetdep (GMD-12-3439-2019) as an option Gan Luo (SUNY-Albany)
Fangqun Yu (SUNY-Albany)
Bob Yantosca (GCST)
CH4 soil absorption from MeMo model Melissa Sulprizio (Harvard)
Removal of most binary punch (aka "bpch") diagnostics GCST
Add netCDF diagnostic for UV fluxes from FAST-JX Jonathan Moch (Harvard)
Bob Yantosca (GCST)
KPP equation reactivity rate and OH reactivity diagnostics Christoph Keller (GMAO)
Bug fix for HEMCO standalone using high-resolution input grids Chris Holmes (FSU)
Incorrect units returned from GET_OH in sulfate_mod.F Rong Tian (NUIST)
Features only affecting GCHP:
Preserve mass conservation when advection is off by adding delta pressure to internal state for mixing ratio scaling during initialization Lizzie Lundgren (GCST)
Use same CEDS anthropogenic emissions inventory as GC Classic, including 1750-1949 and additional VOC species Lizzie Lundgren (GCST)
Assorted GCHP structural changes to facilitate GEOS-Chem in GEOS
  • Move high-level GCHP files to GEOS-Chem repository
  • Move GCHP run directory creation to GEOS-Chem repository
 Lizzie Lundgren (GCST)
Use same precision in non-species Internal state variables and the equivalent GEOS-Chem states (REAL8) Lizzie Lundgren (GCST)
Update ESMF to v8.0.0 public release Lizzie Lundgren (GCST)


Version, resolution, met fields used: GEOS-FP (72L), 4x5, July 2016
1-month benchmark finished on: Mon Jan 6 06:18:07 EST 2020
Performance statistics:
  • Compiled with ifort 17.0.4
  • Ran on 24 CPUs of holyjacob01.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 "Haswell" @ 2.50 GHz)
  • Wall time: 08:40:40
  • CPU time / wall time: 21.1277
  • % of ideal performance: 88.03%
  • Memory: 12.1784 GB
Compared to previous benchmark: 12.6.0
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):
Unit test results may be viewed at: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/GC_12/12.7.0/GCC/Plots/GC_12.7.0_Jan02.results.html
Metrics
Global mean OH from log file (% change): 11.7991194063953 x 105 molec/cm3 (+0.33%)
Methyl chloroform lifetime (% change): 5.3039 years (-0.67%)
Methane lifetime (% change): 8.9168 years (-0.70%)
Overview
Comments on observed differences: Below we summarize the notable changes caused by specific updates.

Small alkyl nitrate chemistry

This update introduced four new advected species: MENO3, ETNO3, IPRNO3, and NPRNO3. These species have been added to the Nitrogen benchmark category. The global mean OH concentrations increase of +0.17% as a result of this chemistry update.


Methanol as part of standard chemical mechanism

With this update, methanol is now a chemically active species as well as a transported species. The overall impact of this update is small, contributing to a global mean OH change of +0.0083%.


Update to Yuan processed MODIS LAI product (covering years 2005-2016)

This update contributed to a global mean OH change of +0.21% and primarily impacts the biogenic emissions. The Yuan-processed MODIS LAI product is used as input in the MEGAN extension (off by default) and in this version we have switched to the updated offline biogenic VOC files generated with that MODIS LAI product. The impact on biogenic emissions is summarized below:
  ###############################################################################
  ### Emissions totals                                                  ###
  ### Ref = GC_12.7.0_Ref; Dev = GC_12.7.0_YuanXLAI                        ###
  ###############################################################################
                                         Ref                 Dev      Dev - Ref
  ACET Biogenic         :           2.982478            2.734815      -0.247663 Tg C
  ALD2 Biogenic         :           1.037183            0.971226      -0.065957 Tg C
  EOH Biogenic          :           0.991817            0.928745      -0.063072 Tg C
  ISOP Biogenic         :          33.723910           33.565337      -0.158573 Tg C
  LIMO Biogenic         :           0.976173            0.930596      -0.045576 Tg
  MTPA Biogenic         :           8.644930            8.089232      -0.555698 Tg
  MTPO Biogenic         :           4.000710            3.756286      -0.244424 Tg
  PRPE Biogenic         :           2.030293            1.855930      -0.174363 Tg C
  SOAP Biogenic         :           1.467334            1.405632      -0.061702 Tg
  SOAS Biogenic         :           1.467334            1.405632      -0.061702 Tg


Latitudinally and monthly resolved fixed surface concentrations for long-lived organohalogen species (1750-2014) and methane (prior to 1979)

This update changes surface concentrations of CH3Br, CCl4, CFCs, CH3Cl, CH2Cl2, CH3CCl3, Halons, HCFCs, and as a result it also impacts concentrations of several other halogen species. Global mean OH changes by -0.12%.


Fix incorrect uptake coefficient for N2O5 in heterogeneous chemistry

This fix causes small changes in N2O5 and in some halogen species. The impact on global mean OH is -0.015%.


Fix offline dust scale factors

This update corrects the scale factor used for offline emissions of DST1 so that the species uses the same factor used for DST2, DST3, and DST4. The impact on emissions is summarized below:
  ###############################################################################
  ### Emissions totals for species DST1                                       ###
  ### Ref = GC_12.7.0_YuanXLAI; Dev = GC_12.7.0_DustSF                        ###
  ###############################################################################
                                         Ref                 Dev      Dev - Ref
  DST1 Natural          :          11.225230            9.550223      -1.675007 Tg


Details
List all SURFACE species, J-Values, and COLUMN AOD values that changed by 10% or more:
  • Oxidants: OH NOx
  • Aerosols: NIT BrSALA BrSALC Complex_SOA Simple_SOA
  • Nitrogen: NOy NOx HNO2 HNO3 HNO4 IPMN NIT NO NO2 NO3 N2O5 MPN PAN PPN NH3
  • ROy: H2O2 OH RO2
  • Sulfur: DMS
  • Iodine: I I2 ICl INO2 IONO2 HI OIO
  • Bromine: Bry BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 CCl4 CH2Cl2 CH3CCl3 HOCl HCl HCFCs OClO
  • Primary_Organics: PRPE XYLE ISOP MTPA MTPO LIMO EOH MOH
  • Secondary_Organics: ACET MEK MVK HPALD MACR ISOPN IEPOX GLYX HCOOH RCHO
  • Secondary_Organic_Aerosols: SOAP TSOA0 TSOA1 TSOA2 TSOA3 TSOG0 TSOG1 TSOG2 TSOG3 ASOG1 ASOG2 ASOG3 INDIOL ISN1OA LVOCOA SOAIE SOAGX SOAME SOAMG
  • J-Values:
  • Column AOD: SOA_from_Aqueous_ISOP Total
List all 500 hPa species and J-Values that changed by 10% or more :
  • Oxidants: NOx
  • Aerosols: NIT BrSALA BrSALC
  • Nitrogen: NOy NOx HNO2 HNO4 IPMN NIT NO NO2 NO3 N2O5 MPN PPN NH3
  • ROy: RO2
  • Sulfur: DMS SO2
  • Iodine: ICl INO2 IONO2 CH2I2 OIO
  • Bromine: BrOx Br Br2 BrCl BrNO2 BrNO3 BrO HOBr HBr
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 CCl4 CH2Cl2 CH3CCl3 HOCl HCl HCFCs OClO
  • Primary_Organics: PRPE TOLU XYLE ISOP MTPA MTPO LIMO EOH MOH
  • Secondary_Organics: ACET MEK MVK HPALD MACR ISOPN IEPOX GLYX HCOOH RCHO
  • Secondary_Organic_Aerosols: LVOCOA SOAIE SOAME
List all ZONAL MEAN species and J-Values that changed by 10% or more:
  • Aerosols: NIT BrSALA
  • Nitrogen: NOy NOx HNO4 IPMN NIT NO NO3 N2O5 MPN PPN NH3
  • ROy: None
  • Sulfur: DMS
  • Iodine: I ICl INO2 CH2I2 OIO
  • Bromine: BrOx Br BrCl BrO HBr
  • Chlorine: Cly ClOx Cl ClO Cl2 Cl2O2 ClOO ClNO2 ClNO3 CCl4 CH2Cl2 HOCl HCl HCFCs OClO
  • Primary_Organics: ALK4 C3H8 PRPE TOLU XYLE ISOP MTPA MTPO LIMO MOH
  • Secondary_Organics: ACET MEK MVK ALD2 HPALD MACR ISOPN IEPOX GLYX HCOOH RCHO
  • Secondary_Organic_Aerosols: None
  • J-Values: None


List all EMISSIONS that changed by 10% or more:
  • Biogenic: ACET ALD2 EOH ISOP LIMO MTPA MTPO PRPE SESQ SOAP SOAS
  • Natural: DST1
  • Ship: O3
  • Total: ACET ALD2 EOH ISOP MTPA PRPE SOAP
Approval
Requires further investigation:
Approved by:
Date of approval:

GCHP 1-month benchmark

The following sections contain validation plots for GCHP 12.7.0.

Comparison of GCHP versions

This table contains plots comparing GCHP 12.6.0 (Ref) and GCHP 12.7.0 (Dev) for a 1-month simulation.

Category Plots Additional Information
Level Map Zonal Mean Emissions
Oxidants sfc 500hPa full column stratosphere full column
Aerosols sfc 500hPa full column stratosphere full column Column AOD
Bromine sfc 500hPa full column stratosphere full column
Chlorine sfc 500hPa full column stratosphere --
Iodine sfc 500hPa full column stratosphere full column
Nitrogen sfc 500hPa full column stratosphere full column
Primary Organics sfc 500hPa full column stratosphere full column
Secondary Organics sfc 500hPa full column stratosphere full column
Secondary Organic Aerosols sfc 500hPa full column stratosphere full column
Sulfur sfc 500hPa full column stratosphere full column
ROy sfc 500hPa full column stratosphere --
J-values sfc 500hPa full column stratosphere --
Emissions by HEMCO category

Aircraft, Anthro, Bioburn, Biogenic,
Lightning, Monoterp, Natural, Ocean, Seabirds, DecayingPlants,
Ship, Soil, Total, VolcDegas, VolcErupt,

Emission totals

Comparison of GCHP and GEOS-Chem Classic

This table contains plots comparing GEOS-Chem Classic 12.7.0 (Ref) against GCHP 12.7.0 (Dev) for a 1-month simulation.

Category Plots Additional Information
Level Map Zonal Mean Emissions
Oxidants sfc 500hPa full column stratosphere full column
Aerosols sfc 500hPa full column stratosphere full column Column AOD
Bromine sfc 500hPa full column stratosphere full column
Chlorine sfc 500hPa full column stratosphere --
Iodine sfc 500hPa full column stratosphere full column
Nitrogen sfc 500hPa full column stratosphere full column
Primary Organics sfc 500hPa full column stratosphere full column
Secondary Organics sfc 500hPa full column stratosphere full column
Secondary Organic Aerosols sfc 500hPa full column stratosphere full column
Sulfur sfc 500hPa full column stratosphere full column
ROy sfc 500hPa full column stratosphere --
J-values sfc 500hPa full column stratosphere --
Emissions by HEMCO category

Aircraft, Anthro, Bioburn, Biogenic,
Lightning, Monoterp, Natural, Ocean, Seabirds, DecayingPlants,
Ship, Soil, Total, VolcDegas, VolcErupt,

Emission totals

GCHP and GEOS-Chem Classic difference of differences

This table contains plots comparing the difference [GCHP 12.7.0 - GCHP 12.6.0] against the difference [GC Classic 12.7.0 - GC Classic 12.6.0], 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=Benchmark/GEOS-Chem_12.7.0&oldid=46494"