Difference between revisions of "GEOS-Chem v9-02 benchmark history"

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== 1-year benchmarks ==
 
== 1-year benchmarks ==
  
=== v9-02f ===
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=== v9-02f-Run0 ===
 
+
==== Run0 ====
+
  
 
Three GEOS-Chem model versions were compared to each other:
 
Three GEOS-Chem model versions were compared to each other:
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--[[User:Melissa Payer|Melissa Payer]] 18:06, 18 March 2013 (EDT)
 
--[[User:Melissa Payer|Melissa Payer]] 18:06, 18 March 2013 (EDT)
  
=== v9-02b ===
+
=== v9-02b-Run0 ===
 
+
==== Run0 ====
+
  
 
''NOTE: A 1-year benchmark simulation was performed for v9-02b to serve as a reference when benchmarking the chemistry updates implemented in v9-02f.''
 
''NOTE: A 1-year benchmark simulation was performed for v9-02b to serve as a reference when benchmarking the chemistry updates implemented in v9-02f.''

Revision as of 20:28, 19 March 2013

On this page we have posted complete information about all benchmark simulations (both 1-month and 1-year) for GEOS-Chem v9-02.

1-year benchmarks

v9-02f-Run0

Three GEOS-Chem model versions were compared to each other:

Color Quantity Plotted Met Type Anthro emissions Soil NOx emissions Tropospheric chemistry mechanism Linoz Annual Mean OH
[105 molec/cm3]
Red v9-01-03r-Run1 GEOS-5, 4x5 Same as v9-01-03r-Run0 Original soil NOx algorithm based on Yienger & Levy [1995] Same as v8-02-01-Run0
+ Bromine chemistry mechanism
ON 11.356
Green v9-02b-Run0 GEOS-5, 4x5 " " New soil NOx emission module " " ON 11.424
Blue v9-02f-Run0 GEOS-5, 4x5 " " " " + Inorganic chemistry updates
+ Methyl peroxy nitrate (MPN) chemistry
ON 11.503
Black Observations            


The output plots for Run0 (both PostScript and PDF format) may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v9-02/v9-02f/Run0/output/ps
mget *
cd gcgrid/geos-chem/1yr_benchmarks/v9-02/v9-02f/Run0/output/pdf
mget *

You may also view the PDF files online by pointing your browser to

http://ftp.as.harvard.edu/pub/index/geos-chem/1yr_benchmarks/v9-02/v9-02f/Run0/output/pdf/

--Melissa Payer 18:06, 18 March 2013 (EDT)

v9-02b-Run0

NOTE: A 1-year benchmark simulation was performed for v9-02b to serve as a reference when benchmarking the chemistry updates implemented in v9-02f.

Three GEOS-Chem model versions were compared to each other:

Color Quantity Plotted Met Type Anthro emissions Soil NOx emissions Tropospheric chemistry mechanism Linoz Annual Mean OH
[105 molec/cm3]
Red v9-01-03r-Run0 GEOS-5, 4x5 Same as v9-01-02-Run1
+ C2H6 emissions from offline simulation
+ PARANOX ship plume emissions
Original soil NOx algorithm based on Yienger & Levy [1995] Same as v8-02-01-Run0 ON 11.858
Green v9-01-03r-Run1 GEOS-5, 4x5 " " " " + Bromine chemistry mechanism ON 11.356
Blue v9-02b-Run0 GEOS-5, 4x5 " " New soil NOx emission module " " ON 11.424
Black Observations            


The output plots for Run0 (both PostScript and PDF format) may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v9-02/v9-02b/Run0/output/ps
mget *
cd gcgrid/geos-chem/1yr_benchmarks/v9-02/v9-02b/Run0/output/pdf
mget *

You may also view the PDF files online by pointing your browser to

http://ftp.as.harvard.edu/pub/index/geos-chem/1yr_benchmarks/v9-02/v9-02b/Run0/output/pdf/

--Melissa Payer 18:06, 18 March 2013 (EDT)

1-month benchmarks

v9-02g

Here is the assessment form for 1-month benchmark simulation v9-02g.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Isoprene scheme: Fabien Paulot (Harvard), Eloise Marais (Harvard), Jingqiu Mao (NOAA/GFDL), Mat Evans (York)
  • RO2+HO2 rate: Fabien Paulot (Harvard)
  • GEOS-5.7.2 fix:: GEOS-Chem Support Team
  • Streets fix: Jenny Fischer (U. Wollongong)
Version, resolution, met fields used: v9-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: TBD
Performance statistics:
  • Ran on TBD
  • Wall time: TBD
  • Scalability: TBD
Compared to previous benchmark: v9-02f
This update will impact:
(select all that apply with boldface)
Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-02g/
Metrics
Global mean OH (from log file): TBD x 105 molec/cm3
Methyl chloroform lifetime: TBD years
Did either of these change by more than 5%? TBD
At the SURFACE, list all species that changed by 10% or more:
Comments on SURFACE differences:
At 500 hPa, list all species that changed by 10% or more:
Comments on 500 hPa differences:
In the ZONAL MEAN differences, list all species that changed by 10% or more:
Comments on ZONAL MEAN differences:
In the EMISSION RATIO maps, list all species that changed by 10% or more:
Comments on EMISSION RATIO differences:
Additional or summary comments:
Approval
Requires further investigation: TBD
Approved: TBD
Date of approval: TBD

--Melissa Payer 10:56, 12 February 2013 (EST)

v9-02f

Here is the assessment form for 1-month benchmark simulation v9-02f.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Inorganic chemistry updates: Mat Evans (York)
  • MPN chemistry: Ellie Browne (UC Berkeley)
  • Nested Hg bug fixes: Yanxu Zhang (U. Washington)
Version, resolution, met fields used: v9-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Wed Jan 30 16:36:48 EST 2013
Performance statistics:
  • Ran on 8 CPUs of bench@titan-10.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 2:32
  • Scalability: 6.3256
Compared to previous benchmark: v9-02e
This update will impact:
(select all that apply with boldface)
Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-02f/
Metrics
Global mean OH (from log file): 12.9589397348900 x 105 molec/cm3
Methyl chloroform lifetime: 4.8396 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: ISOP, MVK, MACR, PMN

N2O5

HNO4

DMS, MSA

Br, BrO, Other bromine compounds

Comments on SURFACE differences: Isoprene related tracers: Concentrations are changing over remote oceanic regions reflecting changes in the initial oxidation steps of these compounds.

N2O5 changes are again is restricted to remote ocean regions. Changes to the NO3+DMS rate constant have made this faster which will tend to reduce NO3 and N2O5 concentrations in regions where DMS is the dominant VOC

DMS, MSA Concentrations are changing due to changes in the DMS+OH and DMS+NO3 rate constants. At the surface changes are small and restricted to continental regions.

Br compounds. These are restricted to the polar regions where concentrations are low and reflects the combination of other changes of longer lived species. The same is the case for HNO3.

At 500 hPa, list all species that changed by 10% or more: NOx

ISOP, MVK, MACR, PMN

N2O5

HNO4

PRPE

DMS, MSA

NIT, NH4

Br species

Comments on 500 hPa differences: The largest changes here are to the DMS and MSA. This reflects the changes in the DMS+OH and DMS+NO3 oxidation routes which essentially both changes the location of DMS oxidation and the branching ratio of the DMS Oxidation

isoprene chemistry changes again reflect changes in the primary oxidation of isoprene and the subsquent branching ration

NIT, NH4 Isoropia seems unstable at cold temperatures and small changes leads to large relative changes in these compounds even though they are at low concentrations.

N2O5, HNO4, Br species see above.

In the ZONAL MEAN differences, list all species that changed by 10% or more: NOx

ISOP, MVK, MACR, PMN

PRPE

CH2O

N2O5

HNO4

MP

DMS, MSA, SO2

Br compounds

Comments on ZONAL MEAN differences: NOx, HNO3, H2O2, CH2O, MP Reflect that changes seen in Browne et al., 2011

DMS, MSA, SO2 reflect changes in the initial DMS oxidation of DMS+OH and DMS+NO3

ISOP, MACR, MVK, PMN changes reflect changes in the ISOP oxidation ISOP+OH, O3, NO3

The N2O5 decrease at ~200 hPa in the zonal mean is also consistent with Browne et al., 2011

In the EMISSION RATIO maps, list all species that changed by 10% or more: No
Comments on EMISSION RATIO differences: N/A
Additional or summary comments: This all seems fine. In general changes are small in absolute concentrations but can be relatively large fractionally.
Approval
Requires further investigation: No
Approved: MJE as long as others are happy.
Date of approval: 07 Feb 2013

--Melissa Payer 09:31, 1 February 2013 (EST)

v9-02e

Here is the assessment form for 1-month benchmark simulation v9-02e.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
Version, resolution, met fields used: v9-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Fri Jan 4 17:01:07 EST 2013
Performance statistics:
  • Ran on 8 CPUs of bench@titan-10.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 2:32
  • Scalability: 6.3584
Compared to previous benchmark: v9-02d
This update will impact:
(select all that apply with boldface)
Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-02/v9-02e/
Metrics
Global mean OH (from log file): 12.9399839759816 x 105 molec/cm3
Methyl chloroform lifetime: 4.8585 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: ISOP, NIT
Comments on SURFACE differences: Differences are attributed to the numerical noise issue in ISORROPIA II.
At 500 hPa, list all species that changed by 10% or more: ISOP, NH3, NIT
Comments on 500 hPa differences: Differences are attributed to the numerical noise issue in ISORROPIA II.
In the ZONAL MEAN differences, list all species that changed by 10% or more: ALK4, PMN, PRPE, C3H8, SO4s, NH3, NIT, NITs
Comments on ZONAL MEAN differences: Differences are seen in ALK4, PMN, PRPE, C3H8, SO4s, NH3, and NITs are in locations where concentrations are already very low. These differences can be attributed to numerical noise.

Differences in NH3 and NITs are attributed to the numerical noise issue in ISORROPIA II.

In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences: The bug fix for regridding of Streets anthropogenic emissions caused CO anthropogenic emissions to change by 0.004 Tg (~0.01%).
Additional or summary comments:
Approval
Requires further investigation: No
Approved: Yes
Date of approval: 07 Jan 2013

--Melissa Payer 16:01, 7 January 2013 (EST)

v9-02d

Here is the assessment form for 1-month benchmark simulation v9-02d.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
Version, resolution, met fields used: v9-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Wed Dec 19 09:33:39 EST 2012
Performance statistics:
  • Ran on 8 CPUs of bench@titan-08.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 2:32
  • Scalability: 6.3638
Compared to previous benchmark: v9-02c
This update will impact:
(select all that apply with boldface)
Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): We expected to see no changes from v9-02d. We have only made structural modifications but not scientific modifications.
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-02/v9-02d/
Metrics
Global mean OH (from log file): 12.9397354478399 x 105 molec/cm3
Methyl chloroform lifetime: 4.8586 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: NIT
Comments on SURFACE differences: Differences in NIT are attributed to the numerical noise issue in ISORROPIA II.
At 500 hPa, list all species that changed by 10% or more: ISOP, NH3, NIT
Comments on 500 hPa differences: Differences are seen in ISOP in locations where concentrations are already very low (i.e. over oceans). These differences are attributed to the bromine bug fix.

Differences in NH3 and NIT are attributed to the numerical noise issue in ISORROPIA II.

In the ZONAL MEAN differences, list all species that changed by 10% or more: ALK4, ISOP, PRPE, C3H8, SO4s, NH3, NIT, NITs, Br2,
Comments on ZONAL MEAN differences: Differences are seen in ALK4, ISOP, PRPE, C3H8, SO4s, and Br2 are in locations where concentrations are already very low. These differences are attributed to the bromine bug fix.

Differences in NH3 and NIT are attributed to the numerical noise issue in ISORROPIA II.

In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences:
Additional or summary comments: When ISORROPIA is turned off, and when the Bug fix for Br2 emissions is also added to v9-02c, then we obtain identical results between v9-02c and v9-02d. This demonstrates that the structural modifications made for grid independence do not change GEOS-Chem's scientific results. Most of these modifications were made to carry data fields in derived-type objects rather than in module arrays, but the data fields themselves have not changed.
Approval
Requires further investigation: No
Approved: Yes
Date of approval: 19 Dec 2012

--Bob Y. 10:39, 19 December 2012 (EST)

v9-02c

Here is the assessment form for 1-month benchmark simulation v9-02c.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • NEI05 Hg emissions: Yanxu Zhang (U. Washington); Lyatt Jaeglé (U. Washington)
  • Nested-grid Hg: Yanxu Zhang (U. Washington); Lyatt Jaeglé (U. Washington)
  • Streets future Hg emissions: Bess Corbitt (Harvard)
  • Updated Hg(0) oxidation kinetics: Bess Corbitt(Harvard); Justin Parrella (Harvard)
  • GEOS-Chem Br/Br fields in Hg simulation: Bess Corbitt(Harvard); Justin Parrella (Harvard)
  • POPs simulation: Carey Friedman (MIT); Noelle Selin (MIT)
  • CAC bug fix: Aaron van Donkelaar (Dalhousie)
Version, resolution, met fields used: v9-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Wed Nov 28 22:37:00 EST 2012
Performance statistics:
  • Ran on 8 CPUs of 8 CPUs of bench@titan-08.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 2:20
  • Scalability: 6.5218
Compared to previous benchmark: v9-02b
This update will impact:
(select all that apply with boldface)
Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): We expect to see no changes from v9-02b
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-02/v9-02c/
Metrics
Global mean OH (from log file): 12.9398281506753 x 105 molec/cm3
Methyl chloroform lifetime: 4.8585 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: None
Comments on SURFACE differences:
At 500 hPa, list all species that changed by 10% or more: None
Comments on 500 hPa differences:
In the ZONAL MEAN differences, list all species that changed by 10% or more: None
Comments on ZONAL MEAN differences:
In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences:
Additional or summary comments:
Approval
Requires further investigation: No
Approved: Yes
Date of approval: 29 Nov 2012

--Melissa Payer 16:58, 27 November 2012 (EST)

v9-02b

Here is the assessment form for 1-month benchmark simulation v9-02b.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Soil NOx: Rynda Hudman Kay (EPA); Neil Moore (formerly of Dalhousie); Bram Maasakkers (Eindhoven)
  • Bug fix in hdf_mod.F: Sajeev Philip (Dalhousie)
  • Tagged CO simulation fixes: Jenny Fisher (Wollongong); GEOS-Chem Support Team
  • Bug fix in nei_anthro_mod.F: Sajeev Philip (Dalhousie)
Version, resolution, met fields used: v9-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Wed Oct 24 16:10:25 EDT 2012
Performance statistics:
  • Ran on 8 CPUs of bench@titan-08.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 2:19
  • Scalability: 6.5256
Compared to previous benchmark: v9-02a
This update will impact:
(select all that apply with boldface)
Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): Soil NOx emissions
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-02/v9-02b/
Metrics
Global mean OH (from log file): 12.9398281506753 x 105 molec/cm3
Methyl chloroform lifetime: 4.8585 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: NOx, Ox, PAN, ALK4, ISOP, HNO3, H2O2, MEk, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, C3H8, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, and OH
Comments on SURFACE differences: The changes are as expected. The new soil NOx parameterization significantly increases the NOx concentrations over North America, the southern part of South America, Central Asia and parts of Africa. Decreases occur over the northern part of South America, central Africa and Indonesia.

Other species are influenced by resulting changes in O3 (and consequently OH). However, some of the reported changes are mainly caused by noise since the absolute differences are very close to zero.

At 500 hPa, list all species that changed by 10% or more: NOx, PAN, ALK4, ISOP, HNO3, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, PRPE, N2O5, HNO4, MP, DMS, SO2, MSA, NH3, NIT, NITs, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, and OH
Comments on 500 hPa differences: See 'Comments on SURFACE differences'
In the ZONAL MEAN differences, list all species that changed by 10% or more: NOx, PAN, ISOP, HNO3, MEK, RCHO, MVK, MACR, PMN, PPN, PRPE, N2O5, HNO4, DMS, SO4s, NH3, NIT, NITs, Br, BrO, BrNO2, BrNO3 and OH.
Comments on ZONAL MEAN differences: See 'Comments on SURFACE differences'
In the EMISSION RATIO maps, list all species that changed by 10% or more: NOx fertilizer emissions and NOx soil emissions
Comments on EMISSION RATIO differences: The NOx soil emissions diagnostic now includes the NOx fertilizer emissions since the emissions related to fertilizer are now calculated using the same procedure as the “regular” soil emissions based on the biome emission coefficients. The soil NOx emission total increases with 0.310 Tg N to 1.028 Tg N for July.

The fertilizer emissions diagnostics gives the soil NOx emissions related to fertilizer use and deposited nitrogen.

Additional or summary comments: The occurring changes are as expected. The benchmark is performed using a new soil NOx restart file which saves per grid cell:
  • The Dry Period (hours)
  • Pulsing factor (unitless)
  • GWET from the previous timestep (unitless)
  • N reservoir from dry/wet deposition (ngN/m2)

The overall changes are in NOx emissions are consistent with those in Hudman et al. (2012) with the additional canopy reduction that Bram added. The changes in O3 and OH follow the changes in NOx emissions.

Approval
Requires further investigation: No
Approved: Randall Martin, Bram Maasakkers
Date of approval: 29 Oct 2012

--Melissa Payer 13:42, 24 October 2012 (EDT)

v9-02a

Here is the assessment form for 1-month benchmark simulation v9-02a.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Sajeev Philip (Dalhousie)
Version, resolution, met fields used: v9-02, GEOS-5 (47L), 4x5
1-month benchmark finished on: Fri Oct 12 17:58:19 EDT 2012
Performance statistics:
  • Ran on 8 CPUs of bench@titan-10.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 2:19
  • Scalability: 6.5621
Compared to previous benchmark: v9-01-03-Fix_for_IFORT12
This update will impact:
(select all that apply with boldface)
Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):
Plots may be viewed at: ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-02/v9-02a/
Metrics
Global mean OH (from log file): 12.8727104044567 x 105 molec/cm3
Methyl chloroform lifetime: 4.8983 years
Did either of these change by more than 5%? No
At the SURFACE, list all species that changed by 10% or more: All species
Comments on SURFACE differences: Expected. Change in boundary layer mixing
At 500 hPa, list all species that changed by 10% or more: DST4, NITS, NH3, DMS, PRPE, MACR, ISOP (over Ocean) and NIT (over Land)
Comments on 500 hPa differences: Change in boundary layer mixing
In the ZONAL MEAN differences, list all species that changed by 10% or more: All species
Comments on ZONAL MEAN differences: Change in boundary layer mixing
In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences: None
Additional or summary comments: None
Approval
Requires further investigation: No
Approved: Yes
Date of approval: Approved 16 Oct 2012

--Melissa Payer 12:00, 15 October 2012 (EDT)