GEOS-Chem v11-01 benchmark history

From Geos-chem
Jump to: navigation, search

On this page we have posted complete information about all benchmark simulations (both 1-month and 1-year) for GEOS-Chem v11-01.

1-year full-chemistry benchmarks

Comparison with GEOS-Chem v10-01

GEOS-Chem v11-01 was compared to GEOS-Chem v10-01 as summarized below:

Color Quantity Plotted Met Type Year Major updates Annual Mean OH
[105 molec/cm3]
Red v10-01 GEOS-FP,
72L, 4x5
2013 11.092
Green v11-01 GEOS-FP,
72L, 4x5
2013 12.001
Black Observations        

The output plots for Run0 may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01-public-release/Run0/compare_to_v10-01
mget *

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

http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01-public-release/Run0/compare_to_v10-01/

--Melissa Sulprizio (talk) 20:51, 31 January 2017 (UTC)

v11-01-public-release-Run0

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

Color Quantity Plotted Met Type Year Updates affecting the benchmark simulation Annual Mean OH
[105 molec/cm3]
Red v11-01g-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01g:

12.069
Green v11-01k-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01h:

Updates introduced in v11-01i:

Updates introduced in v11-01j:

Updates introduced in v11-01k:

12.004
Blue v11-01-public-release-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01 public release:

12.001
Black Observations        

The output plots for Run0 may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01-public-release/Run0/output
mget *

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

http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01-public-release/Run0/output/

**New in v11-01** Tables comparing the global tropospheric aerosol burdens and the global tropospheric mean AODs for this version and past 1-year benchmarks can be viewed on our Global Burden History wiki page.

--Melissa Sulprizio (talk) 20:15, 31 January 2017 (UTC)

v11-01k-Run0

This 1-year benchmark simulation was approved by the GEOS-Chem Steering Committee on 19 Dec 2016.

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

Color Quantity Plotted Met Type Year Updates affecting the benchmark simulation Annual Mean OH
[105 molec/cm3]
Red v11-01f-geosfp-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01e:

Updates introduced in v11-01f:

12.044
Green v11-01g-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01g:

12.069
Blue v11-01k-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01h:

Updates introduced in v11-01i:

Updates introduced in v11-01j:

Updates introduced in v11-01k:

12.004
Black Observations        

The output plots for Run0 may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01k/Run0/output
mget *

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

http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01k/Run0/output/

**New in v11-01** Tables comparing the global tropospheric aerosol burdens and the global tropospheric mean AODs for this version and past 1-year benchmarks can be viewed on our Global Burden History wiki page.

--Melissa Sulprizio (talk) 22:52, 15 December 2016 (UTC)

v11-01g-Run0

This 1-year benchmark simulation was approved by the GEOS-Chem Steering Committee on 28 Sep 2016.

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

Color Quantity Plotted Met Type Year Updates affecting the benchmark simulation Annual Mean OH
[105 molec/cm3]
Red v11-01d-Run1 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01c:

Updates introduced in v11-01d:

12.011
Green v11-01f-geosfp-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01e:

Updates introduced in v11-01f:

12.044
Blue v11-01g-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01g:

12.069
Black Observations        

The output plots for Run0 may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01g/Run0/output
mget *

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

http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01g/Run0/output/

**New in v11-01** Tables comparing the global tropospheric aerosol burdens and the global tropospheric mean AODs for this version and past 1-year benchmarks can be viewed on our Global Burden History wiki page.

--Melissa Sulprizio (talk) 19:54, 14 September 2016 (UTC)

v11-01f-merra2-Run0

This 1-year benchmark simulation was approved by the developers and the GEOS-Chem Steering Committee on 16 Apr 2016.

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

Color Quantity Plotted Met Type Year Updates affecting the benchmark simulation Annual Mean OH
[105 molec/cm3]
Red v11-01d-Run1 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01c:

Updates introduced in v11-01d:

12.011
Green v11-01f-geosfp-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01e:

Updates introduced in v11-01f:

12.044
Blue v11-01f-merra2-Run0 MERRA-2,
72L, 4x5
2013

Updates introduced in v11-01f:

12.269
Black Observations        

The output plots for Run0 may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01f/MERRA2/Run0/output
mget *

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

http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01f/MERRA2/Run0/output/

**New in v11-01** Tables comparing the global tropospheric aerosol burdens and the global tropospheric mean AODs for this version and past 1-year benchmarks can be viewed on our Global Burden History wiki page.

--Melissa Sulprizio (talk) 21:25, 11 April 2016 (UTC)

v11-01f-geosfp-Run0

This 1-year benchmark simulation was approved by the developers and the GEOS-Chem Steering Committee on 16 Apr 2016.

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

Color Quantity Plotted Met Type Year Updates affecting the benchmark simulation Annual Mean OH
[105 molec/cm3]
Red v11-01b-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01a:

Updates introduced in v11-01b:

12.000
Green v11-01d-Run1 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01c:

Updates introduced in v11-01d:

12.011
Blue v11-01f-geosfp-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01e:

Updates introduced in v11-01f:

12.044
Black Observations        

The output plots for Run0 may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01f/GEOSFP/Run0/output
mget *

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

http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01f/GEOSFP/Run0/output/

**New in v11-01** Tables comparing the global tropospheric aerosol burdens and the global tropospheric mean AODs for this version and past 1-year benchmarks can be viewed on our Global Burden History wiki page.

--Melissa Sulprizio (talk) 21:25, 11 April 2016 (UTC)

v11-01d-Run1

This 1-year benchmark simulation was approved by the developers and the GEOS-Chem Steering Committee on 12 Dec 2015.

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

Color Quantity Plotted Met Type Year Updates affecting the benchmark simulation Annual Mean OH
[105 molec/cm3]
Red v10-01-public-release-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v10-01 public release:

11.723
Green v11-01b-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01a:

Updates introduced in v11-01b:

12.000
Blue v11-01d-Run1 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01c:

Updates introduced in v11-01d:

12.011
Black Observations        

The output plots for Run1 may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01d/Run1/output
mget *

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

http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01d/Run1/output/

**New in v11-01** Tables comparing the global tropospheric aerosol burdens and the global tropospheric mean AODs for this version and past 1-year benchmarks can be viewed on our Global Burden History wiki page.

--Melissa Sulprizio (talk) 19:49, 9 December 2015 (UTC)

v11-01d-Run0

NOTE: The original v11-01d benchmark included a quick fix for low Pb tropospheric lifetime against deposition in GEOS-FP and MERRA-2. Due to the high impact on aerosols, the GEOS-Chem Steering Committee rejected the quick fix. We have subsequently removed this fix from v11-01d and performed additional 1-year benchmark simulations with the updated model. The values below do not reflect the approved version of v11-01d. Please refer to the results for v11-01d-Run1.

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

Color Quantity Plotted Met Type Year Updates affecting the benchmark simulation Annual Mean OH
[105 molec/cm3]
Red v10-01-public-release-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v10-01 public release:

11.723
Green v11-01b-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01a:

Updates introduced in v11-01b:

12.000
Blue v11-01d-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01c:

Updates introduced in v11-01d:

12.567
Black Observations        

The output plots for Run0 may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01d/Run0/output
mget *

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

http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01d/Run0/output/

--Melissa Sulprizio (talk) 22:00, 30 October 2015 (UTC)

v11-01b-Run0

This 1-year benchmark simulation was approved by the developers and the GEOS-Chem Steering Committee on 19 Aug 2015.

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

Color Quantity Plotted Met Type Year Updates affecting the benchmark simulation Annual Mean OH
[105 molec/cm3]
Red v10-01i-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v10-01i:

11.125
Green v10-01-public-release-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v10-01 public release:

11.723
Blue v11-01b-Run0 GEOS-FP,
72L, 4x5
2013

Updates introduced in v11-01a:

Updates introduced in v11-01b:

12.000
Black Observations        

The output plots for Run0 may be downloaded from:

ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01b/Run0/output
mget *

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

http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01b/Run0/output/

--Melissa Sulprizio (talk) 20:24, 11 August 2015 (UTC)

Comments about the 1-year benchmark v11-01b-Run0

Aerosol differences

Colette Heald wrote:

I took a look at the aerosols in the benchmark. There's one thing I don't quite understand: why are the differences between v11-01b and v10-01i so much larger than the differences between v11-01b and v10-01-public at the surface for NIT, NH4, OCPI (see for example the difference plots for Jan or Jul)? According to the table that Melissa linked to the only difference between the two v10-01 runs are bug fixes and the inclusion of UCX and SOA. The NIT/NH4 may be a knock-on effect from changes in SO4 & HNO3, but I'm at a loss for why OCPI changes so significantly. Perhaps I've misunderstood the changes included those simulations?

Melissa Sulprizio wrote:

The large differences in OCPI are due to the fact that biogenic OC emissions are not calculated in the SOA chemistry mechanism. Before HEMCO, we had the following code in carbon_mod.F:
        IF ( LSOA ) THEN

           ! Total HYDROPHILIC OC source [kg]
           ! (Don't use archived TERP_ORGC if LSOA=T)
           OCSRC(I,J,1) = ANTH_ORGC(I,J,1) + 
    &                     BIOF_ORGC(I,J,1) + 
    &                     BIOB_ORGC(I,J,1)

        ELSE

           ! Total HYDROPHILIC OC source [kg]
           ! (Use archived TERP_ORGC for if LSOA=F)
           OCSRC(I,J,1) = ANTH_ORGC(I,J,1) + 
    &                     BIOF_ORGC(I,J,1) + 
    &                     BIOB_ORGC(I,J,1) + 
    &                     TERP_ORGC(I,J)

        ENDIF
Christoph Keller has treated OCPI in the same manner in HEMCO. If SOA is turned in in GEOS-Chem v10-01 and later versions, HEMCO will not calculate biogenic OCPI emissions.
Many of the other differences between v11-01b and v10-01i can be attributed to last-minute fixes that went into v10-01 prior to the public release (see the complete table of fixes and updates). In particular, the following fixes may have contributed to the differences we’re seeing:
  1. Remove Russia from MIX Asia mask file
  2. Switching to the officially released GFED4 data files
  3. Bug fix in I3 field interpolation (affected temperature-dependent emissions)

Jeff Pierce wrote:

Thanks Melissa. Just to be clear, the SOA mass goes to to the OCPI tracer when the interactive SOA is turned off, but SOA mass goes to other, SOA-specific tracers when the interactive SOA is turned on.

Colette Heald wrote:

Thanks for the clarifications Melissa. I believe then, that other than the dust issue that Li has flagged up, the aerosols look fine for v11.1
Dust differences

Li Zhang wrote:

After checking the results, I found that there are some problems with the Dust3 (DST3) concentrations both at the surface and 500 hPa. It is not only different to the 1-month benchmarks that Lizzie sent me, but also different to the results of our simulations based on GEOS-Chem adjoint code. Both in Lizzie's and my results, that the DST3 concentrations are larger after using our dust scheme.
The DST3 should be supposed to increase, especially over the dust source regions after applying our improved dust scheme. From the dust emission map of DST3, I did see this increase in this benchmarks. However I am surprised that it shows decrease in the concentrations both at the surface and 500 hPa. I am not sure it is due to the coding or only the plotting mistake. It would be great that someone can double check it.

Melissa Sulprizio wrote:

The dust differences that we see in the 1-year benchmark plots for v11-01b are a combination of the following updates:
  1. Improved dust size distribution scheme
  2. Now treat DST2-DST4 as coarse mode in wet scavenging
The second item was identified by Duncan Fairley when we implemented his acid uptake on dust scheme (default off) into the standard code.
The improved dust size distribution scheme decreased DST1 and DST2, while it increased DST3 and DST4. The wet scavenging fix to dust decreased DST2 and DST3.

Colette Heald wrote:

Thanks for the clarification. I can see that this makes sense given the changes. I discussed this with Dave, and I'll just note here (more for the benefit of Jeff and Peter) that the net effect of these changes does appear to be moving us in the wrong direction. The model already underestimates dust export/transport and these further reductions will exacerbate that. Something for us to keep an eye out in the future...

David Ridley wrote:

We’ve mainly been focusing on removal in the outflow from Africa, but there seems to be too much removal in general based on the gradient in dust AOD away from source. However, I’m finding a general lack of dust from Asia in GC too, which is contrary to some previous work. Much of low bias we’re seeing (relative to satellite) comes from earlier and later in the year than the Wang et al. (2012) and Ku et al. (2011) studies that I know of – although the latter study shifts dust emissions around, rather than decreasing them substantially. We’ve been looking over a period of several years, so it is tricky to relate that to the above studies that focus on periods of days to weeks.
It sounds like Duncan’s fix makes sense, but it does highlight potential issues with emission and removal of dust in the model.

--Melissa Sulprizio (talk) 13:46, 19 August 2015 (UTC)

1-month benchmarks

v11-01 public release

Here is the assessment form for 1-month benchmark simulation v11-01 public release.

Description
New features added into GEOS-Chem:

Features affecting the full-chemistry simulation in this benchmark:

Features not affecting the full-chemistry simulation in this benchmark:

Developer name(s) and institution(s):
  • MAP_A2A fix: Seb Eastham (Harvard), GCST
  • Timezone update: Seb Eastham (Harvard)
  • GMI HCOOH fix: Seb Eastham (Harvard)
  • Turn on traceback: Bob Yantosca (GCST)
  • Fix HEMCO seg fault: Bob Yantosca (GCST)
  • GEOS-Chem error message: Bob Yantosca (GCST)
  • Brown carbon fix: Melissa Sulprizio (GCST)
  • Time interpolation fix: Christoph Keller (NASA/GSFC), Seb Eastham (Harvard)
  • nAdvect fix in EMISSCO2: Bob Yantosca (GCST)
  • ND43 unit fix: Chris Holmes (Florida State)
  • CHEM=Custom fix: Prasad Kasibhatla (Duke)
  • OpenMP debug: Melissa Sulprizio (GCST)
  • ND65 unit fix: Chris Holmes (Florida State), Melissa Sulprizio (GCST)
  • NetCDF write speed improvement: Chris Holmes (Florida State)
  • NetCDF restart read in GAMAP: Bob Yantosca (GCST)
  • ND68 tracerinfo.dat fix: Melissa Sulprizio (GCST)
Version, resolution, met fields used: v11-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Mon Jan 23 23:12:21 EST 2017
Performance statistics:
  • Ran on 16 CPUs of regal05.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50 GHz)
  • Wall time: 09:25:11
  • CPU time / wall time: 12.6859
  • % of ideal performance: 79.29%
  • Memory: 5.1574 GB
Compared to previous benchmark: v11-01 provisional release
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):
Unit test results may be viewed at: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01-public-release/v11-01-public-release.results.html
Plots may be viewed at: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01-public-release/
Metrics
Global mean OH (from log file): 12.637496674870 x 105 molec/cm3
Methyl chloroform lifetime: 4.9699 years
Did either of these change by more than 5%? No. Mean OH changed by -0.04% and MCF lifetime changed by 0.06%.
At the SURFACE, list all species that changed by 10% or more: NO, O3, PAN, ALK4, ISOP, HNO3, H2O2, RCHO, MVK, MACR, PMN, PPN, PRPE, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, Br, BrO, HBr, BrNO2, BrNO3, MPN, ISOPND, ISOPNB, MOBA, HAC, GYLC, MVKN, MACRN, RIP, IEPOX, MAP, NO2, NO3, HNO2, BrCl, Cl, ClO, HOCl, ClNO3, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, ISOG2, ISOA2, TOLU, XYLE, ASOG3, ASOA3, OH, HO2
Comments on SURFACE differences:
  • Differences in most species concentrations are primarily found at the surface over the mid-Atlantic. These differences are caused by the fix for MAP_A2A regridding.
  • Differences in ISOP, PRPE, DMS, ISOPND, ISOPNB, MOBA, MTPA, LIMO, MTPO, and XYLE are likely small number differences where concentrations are near zero.
  • Randomly distributed small differences in NH3 and NIT can be attributed to numerical noise caused by ISORROPIA.
At 500 hPa, list all species that changed by 10% or more: ISOP, PRPE, DMS, NH3, NIT, ISOPND, ISOPNB, MOBA, RIP, MTPA, LIMO, MTPO
Comments on 500 hPa differences: See comments on surface differences.
In the ZONAL MEAN differences, list all species that changed by 10% or more: NH3, NIT, OClO, Cl2O2
Comments on ZONAL MEAN differences: See comments on surface differences.
In the EMISSION RATIO maps, list all species that changed by 10% or more: Anthro+biofuel: CO, NH3, NO, SO2, SO4
Comments on EMISSION RATIO differences:
  • Differences in anthropogenic emissions are the mid-Atlantic. These differences are caused by the fix for MAP_A2A regridding.
  • The striping pattern in the NO anthropogenic+biofuel emissions over the oceans is caused by the timezone file update
Additional or summary comments:
Approval
Requires further investigation: No
Approved by: GEOS-Chem Support Team
Date of approval: 31 Jan 2017

--Melissa Sulprizio (talk) 18:47, 31 January 2017 (UTC)

v11-01 with PRECISION=4

In order to test Flexible precision in GEOS-Chem, we performed a 1-month benchmark with the PRECISION=4 setting turned on. This will declare most of GEOS-Chem's floating-point variables as REAL*4 instead of REAL*8. Here is the benchmark approval form for v11-01 with PRECISION=4:

Description
New features added into GEOS-Chem:

Features affecting the full-chemistry simulation in this benchmark:

  • None

Features not affecting the full-chemistry simulation in this benchmark:

Developer name(s) and institution(s):
  • Traceback error output: Seb Eastham (Harvard) and GCST
  • Avoid HEMCO seg fault: Bob Yantosca (GCST)
  • Error output advising to check HEMCO log file: GCST
  • Out-of-bounds error fix: Melissa Sulprizio (GCST)
Version, resolution, met fields used: v11-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Sat Jan 7 13:19:52 EST 2017
Performance statistics:
  • Ran on 24 CPUs of holyjacob04.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50 GHz)
  • Wall time: 05:29:17
  • CPU time / wall time: 17.2081
  • % of ideal performance: 71.70%
  • Memory: 3.3605 GB
Compared to previous benchmark: v11-01k
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 small differences across-the-board caused by the change in default precision from 8-byte reals to 4-byte reals.
Unit test results may be viewed at: TBD
Plots may be viewed at: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01.prec4/
Metrics
Global mean OH (from log file): 12.64273 x 105 molec/cm3
Methyl chloroform lifetime: 4.9666 years
Did either of these change by more than 5%? No. Mean OH changed by -0.00098% and MCF lifetime changed by -0.0020%.
At the SURFACE, list all species that changed by 10% or more:
  • Diffs near N. Pole only: NO, ALK4, RCHO, PRPE, N2O5, HNO4, BCPO, OCPO, BrNO2, BrNO3, MPN, NO2, NO3, HNO2, ClO, ClOO, Cl2, Cl2O2, TOLU, XYLE, OH. HO2
  • Diffs over oceans: LIMO, MTPO
  • The usual ISORROPIA noise: NH3, NIT
Comments on SURFACE differences: These might be small-number differences (due to roundoff etc.) where the concentrations are probably already very small.
At 500 hPa, list all species that changed by 10% or more:
  • Diffs over oceans: LIMO, MTPO,
  • The usual ISORROPIA noise: NH3, NIT
Comments on 500 hPa differences: N/A
In the ZONAL MEAN differences, list all species that changed by 10% or more:
  • Diffs near surface N. Pole only: NO, ALK4, RCHO, PRPE, CH2O, N2O5, HNO4, BCPO, OCPO, BrNO2, MPN, ISOPND, NO2, NO3, HNO2, ClO, ClNO3, OClO. Cl2, Cl2O2, MTPA, TOLU, XYLE
  • Diffs near top of atmospehre: O3, ISOP, MVK, MACR, PMN, PRPE, SO4s, NITs, BCPO, OCPO, DST1, DST2, DST3, DST4, Br2, NO3, OCS, BrCl, CCl4, CHCCl3, CFC11, H1211, H1301, H2402,
  • Other diffs: LIMO, MTPO
  • The usual ISORROPIA noise: NH3, NIT
Comments on ZONAL MEAN differences: N/A
In the EMISSION RATIO maps, list all species that changed by 10% or more:
  • Diffs in sporadic grid boxes: NO, CO, BC, OC, SO2, SO4, NH3
Comments on EMISSION RATIO differences: The emissions summary table shows total emissions differing by +/- 0.001 Tg or less. The differences in the ratio plots are probably caused by either small-number differences or roundoff errors between REAL*4 and REAL*8 precision.
Additional or summary comments:
  • Most of the differences are small and are likely caused by the shift from REAL*8 to REAL*4 as the default precision.
  • The differences of several tracers at the poles appear to be in locations where concentrations are already very low.
  • With respect to the v11-01 provisional release benchmark:
    • The wall clock time was 20 minutes faster (05:29 vs. 05:49)
    • GEOS-Chem used approximiately 40% less memory (3.3605 GB vs. 5.3816 GB)

Daniel Jacob wrote:

Thanks Bob. I went through your summary and checked out the emission ratio maps that you flagged, and the differences there are really negligible. Bottom line is, it all looks good, and I think the 1-month benchmark is sufficient. 10% gain in runtime is nothing to sneeze at, and the memory reduction is great.
Approval
Requires further investigation: No
Approved by: Daniel Jacob
Date of approval: 08 Feb 2017

--Bob Yantosca (talk) 20:19, 8 February 2017 (UTC)

v11-01 provisional release

Here is the assessment form for 1-month benchmark simulation v11-01 provisional release.

Description
New features added into GEOS-Chem:

Features affecting the full-chemistry simulation in this benchmark:

  • None

Features not affecting the full-chemistry simulation in this benchmark:

Developer name(s) and institution(s):
  • gckpp_Integrator.F90 workaround: GCST
  • TOMAS temporary fix: Sal Farina (TOMAS team)
  • GNU profiler support: Bob Yantosca (GCST)
Version, resolution, met fields used: v11-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Fri Dec 9 06:09:45 EST 2016
Performance statistics:
  • Ran on 24 CPUs of holyjacob03.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50 GHz)
  • Wall time: 05:49:34
  • CPU time / wall time: 17.9054
  • % of ideal performance: 74.61%
  • Memory: 5.3816 GB
Compared to previous benchmark: v11-01k
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 v11-01k
Unit test results may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01-provisional-release.tar.gz
Plots may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01-provisional-release.tar.gz
Metrics
Global mean OH (from log file): 12.6428535892599 x 105 molec/cm3
Methyl chloroform lifetime: 4.9667 years
Did either of these change by more than 5%? No. Mean OH and MCF lifetime were identical to v11-01k.
At the SURFACE, list all species that changed by 10% or more: None
Comments on SURFACE differences: N/A
At 500 hPa, list all species that changed by 10% or more: None
Comments on 500 hPa differences: N/A
In the ZONAL MEAN differences, list all species that changed by 10% or more: None
Comments on ZONAL MEAN differences: N/A
In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences: N/A
Additional or summary comments:
Approval
Requires further investigation: No
Approved by: GEOS-Chem Support Team
Date of approval: 20 Dec 2016

--Melissa Sulprizio (talk) 19:27, 9 January 2017 (UTC)

v11-01k

Here is the assessment form for 1-month benchmark simulation v11-01k.

Description
New features added into GEOS-Chem:

Features affecting the full-chemistry simulation in this benchmark:

Features not affecting the full-chemistry simulation in this benchmark:

Developer name(s) and institution(s):
  • Lightning NOx update: Katie Travis (Harvard)
  • Updates for Beijing Climate Center Model: GCST
  • Memory updates: GCST
  • State_Met fixes: GCST
  • Temporary TOMAS fix: GCST
Version, resolution, met fields used: v11-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Sat Dec 3 03:06:41 EST 2016
Performance statistics:
  • Ran on 24 CPUs of holyjacob03.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50 GHz)
  • Wall time: 07:14:01
  • CPU time / wall time: 18.1264
  • % of ideal performance: 75.53%
  • Memory: 5.3838 GB
Compared to previous benchmark: v11-01j
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): Lightning NOx emissions
Unit test results may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01k.tar.gz
Plots may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01k.tar.gz
Metrics
Global mean OH (from log file): 12.6428535892599 x 105 molec/cm3
Methyl chloroform lifetime: 4.9667 years
Did either of these change by more than 5%? No. Mean OH changed by -0.45% and MCF lifetime changed by 0.47%.
At the SURFACE, list all species that changed by 10% or more: MTPO
Comments on SURFACE differences:
  • See comments on 50 hPa differences
At 500 hPa, list all species that changed by 10% or more: NO, ALK4, ISOP, HNO3, RCHO, MVK, MACR, PMN, N2O5, HNO4, MP, DMS, NH3, NIT, BrNO2, MPN, ISOPND, ISOPNB, HAC, GLYC, MVKN, RIP, IEPOX, MAP, NO2, NO3, HNO2, BrCl, Cl, ClNO3, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, BENZ, TOLU, XYLE, OH
Comments on 500 hPa differences:
  • The lightning NOx update involves moving the boundary between tropical and midlatitude lightning from 23° N to 35° N to reduce ozone concentrations in the southern US. Changes in species concentrations can be seen over the southern US at mid and upper levels where emissions from lightning NOx are impacted.
  • Randomly distributed small differences in NH3 and NIT can be attributed to numerical noise caused by ISORROPIA.
In the ZONAL MEAN differences, list all species that changed by 10% or more: NO, NH3, NIT
Comments on ZONAL MEAN differences:
  • See comments on 500 hPa differences
In the EMISSION RATIO maps, list all species that changed by 10% or more: NO column lightning emissions
Comments on EMISSION RATIO differences:
  • NOx lightning emissions decrease in the band from 23° N to 35° N as expected.
Additional or summary comments:
Approval
Requires further investigation: No
Approved by: Katie Travis, Daniel Jacob
Date of approval: 06 Dec 2016

--Melissa Sulprizio (talk) 17:38, 5 December 2016 (UTC)

v11-01j

Here is the assessment form for 1-month benchmark simulation v11-01j.

Description
New features added into GEOS-Chem:

Features affecting the full-chemistry simulation in this benchmark:

Features not affecting the full-chemistry simulation in this benchmark:

Developer name(s) and institution(s):
  • HEMCO v2.0.003: Christoph Keller (NASA GSFC)
  • High-resolution CAC: Aaron van Donkelaar (Dalhousie)
  • Replace RETRO C3h8 with Xiao: Emily Fischer (CSU), Zitely Tzompa (CSU)
  • EDGAR SO2 fix: Jaegun Jung (Ramboll Environ)
  • EDGAR biofuel fix: Jaegun Jung (Ramboll Environ)
  • GMI HCOOH rate fix: Eloise Marais (Harvard), Xin Chen (UMN)
  • Set ACTA and HCOOH to active: Katie Travis (Harvard)
  • Mesospheric NOx fixes: Seb Eastham (Harvard)
  • N2O5 MW fix: Chi Li (Dalhousie)
  • QFED & FINN for Hg: Jenny Disher (Wollongong)
  • TOMAS Jeagle sea salt extension: Jack Kodros (CSU)
  • Fix KPP prod/loss diagnostic: Mike Long (Harvard)
  • TOMS fix: Barron Henderson (U. Florida)
  • HEMCO strat P/L fix: Christoph Keller (NASA GSFC)
  • NOx diurnal scale factor fix:Brian Boys (Dalhousie), Christoph Keller (NASA GSFC)
  • PM2.5 diagnostic: Melissa Sulprizio (GCST)
  • Support for Gfortran: Seb Eastham (Harvard), Bob Yantosca (Harvard)
  • Fixes for Gfortran: Bob Yantosca (Harvard)
Version, resolution, met fields used: v11-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Thu Dec 1 10:06:54 EST 2016
Performance statistics:
  • Ran on 24 CPUs of holyjacob03.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50 GHz)
  • Wall time: 07:13:30
  • CPU time / wall time: 18.1093
  • % of ideal performance: 75.46%
  • Memory: 5.3702 GB
Compared to previous benchmark: v11-01i
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):
Unit test results may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01j.tar.gz
Plots may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01j.tar.gz
Metrics
Global mean OH (from log file): 12.7001495110158 x 105 molec/cm3
Methyl chloroform lifetime: 4.9436 years
Did either of these change by more than 5%? No. Mean OH changed by -0.40% and MCF lifetime changed by 0.71%.
At the SURFACE, list all species that changed by 10% or more: NO, O3, PAN, CO, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, RIP, IEPOX, MAP, NO2, NO3, HNO2, BrCl, Cl, ClO, HOCl, ClNO3, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG3, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, ISOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, BENZ, TOLU, XYLE, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3, OH, HO2
Comments on SURFACE differences:
  • The update to HEMCO v2.0.003 causes differences in many species. These differences are mainly attributed to:
    • New timezones file: Large differences in species concentrations in Southeast Asia and globally along coastlines are attributed to the new timezones file that was introduced in this update to correct for cells with large ocean overlap.
    • PARANOX fix: Differences in NOx-related species over the oceans are caused by the bug fix in hcox_paranox_mod.F90 to archive deposition flux as an absolute number.
    • NOTE: This update also causes large percent increases in ISOP, MVK, MACR, PMN, ISOPND, ISOPNB, MOBA, GLYC, MVKN, MACRN, RIP, IEPOX, MTPA, LIMO, and MTPO over the oceans. These are likely small number differences where concentrations are near zero.
  • The increases in many species over Canada and Mexico can be attributed to the 0.1° x 0.1° CAC emissions. This update applies a new NEI2011 mask file to correct for zeroing of emissions over Northern Canada and parts of Mexico.
  • The large increase in C3H8 is caused by replacing RETRO C3H8 with emissions from Xiao et al. (2008). This update also causes increases in ACET, ALD2, RCHO, and PPN over land. With this update, C2H6 emissions are now overwritten by NEI2011 and MIX over the US and Asia, causing large positive and negative differences over those regions.
  • The large differences in SO2 and SO4 concentrations are caused by the fix for EDGAR v4.2 SO2 units. This update also causes large percent changes in N2O5, DMS, SO4s, MSA, NH3, NH4, NIT, NITs where concentrations are very low.
  • The decreases in many species (especially NO, HNO3, N2O5, HNO4, NIT, NO3, HNO2) over Africa, South America, and Russia are caused by the fix to EDGAR v4.2 to prevent biofuel emissions from being double counted.
At 500 hPa, list all species that changed by 10% or more: NO, PAN, ALK4, ISOP, HNO3, ACET, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, C2H8, C2H6, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, RIP, IEPOX, MAP, NO2, NO3, HNO2, BrCl, Cl, ClNO3, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG3, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, ISOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, BENZ, TOLU, XYLE, ASOAN, ASOA1, ASOA2, ASOA3
Comments on 500 hPa differences:
  • See comments on surface differences.
In the ZONAL MEAN differences, list all species that changed by 10% or more: NO, ALK4, ISOP, HNO3, ACET, MEK, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, C3H8, C2H6, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, BCPO, OCPO, Br, BrNO2, BrNO3, MPN, ISOPND, ISOPNB, MOBA, PROPNN, HAC, GLYC, MVKN, MACRN, RIP, IEPOX, MAP, NO2, NO3, HNO2, N2O, Cl, ClNO3, ClOO, OClO, Cl2O2, MTPA, LIMO, MTPO, TSOA0, ISOG1, ISOG3, ISOA1, ISOA2, ISOA3, TOLU, XYLE, ASOA2
Comments on ZONAL MEAN differences:
  • The large differences in NO, NO2, NO3, N2O at the top of the zonal mean plots are caused by the fix for mesospheric NOx chemistry.
  • Also see comments on surface differences.
In the EMISSION RATIO maps, list all species that changed by 10% or more:
  • Anthro+biofuel: ACET, ALD2, ALK4, BC, C2H6, C3H8, CH2O, CO, MEK, NH3, NO, OC, PRPE, SO2, SO4
  • Biogenic: ACET, ALD2, ISOP, PRPE
  • ACET from MONOT, ACET from MBO, ACET direct
  • CO from MONOT
Comments on EMISSION RATIO differences:
  • The differences in anthropogenic emissions over Canada and Mexico are caused by the update to 0.1° x 0.1° CAC emissions. This update impacts emissions over Mexico because it applies a new NEI2011 mask file to correct for zeroing of emissions over Northern Canada and parts of Mexico.
  • The increases in anthropogenic SO2 and SO4 emissions over South America, Africa, Australia, and Russia are caused by the fix for EDGAR v4.2 SO2 units.
  • The differences in NO anthropogenic emissions over the oceans are caused by the fix to PARANOX that was included in HEMCO v2.0.003.
  • Differences in anthropogenic C3H8 emissions globally are caused by replacing RETRO C3H8 with Xiao. That update also includes overwriting C2H6 emissions over the US and Asia with NEI2011 and MIX, which causes large differences in C2H6 anthropogenic emissions over those regions. C3H8 anthropogenic emissions remain unchanged over the US and Asia because NEI2011 and MIX were already used in those regions in v11-01i.
  • Differences in biogenic emissions, ACET emission from MONOT and MBO, direct ACET emissions, and CO from MONOT emissions are caused by the update to HEMCO v2.0.003. In that update, the timezones file was updated to correct for cells with large ocean overlap, which causes large differences in emissions along coastlines.
Additional or summary comments:
Approval
Requires further investigation: No
Approved by: Daniel Jacob, Randall Martin, Aaron van Donkelaar
Date of approval: 03 Dec 2016

--Melissa Sulprizio (talk) 19:32, 1 December 2016 (UTC)

v11-01i

Here is the assessment form for 1-month benchmark simulation v11-01i.

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • Re-evaporation fix: Virah Shah (UW), Bo Zhang (NIA), Hongyu Liu (NIA/NASA Langley)
Version, resolution, met fields used: v11-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Wed Oct 12 04:53:29 EDT 2016
Performance statistics:
  • Ran on 24 CPUs of holyjacob05.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50 GHz)
  • Wall time: 05:40:57
  • CPU time / wall time: 17.3977
  • % of ideal performance: 72.49%
  • Memory: 5.4688 GB
Compared to previous benchmark: v11-01h
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):
Unit test results may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01i.tar.gz
Plots may be viewed at: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01i.tar.gz
Metrics
Global mean OH (from log file): 12.7515965946309 x 105 molec/cm3
Methyl chloroform lifetime: 4.9088 years
Did either of these change by more than 5%? No. Mean OH changed by 0.27% and MCF lifetime changed by -0.29%.
At the SURFACE, list all species that changed by 10% or more: NO, PAN, ISOP, HNO3, H2O2, MVK, MACR, PMN, PPN, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, ISOPND, ISOPNB, MOBA, PROPNN, GLYC, MVKN, MACRN, RIP, IEPOX, MAP, NO3, HNO2, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG3, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, IGOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3, HO2
Comments on SURFACE differences:
  • See summary comments below
At 500 hPa, list all species that changed by 10% or more: NO, ISOP, HNO3, MVK, MACR, PMN, PRPE, N2O5, HNO4, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, ISOPND, ISOPNB, MOBA, MVKN, MACRN, RIP, IEPOX, NO3, HNO2, BrCl, HCl, Cl, ClO, ClNO3, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG3, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, IGOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3
Comments on 500 hPa differences:
  • See summary comments below
In the ZONAL MEAN differences, list all species that changed by 10% or more: NO, ISOP, HNO3, H2O2, MACR, N2O5, DMS, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, ISOPND, ISOPNB, MOBA, GLYC, MVKN, MACRN, IEPOX, NO3, HNO2, BrCl, HCl, Cl, ClO, ClNO3, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG3, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, IGOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3
Comments on ZONAL MEAN differences:
  • See summary comments below
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:

Viral Shah wrote:

[Prior to this version], the re-suspension of aerosols and highly soluble gases (species for which washout is treated as a kinetic process) is not performed when running GEOS-Chem with GEOSFP/MERRA fields. This fix corrects that. Thus there is a widespread increase in the concentrations of these species at the surface and to a smaller extent at 500 hPa. There is also an increase in species (or decrease for a few species) with low solubility likely because they are connected chemically to the species that are directly affected by the fix. The relative increases seem fairly large (factor of 2), but for the most part the highest ratios are in places with low concentrations.
Approval
Requires further investigation: No
Approved by: Viral Shah
Date of approval: 19 Oct 2016

--Melissa Sulprizio (talk) 16:32, 18 October 2016 (UTC)

v11-01h

Here is the assessment form for 1-month benchmark simulation v11-01h.

Description
New features added into GEOS-Chem:

Features affecting the full-chemistry simulation in this benchmark:

Features not affecting the full-chemistry simulation in this benchmark:

Developer name(s) and institution(s):
  • Moisture fix: Meemong Lee (JPL), Richard Weidner, Lizzie Lundgren (GCST), Kevin Bowman (JPL)
  • MERRA-2 nested AS: Melissa Sulprizio (GCST)
Version, resolution, met fields used: v11-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Sat Oct 1 03:05:57 EDT 2016
Performance statistics:
  • Ran on 24 CPUs of holyjacob04.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50 GHz)
  • Wall time: 05:37:13
  • CPU time / wall time: 17.3384
  • % of ideal performance: 72.24%
  • Memory: 5.4620 GB
Compared to previous benchmark: v11-01g
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):
Unit test results may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01h.tar.gz
Plots may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01h.tar.gz
Metrics
Global mean OH (from log file): 12.7172819332578 x 105 molec/cm3
Methyl chloroform lifetime: 4.9230 years
Did either of these change by more than 5%? No. Mean OH changed by -0.07% and MCF lifetime changed by 0.06%.
At the SURFACE, list all species that changed by 10% or more: HNO3, NIT, LIMO
Comments on SURFACE differences:
  • Randomly distributed small differences in NH3 and NIT can be attributed to numerical drift caused by ISORROPIA.
At 500 hPa, list all species that changed by 10% or more: NO, NH3, NIT, MTPA, LIMO, MTPO
Comments on 500 hPa differences:
  • See comments for surface differences above
In the ZONAL MEAN differences, list all species that changed by 10% or more: ISOP, MACR, PMN, SO4s, NH3, NIT, MTPO
Comments on ZONAL MEAN differences:
  • Zonal mean differences are consistent with a change in advection with respect to moisture (<3%).
  • Zonal mean concentrations generally decreased most towards the equator near the surface due to greater reductions in the pressure used in advection, from moist to dry, in those areas.
  • Away from the surface, concentrations generally increased due to the difference in vertical pressure profiles used in advection. While v11-01g uses vertical pressure profiles constructed from moist surface pressure, v11-01h uses pressure profiles constructed from dry surface pressure; both profiles are constructed using the same GMAO vertical grid parameters.
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:
  • The moisture fix corrects the remaining issue after implementation of moisture in GEOS-Chem air quantities in v11-01a, specifically preferential pooling of species mass in grid boxes with greater humidity. Differences resulting with this fix are as expected, with order of magnitude comparable to the difference between dry and moist air pressure.
  • While this update corrects a problem in advection and therefore impacts advected species concentrations, it also causes small differences in concentrations of non-advected species. Since advected and non-advected species are stored together, non-advected species undergo the same unit conversions as advected species. To preserve mass conservation, species unit conversions now use dry air mass derived from the new dry surface pressure used in advection, values that are slightly different than in v11-01g.
  • After this 1-month benchmark simulation was completed, Hongyu Liu pointed out an imbalance in the Pb210 budget from 1-year benchmark v11-01h-RnPbBe. The imbalance was caused by bugs in the dry deposition diagnostic when the TURBDAY mixing scheme is used. The diagnostic bug fixes went into v11-01h, but they do not impact this 1-month full-chemistry benchmark because the non-local PBL (VDIFF) mixing scheme is used.
Approval
Requires further investigation: No
Approved by: Lizzie Lundgen (GCST), Daniel Jacob
Date of approval: 11 Oct 2016

--Lizzie Lundgren (talk) 19:42, 3 October 2016 (UTC)

v11-01g

Here is the assessment form for 1-month benchmark simulation v11-01g.

Description
New features added into GEOS-Chem:

Features affecting the full-chemistry simulation in this benchmark:

Features not affecting the full-chemistry simulation in this benchmark:

Developer name(s) and institution(s):
  • FlexChem: Mike Long (Harvard); GCST
  • Soil Hg updates: Jenny Fisher (Wollongong)
  • Hg parallelization fixes: Bob Yantosca (GCST)
  • HEMCO bug fixes: Christoph Keller (NASA GSFC); GCST
  • Hg netCDF restart files: Lizzie Lundgren (GCST)
  • Tagged CO updates: GCST
  • GCHP DevKit updates: Seb Eastham (Harvard); GCST
  • Pointers fix: Bob Yantosca (GCST)
  • Species indexing: GCST
Version, resolution, met fields used: v11-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Sat Sep 10 00:31:03 EDT 2016
Performance statistics:
  • Ran on 24 CPUs of holyjacob03.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50 GHz)
  • Wall time: 05:39:22
  • CPU time / wall time: 17.4727
  • % of ideal performance: 72.80%
  • Memory: 5.4582 GB
Compared to previous benchmark: v11-01f
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):
Unit test results may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01g.tar.gz
Plots may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01g.tar.gz
Metrics
Global mean OH (from log file): 12.7263760623542 x 105 molec/cm3
Methyl chloroform lifetime: 4.9202 years
Did either of these change by more than 5%? No. Mean OH changed by 0.11% and MCF lifetime changed by -0.12%.
At the SURFACE, list all species that changed by 10% or more: NO, ISOP, HNO3, MVK, MACR, PMN, N2O5, DMS, SO2, NH3, NH4, NIT, HBr, BrNO3, ISOPND, ISOPNB, MOBA, PROPNN, MVKN, MACRN, RIP, NO3, CFC113, CFC114, CFC115, HCFC141b, HCFC142b, Cl, ClNO2, ClOO, OClO, Cl2, Cl2O2, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3
Comments on SURFACE differences:
  • Large differences appear for ISOPND, ISOPNB, MVKN, MACRN, CFC113, CFC114, CFC115, HCFC1241b, and HCFC142b. These advected species are new in this version and were introduced as part of the family tracer removal updates. The ratio plots for these species are an approximation and were created by comparing the new species concentrations to the former family tracer concentration divided by the number of species in that chemical family.
  • Widespread < -10% ratios in Cl2 and Cl2O2 are also caused by the family tracer removal updates. These differences are small and occur where the species concentrations are very low.
  • Differences in N2O5 can be attributed to a bug in NIT units in calcrate.F. With the fix to NIT units in this version (in code now found in gckpp_HetRates.F90), we see > +10% ratios over regions of Europe, Asia, and Antarctica.
  • In previous versions, default background concentrations were obtained from the now obsolete globchem.dat file to initialize non-advected species just prior to chemistry. In v11-01g, these background values are stored in the species database and are used to initialize species if values are not present in the netCDF restart file. The initialization now occurs in a different dynamic timestep and therefore results in small differences due to different met field values in the unit conversion.
  • With the removal of tracers, the species unit is dynamic while previously it was static (molecules/cm3). To conserve species mass, mixing ratio updates are now applied to species when the met fields change as was done previously for tracers. This change results in small differences on the order of magnitude of relative humidity differences between two timesteps.
  • All other differences are small number differences where concentrations are very low.
At 500 hPa, list all species that changed by 10% or more: NO, ISOP, MVK, MACR, PMN, DMS, SO2, SO4s, NH3, NIT, NITs, HBr, BrNO3, ISOPND, ISOPNB, MOBA, MVKN, MACRN, RIP, CFC113, CFC114, CFC115, HCFC141b, HCFC142b, ClO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, XYLE, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3
Comments on 500 hPa differences:
  • See comments on surface differences.
In the ZONAL MEAN differences, list all species that changed by 10% or more: NO, ISOP, HNO3, ACET, MVK, MACR, PMN, PRPE, CH2O, N2O5, HNO4, MP, DMS, SO4s, NH3, NIT, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPND, ISOPNB, MOBA, MVKN, MACRN, MAP, NO2, NO3, HNO2, N2O, BrCl, CFC113, CFC114, CFC115, HCFC123, HCFC141b, HCFC142b, Cl, ClO, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3, OH, HO2
Comments on ZONAL MEAN differences:
  • See comments on surface differences.
  • Above the stratopause (LLCHEM), non-advected chemical species concentrations are now set to 1e-30 mol/mol. In previous model versions, all non-advected species were set to zero above LLCHEM. This change causes some differences in species like OH and HO2 at upper levels.
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:

J-value differences:

  • Chris Holmes noted, "J-values changed everywhere by -50% for O(1D) and O(3P). There’s also a 50% J-value change over Antarctica for all species, but I suspect that might be a divide by zero artifact since it’s dark there in July." The changes in J-values for O(1D) and O(3P) are caused by an apparent bug in the ND22 diagnostic that was present in previous versions. This issue is described in this wiki post.

FlexChem updates in the pipeline:

  • The KPP prod/loss diagnostic capability still needs to be updated to account for reactions where there is cycling between species within a chemical family. This fix should be included in GEOS-Chem v11-01 prior to the public release. The prod/loss diagnostic (ND65) should not be used with this version as it will return unrealistic values.
  • The pre-built chemistry mechanisms (Standard, Tropchem, UCX, SOA, SOA-SVPOA) will be rebuilt with Kppa prior to GEOS-Chem v11-01 release. This update should improve model performance when compared to mechanisms built with the standard KPP code.
Approval
Requires further investigation: No
Approved by: Mat Evans, Daniel Jacob
Date of approval: 14 Sep 2016

--Melissa Sulprizio (talk) 17:48, 12 September 2016 (UTC)

v11-01f

We performed two 1-month benchmark simulations for GEOS-Chem v11-01f:

  1. v11-01f: 1-month benchmark with GEOS-FP
  2. v11-01f-merra2: 1-month benchmark with MERRA-2

1-month benchmark v11-01f with GEOS-FP

Here is the assessment form for 1-month benchmark simulation v11-01f with GEOS-FP meteorology (aka v11-01f).

Description
New features added into GEOS-Chem:

Features affecting the full-chemistry simulation in this benchmark:

Features not affecting the full-chemistry simulation in this benchmark:

Developer name(s) and institution(s):
  • Hydrophobic aerosol fix: Seb Eastham (Harvard)
  • MOBA globchem.dat fix: Will Porter (MIT)
  • ISNOOA + NO2 globchem.dat fix: Mike Long (Harvard)
  • Consistent physical constants: Lizzie Lundgren (GCST)
  • Optimal timesteps: Sajeev Philip (Dalhousie), Randall Martin (Dalhousie)
  • EMEP mask fix: Eloise Marais (Harvard)
  • Hg2 emissions fix: Amanda Giang (MIT)
  • HEMCO RnPbBe extension fix: Mat Evans (U. York)
  • SOA-SVPOA fix: Prasad Kasibhatla (Duke), Melissa Sulprizio (GCST)
  • isCoards script: Bob Yantosca (GCST)
  • MERRA-2 fullchem: Melissa Sulprizio (GCST), Lee Murray (NASA GISS/LDEO)
  • NetCDF restart file: Lizzie Lundgren (GCST)
  • PGI fixes: Bob Yantosca (GCST)
  • Stratospheric emissions bug fix: Lizzie Lundgren (GCST)
Version, resolution, met fields used: v11-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Mon Mar 21 21:37:17 EDT 2016
Performance statistics:
  • Ran on 24 CPUs of holyjacob02.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50 GHz)
  • Wall time: 04:42:42
  • CPU time / wall time: 17.2314
  • % of ideal performance: 71.80%
  • Memory: 6.7622 GB
Compared to previous benchmark: v11-01e
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): Minor numerical differences may occur as a result of the physical constants update
Unit test results may be downloaded from http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01f.tar.gz
  • NOTE: Unit tests for tagged CO were not performed, since this simulation is not yet 100% compatible with HEMCO.
Plots may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01f.tar.gz
Metrics
Global mean OH (from log file): 12.7130056846517 x 105 molec/cm3
Methyl chloroform lifetime: 4.9263 years
Did either of these change by more than 5%? No. Mean OH changed by 0.29% and MCF lifetime changed by -0.25%.
At the SURFACE, list all species that changed by 10% or more: NO, PAN, ALK4, IOSP, HNO3, H2O2, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, OCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, PROPNN, GLYC, MMN, RIP, IEPOX, NO2, NO3, HNO2, BrCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, H2O, MTPA, LIMO, MTPO, TSOG1, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, ISOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, TOLU, XYLE, ASOG1, ASOAN, ASOA1, ASOA2, ASOA3, OH, HO2.
Comments on SURFACE differences:
  • Differences in the following species were caused by the reduction of the chemistry timestep to 20 minutes and transport timestep to 10 minutes: NO, PAN, ISOP, HNO3, H2O2, MVK, MACR, PPN, N2O5, HNO4, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, OCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPN, PROPNN, GLYC, MMN, RIP, IEPOX, NO2, NO3, BrCl, H2O, MTPA, LIMO, MTPO, TSOG0, TSOG1, TSOA0, TSOA1, TSOA2, TSOA3, ISOG1, ISOG2, ISOA3, ISOA1, ISOA2, ISOA3, TOLU, ASOG1, ASOG2, ASOAN, ASOA1, ASOA2, ASOA3, and OH.
  • Differences for Br2, BrO, BrNO2, BrNO3, and BrCl appear in a splotchy geometric pattern. This may be due to the impact of the reduced chemistry timestep on photolysis.
  • Differences in the following species may be attributed to bug fixes in the MOBA + OH -> MOBAOO reaction in globchem.dat, the ISNOOA + NO2 --> PMN reaction in globchem.dat, or the hydrophobic aerosol property calculations: PAN, ALK4, MEK, ALD2, RCHO, PMN, PPN, PRPE, DMS, SO2, NH3, NIT, BrNO2, NO2, HNO2, HOCl, ClNO3, and HO2.
  • Changes in R4N2 are due to bug fix in reaction ISNOOA + NO2 --> PMN in globchem.dat.
  • MOBA uniformly decreased over most of the globe by approximately 50% due to the syntax error fix in the MOBA + OH -> MOBAOO reaction in globchem.dat.
  • ClNO2 shows change ratios of up to 2.0 in an instantaneous day/night signature pattern. However, all concentrations and differences are very low and therefore differences are likely due to numerical noise. It is unclear why the numerical noise appears in the day/night pattern.
  • All other differences can be attributed to small numerical differences when concentrations are very low.
At 500 hPa, list all species that changed by 10% or more: NO, IOSP, MVK, MACR, PMN, R4N2, PRPE, N2O5, DMS, SO2, SO4, SO4s, NH3, NIT, NITs, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HBr, BrNO2, BrNO3, ISOPN, MOBA, GLYC, MMN, RIP, IEPOX, NO3, BrCl, Cl, ClO, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, TSOG1, TSOA1, TSOA2, TSOA3, TSOA0, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, XYLE, ASOA1, ASOA2, and ASOA3.
Comments on 500 hPa differences:
  • See comments on surface differences.
In the ZONAL MEAN differences, list all species that changed by 10% or more: NO, PAN, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, PMN, R4N2, PRPE, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, NITs, BCPO, OCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, CHBr3, CH2Br2, MPN, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO2, NO3, HNO2, OCS, BrCl, HCl, CCl4, CH3CCl3, CFC11, H1211, H2402, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, H2O, MTPA, LIMO, MTPO, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, ISOG2, ISOA1, ISOA2, ISOA3, TOLU, XYLE, ASOA1, ASOA2, ASOA3, OH, and HO2.
Comments on ZONAL MEAN differences:
  • See comments on surface differences.
In the EMISSION RATIO maps, list all species that changed by 10% or more:
  • ISOP biogenic emissions
  • NO anthropogenic + biofuel emissions
Comments on EMISSION RATIO differences:
  • Isoprene biogenic emissions increased by up to a factor of two along Asian coasts, particularly over southeast Asia, due to the chemistry timestep update. Global emissions increased by 0.0096 Tg C (2.27%).
  • NO anthropogenic and biofuel emissions decreased by over 10% in parts of the Atlantic ocean and Mexico due to the timestep update.
    • This timestep update affects when the PARANOX ship plume model runs, thus leading to small differences over the ocean.
    • However, these decreases occurred where emissions are very small and global emissions actually increased by a small amount (0.00575 Tg N, or 0.04%).
Additional or summary comments: A note about increased "wall clock" run times:

The addition of the optimal timestep configuration (i.e. transport/convection/PBL mixing/wetdep every 10 minutes and emissions/drydep/chemistry every 20 minutes) caused a doubling of the wall clock time when using 8 CPUS, as shown below.

  • v11-01e, 8 CPUS: 04:16:08
  • v11-01f, 8 CPUs: 08:41:54
  • v11-01f, 24 CPUS: 04:42:42 (reported in this form)

We attribute this increase in wall clock time to the following factors:

  • Transport is now being called 3X more frequently
  • Chemistry is now being called 1.5X more freqently
    • We know that the SMVGEAR chemistry solver is very inefficient, as it spends a lot of overhead in copying large 3-D arrays to large 1-D arrays, and then back again.
    • We anticipate that performance will improve in v11-01g, with the addition of the FlexChem package (which will be a clean implementation of the KPP solver)
  • We now are writing out data to the netCDF restart file, which incurs some additional computational overhead

Other observations:

  • Most differences observed are due to the reduction in chemistry timestep to 20 minutes.
  • Several species are impacted by bug fixes in the MOBA + OH -> MOBAOO and the ISONOOA + NO2 -> PMN reactions in globchem.dat.
Approval
Requires further investigation: No
Approved by: Randall Martin, Sajeev Philip, Daniel Jacob
Date of approval: 29 Mar 2016

--Lizzie Lundgren (talk) 15:55, 22 March 2016 (UTC)

1-month benchmark v11-01f with MERRA-2

Here is the assessment form for 1-month benchmark simulation v11-01f with MERRA-2 meteorology (aka v11-01f-merra2).

Description
New features added into GEOS-Chem:
Developer name(s) and institution(s):
  • MERRA-2 fullchem: Melissa Sulprizio (GCST), Lee Murray (NASA GISS/LDEO)
Version, resolution, met fields used: v11-01, MERRA-2 (72L), 4x5, July 2013
1-month benchmark finished on: Tue Mar 22 00:21:33 EDT 2016
Performance statistics:
  • Ran on 24 CPUs of holyjacob-3.rc.fas.harvard.edu (Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50 GHz)
  • Wall time: 04:40:19
  • CPU time / wall time: 17.3069
  • % of ideal performance: 72.11%
  • Memory: 6.8440 GB
Compared to previous benchmark: v11-01f with GEOS-FP
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):
Unit test results may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01f.tar.gz
  • NOTE: Unit tests for tagged CO were not performed, since this simulation is not yet 100% compatible with HEMCO.
Plots may be viewed at: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01f-merra2.tar.gz
Metrics
Global mean OH (from log file): 12.6308637279271 x 105 molec/cm3
Methyl chloroform lifetime: 4.8960 years
Did either of these change by more than 5%? No. Mean OH changed by -0.65% and MCF lifetime changed by -0.62%.
At the SURFACE, list all species that changed by 10% or more: NO, O3, PAN, CO, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, CHBr3, MPN, ISOPN, MOBA, PROPNN, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO2, NO3, HNO2, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, H2O, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG3, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, ISOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, BENZ, TOLU, XYLE, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3, OH, HO2
Comments on SURFACE differences:
  • Observed differences in tracer concentrations can be attributed to differences between GEOS-FP and MERRA-2
  • See additional comments below for useful links comparing these two met fields.
At 500 hPa, list all species that changed by 10% or more: NO, O3, PAN, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, CHBr3, MPN, ISOPN, MOBA, PROPNN, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO2, NO3, HNO2, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, H2O, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG3, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, ISOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, BENZ, TOLU, XYLE, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3, OH, HO2
Comments on 500 hPa differences:
  • Observed differences in tracer concentrations can be attributed to differences between GEOS-FP and MERRA-2
  • See additional comments below for useful links comparing these two met fields.
In the ZONAL MEAN differences, list all species that changed by 10% or more: All species: NO, O3, PAN, CO, ALK4, ISOP, HNO3, H2O2, ACET, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, CHBr3, CHBr2, CH3Br, MPN, ISOPN, MOBA, PROPNN, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO2, NO3, HNO2, N2O, OCS, CH4, BrCl, HCl, CCl4, CH3Cl, CH2CCl3, CFCX, HCFCX, CFC11, CFC12, HCFC22, H1211, H1301, H2402 Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, H2O, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG3, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, ISOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, BENZ, TOLU, XYLE, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3, OH, HO2
Comments on ZONAL MEAN differences:
  • Observed differences in tracer concentrations can be attributed to differences between GEOS-FP and MERRA-2
  • See additional comments below for useful links comparing these two met fields.
In the EMISSION RATIO maps, list all species that changed by 10% or more:
  • Anthro + biofuel: NO
  • Biogenic: ACET, ALD2, DMS, ISOP, PRPE
  • ACET from MONOT, ACET from MBO, ACET direct, ACET ocean source
  • CO from MONOT
  • DST1, DST2, DST3, and DST4 emissions
  • NO fertilizer emissions, NO soil emissions, NO lightning emissions
  • SALA and SALC emissions
Comments on EMISSION RATIO differences:
  • Changes in most emissions can be attributed to the differences in the GEOS-FP and MERRA-2 met fields.
    • The dust and sea-salt tracers are very sensitive to the 10-m wind speed
    • The biogenic emissions are sensitive several met fields, including T2M, PARDF, PARDR, GWETROOT, and SUNCOS
    • The fertilizer and soil NOx emissions are sensitive to several met fields, including T2M, GWETTOP, SUNCOS, U10M, and V10M
  • Differences in anthropogenic NO emissions are concentrated over the oceans. Changes in ship emissions may result from slight changes in NO or NO2 concentrations.
Additional or summary comments: Summary:

This benchmark can be used to evaluate the differences caused by running GEOS-Chem with GEOS-FP or MERRA-2 meteorology. GEOS-FP met fields for July 2013 are based on GEOS-5.11.0 from GMAO, while MERRA-2 is based on GEOS-5.12.4. For more information, see these useful links:

We also invite you to view benchmark plots comparing select 2D and 3D met fields for GEOS-FP and MERRA-2, which are contained in file
http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01f.tar.gz

  • v11-01f-merra2.2d_met_differences.dyn_range.pdf: Differences in 2D met fields
  • v11-01f-merra2.3d_met_differences.dyn_range.pdf: Differences in 3D met fields

A note about increased "wall clock" run times:

For an explanation of the increase in "wall-clock" run times, please see the "Additional or Summary Comments" section of the v11-01f benchmark with GEOS-FP.

Other observations:

  • Chris Holmes noted, "Most photolysis rates are 10-50% faster at the surface and 0-20% slower at 500 hPa in MERRA-2 compared to GEOS-FP." The J-value differences can be attributed to differences in the cloud fraction and cloud optical depth fields between GEOS-FP and MERRA-2 as observed in the new cloud difference benchmark plots.
Approval
Requires further investigation: No
Approved by: Daniel Jacob
Date of approval: 29 Mar 2016

--Melissa Sulprizio (talk) 15:15, 22 March 2016 (UTC)

v11-01e

Here is the assessment form for 1-month benchmark simulation v11-01e.

Description
New features added into GEOS-Chem:

Features affecting the full-chemistry simulation in this benchmark:

Features not affecting the full-chemistry simulation in this benchmark:

Developer name(s) and institution(s):
  • HEMCO update: Christoph Keller (Harvard)
  • netCDF read frequency: Bob Yantosca (GCST)
  • Arctic Hg: Jenny Fisher (Wollongong)
  • Air quantity bug fix: Lizzie Lundgren (GCST)
  • Species Units Phase 1: Lizzie Lundgren (GCST)
  • MERRA-2 nested simulations: Melissa Sulprizio (GCST)
  • Species Database Phase 2a: Bob Yantosca (GCST)
  • Species Database Phase 2b: Bob Yantosca (GCST)
Version, resolution, met fields used: v11-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Fri Dec 18 01:54:44 EDT 2015
Performance statistics:
  • Ran on 8 CPUs of regal12.rc.fas.harvard.edu (Intel(R) Xeon CPU E5-2660 0 @ 2.20 GHz)
  • Wall time: 04:16:08
  • CPU time / wall time: 6.4373
  • % of ideal performance: 80.47%
Compared to previous benchmark: v11-01d
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):
Unit test results may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01e.tar.gz
  • NOTE: Unit tests for tagged CO were not performed, since this simulation is not yet 100% compatible with HEMCO.
Plots may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01e.tar.gz
Metrics
Global mean OH (from log file): 12.6756714604872 x 105 molec/cm3
Methyl chloroform lifetime: 4.9388 years
Did either of these change by more than 5%? No. Mean OH changed by 0.0094% and MCF lifetime changed by -0.018%.
At the SURFACE, list all species that changed by 10% or more: ACET, N2O5, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, MPN, ISOPN, NO3, MTPA, LIMO, MTPO, ISOG2, ISOA2
Comments on SURFACE differences:
  • Updates to HEMCO resulted in small differences in ACET, DMS, MSA, and MPN.
  • Randomly distributed small differences in NH3 and NIT can be attributed to numerical drift caused by ISORROPIA.
  • Corrections in molecular weights of SO4s (from 96 to 31.4 g/mol) and NITs (from 62 to 31.4 g/mol) to match the molecular weight of SALC caused spatially uniform relative increases in those species.
  • All other differences can be attributed to small numerical differences when concentrations are very low.
At 500 hPa, list all species that changed by 10% or more:

DMS, SO4s, NH3, NIT, NITs, MTPA, LIMO, MTPO

Comments on 500 hPa differences:
  • See comments on surface differences.
In the ZONAL MEAN differences, list all species that changed by 10% or more: NO, ISOP, ACET, N2O5, DMS, SO2, SO4s, MSA, NH3, NIT, NO3, MTPO, LIMO
Comments on ZONAL MEAN differences:
  • With the HEMCO updates, several species changed over the northern pole (increases in ACET, N2O5, and NO3 and decreases in DMS, SO2, SO4s, and MSA) and NH3 increased over the northern latitudes.
  • Increases in zonal SO4s and zonal NITs in the PBL can be attributed to the change of their molecular weights.
  • All other differences can be attributed to small numerical differences when concentrations are very low.
In the EMISSION RATIO maps, list all species that changed by 10% or more:
  • ACET biogenic emissions
  • DMS biogenic emissions
  • NO fertilizer emissions.
Comments on EMISSION RATIO differences:
  • ACET biogenic emission decreased by 0.1385 Tg C and DMS biogenic emissions decreased by 0.0448 Tg C. All changes occurred at land edges due to the HEMCO updates where sea fluxes now use the HEMCO land mask instead of land fraction.
  • NO fertilizer emissions decreased by 0.0012 Tg N due to cumulative effects of new tracer concentration units.
Additional or summary comments:
  • The HEMCO updates caused small differences in some species in the PBL near the north pole and decreases in ACET and DMS biogenic emissions at the land edges.
  • Reducing the molecular weights of SO4s and NITs to match the molecular weight of seasalt caused increases in those species approximately proportional to the molecular weight reduction.
  • Updating tracer units throughout GEOS-Chem caused no noticeable differences except small changes in NO fertilizer emissions.
Approval
Requires further investigation: We do not think that v11-01e requires further investigation. The changes to most species are very small and the mean OH and MCF lifetime changed by about 0.01%.
Approved by: Daniel Jacob
Date of approval: January 4, 2016

--Lizzie Lundgren (talk) 21:05, 18 December 2015 (UTC)
--Bob Yantosca (talk) 19:38, 21 December 2015 (UTC)

v11-01d

Here is the assessment form for 1-month benchmark simulation v11-01d.

NOTE: The v11-01d 1-month benchmark results in this form included a quick fix for low Pb tropospheric lifetime against deposition in GEOS-FP and MERRA-2. Due to the high impact on aerosols, the GEOS-Chem Steering Committee rejected the quick fix. We have subsequently removed this fix from v11-01d and performed additional 1-year benchmark simulations with the updated model. The results below do not reflect the updated version of v11-01d except where specified.

Description
New features added into GEOS-Chem:

Features affecting the full-chemistry simulation in this benchmark:

Features not affecting the full-chemistry simulation in this benchmark:

Developer name(s) and institution(s):
  • CO2 inhibition: Amos Tai (CUHK)
  • Criegee intermediates: Dylan Millet (U. Minnesota), Eloïse Marais (Harvard)
  • GFED4.1: Prasad Kasibhatla (Duke), Christoph Keller (Harvard)
  • Wet dep fix for high concentrations: Viral Shah (UW)
  • Wet dep fix for low Pb lifetimes: Bo Zhang, Hongyu Liu (NIA / NASA Langley)
  • NEI2011 fix: Viral Shah (UW)
  • Brown carbon updates: Melanie Hammer (Dalhousie)
  • Species database: GCST
  • Tagged Ox fixes: GCST
  • Marine POA fix: GCST
  • Offline Dust Aerosols fix: Seb Eastham (Harvard)
Version, resolution, met fields used: v11-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Thu Oct 29 04:51:06 EDT 2015
Performance statistics:
  • Ran on 8 CPUs of holyseas02
  • Wall time: 10:41:39
  • CPU time / wall time: 6.1824
  • % of ideal performance: 77.28%
Compared to previous benchmark: v11-01c
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):
Unit test results may be downloaded from:: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01d.tar.gz
  • NOTE: Unit tests for tagged CO were not performed, since this simulation is not yet 100% compatible with HEMCO.
Plots may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01d.tar.gz
Metrics
Global mean OH (from log file):
  • 12.9458396071682 x 105 molec/cm3
  • Updated version without quick fix: 12.6744768934603 x 105 molec/cm3
Methyl chloroform lifetime:
  • 4.8665 years
  • Updated version without quick fix: 4.9397
Did either of these change by more than 5%?
  • No. The mean OH differs by 2.39%, and the MCF lifetime differs by -1.83%.
  • Updated version without quick fix: No. The mean OH differs by 0.245%, and the MCF lifetime differs by -0.349%.
At the SURFACE, list all species that changed by 10% or more: NO, PAN, CO, ALK4, ISOP, HNO3, H2O2, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO2, NO3, HNO2, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG3, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, ISOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, BENZ, TOLU, XYLE, ASOG1, ASOG2, ASOG3, ASOGAN, ASOA1, ASOA2, ASOA3, OH, HO2
Comments on SURFACE differences:
  • The biomass burning emissions update to GFED4.1 reduced the concentrations of species in the northern latitudes, particularly over Canada and northern Asia. These species include NO, PAN, CO, ALK4, HNO3, ACET, MEK, ALD2, RCHO, R4N2, PPN, PRPE, C3H8, CH2O, C2H6, N2O5, HNO4, SO2, SO4, NH3, NH4, NIT, BCPI, OCPI, BCPO, OCPO, MPN, ISOP, NO2, HNO2, TSOA0, TSOA2, TSOA3, ISOA1, ISOA2, and ISOA3. There are also increases in the northern latitudes for some species, including H2O2, MP, TSOG2, ASOAN, OH, and HO2.
  • The fix for reading hourly NEI2011 emissions reduced concentrations of species primarily over the United States. These species include: NO, ALK4, MEK, ALD2, RCHO, PPN, R4N2, C3H8, N2O5, DMS, OCPI, BCPO, OCPO, RIP, NO2, NO3, HNO2, TSOA2, TSOA3, ISOA2, ISOA3, BENZ, TOLU, XYLE, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, and ASOA3. Concentrations for NH3 and NIT decreased over the western part of the United States and increased over the eastern part.
  • The wet deposition quick fix caused widespread increase in concentrations for many species including all aerosols. Species impacted include: NO, ISOP, HNO3, H2O2, MVK, MACR, PMN, PPN, PRPE, N2O5, HNO4, DMS, SO2, SO4, SO4, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, DST1, DST2, DST3, DST4, SALC, SALA, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPN, GLYC, MMN, MOBA, RIP, IEPOX, NO2, NO3, HNO2, BrCl, HCl, Cl, ClO, ClNO3, HOCl, ClOO, OClO, Cl2, Cl202, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG3, TSOG0, TSOA1, TSOA2, TSOA2, TSOA3, TSOA0, ISOG1, ISOG2, ISOG3, ISOA1, ISOA3, TOLU, XYLE, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3, OH, and HO2.
  • The addition of Criegee intermediates resulted in widespread increases in MPN but concentrations are all low.
  • Randomly distributed small differences in NH3 and NIT can be attributed to numerical drift caused by ISORROPIA.
  • All other differences can be attributed to small numerical differences when concentrations are very low.
At 500 hPa, list all species that changed by 10% or more: NO, ALK4, ISOP, HNO3, H2O2, MEK, RCHO, MVK, MACR, PMN, R4N2, PRPE, C3H8, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO2, NO3, HNO2, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG3, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, ISOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, BENZ, TOLU, XYLE, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3, OH, HO2
Comments on 500 hPa differences:
  • See comments for surface differences above
In the ZONAL MEAN differences, list all species that changed by 10% or more: NO, PAN, ISOP, HNO3, H2O2, ALD2, MVK, MACR, PMN,PPN, PRPE, C3H8, N2O5, HNO4, MP,

DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, HAC, GLYC, MMN, IEPOX, MAP, NO2, NO3, HNO2, BrCl, HCl, Cl, ClO, HOCl, ClNO3, ClNO2, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG3, TSOG0, TSOA1, TSOA2, TSOA3, TSOA0, ISOG1, ISOG2, ISOG3, ISOA1, ISOA2, ISOA3, TOLU, XYLE, ASOG1, ASOG2, ASOG3, ASOAN, ASOA1, ASOA2, ASOA3, OH, HO2

Comments on ZONAL MEAN differences:
  • Most of the differences are explained by the wet deposition quick fix which impacted the troposphere.
  • Some of the decreases in the zonal mean in the upper latitudes is explained by the GFED and NEI updates.
In the EMISSION RATIO maps, list all species that changed by 10% or more:
  • Anthro emissions: BC, NH3, OC, SO2
  • Anthro + Biofuel emissions: ACET, ALD2, ALK4, C3H8, CH2O, CO, MEK, NO, PRPE, SO4
  • Biomass emissions: C2H6, BC, NH3, OC, ACET, ALD2, ALK4, C3H8, CH2O, CO, MEK, NO, PRPE, SO2
Comments on EMISSION RATIO differences:
Additional or summary comments:
  • The quick fix for wet deposition in GEOS-FP and MERRA-2 turns off scavenging of aerosol species where T < 258 K. As explained above, this attributes for some of the increased concentration of aerosol species above 500 hPa in the zonal mean ratio and difference plots.
Approval
Requires further investigation: Peter Adams writes:
The “quick fix” implemented by Hongyu to wet scavenging has significant effects on aerosols species. Most notably, free tropospheric levels of sulfate and black carbon increase by a factor of ~2. Changes in overall burdens are less, of course, but still significant.
With a change of this magnitude for aerosols, we would much rather proceed with something that has undergone some substantial vetting. Based on our communications with Hongyu, this is very much a “quick fix” – one that his group will be evaluating in much more detail in the next months. We all know that wet deposition lifetimes are the result of a bunch of contributing processes. As far as I can tell, we are not sure that making a change specifically to cold cloud scavenging pushes us in the right direction for the right reasons.
For these reasons, both Colette and I recommend removing – at least for now – Hongyu’s cold cloud fix until it gets more evaluation. To be clear, this is more for the sake of making significant changes to physics only after careful evaluation rather than clear-cut observational evidence that model predictions are better/worse with or without the fix.
Approved by: GCSC
Date of approval: 12 Dec 2015
  • v11-01d including Pb lifetime "quick fix" was not approved, and was removed from this benchmark. (see note above table)

--Lizzie Lundgren (talk) 16:47, 2 December 2015 (UTC)
--Bob Yantosca (talk) 19:17, 21 December 2015 (UTC)

v11-01c

Here is the assessment form for 1-month benchmark simulation v11-01c.

Description
New features added into GEOS-Chem:

Features affecting the full-chemistry simulation in this benchmark:

Features not affecting the full-chemistry simulation in this benchmark:

Developer name(s) and institution(s):
  • Sea salt alkalinity fix: Johan Schmidt (Harvard)
  • ND21 fix: Sebastian Eastham (MIT)
  • ND46 fix: Jared Brewer (CSU)
  • PAH updates: Carey Friedman (MIT)
  • Hg MLD fixes: Amanda Giang (MIT)
  • Hg ocean rates: Shaojie Song (MIT)
  • Hg Arctic updates: Jenny Fisher (Wollongong)
  • Hg emission updates: Yanxu Zhang (Harvard), Amanda Giang (MIT)
  • GEOS-5 OTD-LIS fix: Christoph Keller (Harvard), Lu Hu (Harvard)
  • Custom nested grid fix: Shannon Koplitz (Harvard), GCST
  • GC Timers: Matt Yannetti (GCST)
  • MERRA-2: Bob Yantosca (GCST)
Version, resolution, met fields used: v11-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Thu Sep 10 02:22:53 EDT 2015
Performance statistics:
  • Ran on 8 CPUs of holy2a11201
  • Wall time: 8:27:55
  • CPU time / wall time: 6.7299
  • % of ideal performance: 84.12%
Compared to previous benchmark: v11-01b
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): Diagnostics, Mercury simulation, POPs simulation
Unit test results may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01c.tar.gz
  • NOTE: Unit tests for tagged CO were not performed, since this simulation is not yet 100% compatible with HEMCO.
Plots may be downloaded from http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01c.tar.gz
Metrics
Global mean OH (from log file): 12.6434767011206 x 105 molec/cm3
Methyl chloroform lifetime: 4.9570 years
Did either of these change by more than 5%? No. The mean OH differs by -0.01%, and the MCF lifetime differs by 0.02%.
At the SURFACE, list all species that changed by 10% or more: HNO3, N2O5, SO2, SO4, SO4s, NH3, NH4, NIT, NITs
Comments on SURFACE differences:
At 500 hPa, list all species that changed by 10% or more: SO4s, NH3, NH4, NIT, NITs
Comments on 500 hPa differences:
  • See comments for SURFACE DIFFERENCES above.
In the ZONAL MEAN differences, list all species that changed by 10% or more: HNO3, SO2, SO4, SO4s, NH3, NH4, NIT, NITs, LIMO
Comments on ZONAL MEAN differences:
  • See comments for SURFACE DIFFERENCES above.
  • Differences in LIMO can be attributed to small number differences where concentrations are very low.
In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences:
  • Differences in MONX, APIN, BPIN, LIMO, SABI, MYRC, CARE, OCIM, OMON, FARN, BCAR, and OSQT in the v11-01c.emission.fullchem file are caused by the bug fix for the ND46 diagnostic.
Additional or summary comments:
  • The GEOS-5 Hg unit test return inconsistent differences in the HG-SRCE diagnostic and the ocean restart files when using multiple processors vs a single processor. For more information see this wiki post.
  • Peter Adams wrote:
Benchmarks look good to me. As Daniel noted, there are relatively large reductions in HNO3, SO2, sulfate in the oceans (esp SH) of around 25-50% - consistent with the described bug fix for sea salt alkalinity. There are very large (ratio) increases in sea-salt associated sulfate and nitrate (SO4s and NITs) that partly compensate. The absolute magnitude of the sulfate decrease is ~0.1 ug/m3 or less, so these are unlikely to change comparisons to obs much.
Approval
Requires further investigation: No
Approved by: Johan Schmidt, Peter Adams, Daniel Jacob
Date of approval: 14 Sep 2015

--Melissa Sulprizio (talk) 21:36, 11 September 2015 (UTC)

v11-01b

Here is the assessment form for 1-month benchmark simulation v11-01b.

Description
New features added into GEOS-Chem:

Features affecting the full-chemistry simulation in this benchmark:

Features not affecting the full-chemistry simulation in this benchmark:

Developer name(s) and institution(s):
  • Lana DMS: Tom Breider (Harvard)
  • Impaction scavenging for BCPO: Qiaoqiao Wang (Max Planck Institute)
  • Homogeneous IN removal: Qiaoqiao Wang (Max Planck Institute)
  • Density of OA: Melanie Hammer (Dalhousie), Eloïse Marais (Harvard)
  • Improved dust distribution: Li Zhang (Colorado U.), Daven Henze (Colorado U.)
  • Dust fix for wet scavenging: T. Duncan Fairlie (NASA/LARC)
  • globchem.dat fix: Dylan Millet (UMN)
  • UCX fix for BC: Sebastian Eastham
  • BrC UV absorption: Melanie Hammer (Dalhousie)
  • Acid uptake on dust: T. Duncan Fairlie (NASA/LARC)
  • Marine POA: Brett Gantt (NCSU), Matthew Johnson (NASA Ames)
  • RRTMG fixes: Sebastian Eastham (MIT), David Ridley (MIT)
  • PGI compiler fix: GEOS-Chem Support Team
Version, resolution, met fields used: v11-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Mon Jul 27 18:27:44 2015
Performance statistics:
  • Ran on 8 CPUs of bench@titan-10.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 7:56:50
  • CPU time / wall time: 6.7733
  • % of ideal performance: 84.67%
Compared to previous benchmark: v11-0a
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):
Unit test results may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01b.tar.gz
  • NOTE: Unit tests for tagged CO were not performed, since this simulation is not yet 100% compatible with HEMCO.
Plots may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01b.tar.gz
Metrics
Global mean OH (from log file): 12.6447244306942 x 105 molec/cm3
Methyl chloroform lifetime: 4.9562 years
Did either of these change by more than 5%? No. The mean OH differs by 0.57%, and the MCF lifetime differs by -0.73%.
At the SURFACE, list all species that changed by 10% or more: NO, 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, NIT, NITs, BCPI, OCPI, BCPO, OCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO2, NO3, HNO2, BrCl, Cl, ClO, HOCl, ClNO3, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, TSOG1, TSOG3, TSOG0, TSOA1, TSOA2, TSOA3, ISOG2, ISOA1, ISOA2, ISOA3, BENZ, TOLU, XYLE, ASOAN, ASOA1, ASOA2, ASOA3, OH, HO2
Comments on SURFACE differences:
  • Differences in NO, PAN, ALK4, ISOP, R4N2, PRPE, C3H8, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, NO2, BrCl, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTOP, TSOG1, TSOG3, TSOA1, TSOA2, TSOA3, TSOA0, ISOA1, XYLE, ASOAN, ASOA1, ASOA2, and ASOA3 over oceans or the poles are mainly small number differences where concentrations are very low, especially ISOP and its related species
  • The impaction scavenging for hydrophobic BC and homogeneous IN removal updates contributes to changes in N2O5, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, SALA, SALC, Br2, Br, BrO, HBr, BrNO3, Cl, TSOG0, TSOA0-3, ISOA1-3, ASOG1, ASOAN, ASOA1-3.
  • The update to the dust size distribution scheme causes a decrease in DST1 and DST2 concentrations and an increase in DST4 concentrations.
  • The fix for the treatment of dust in wet deposition also impacts the dust tracers, contributing to the decrease in DST2 and DST3 concentrations. In addition, this update causes a decrease in column AOD for dust over Africa, which leads to differences over Africa for the following tracers: H2O2, ALD2, RCHO, MVK, MACR, PMN, PPN, PRPE, N2O5, HNO4, MP, DMS, SO2, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO3, HNO2, BrCl, Cl, ClO, HOCl, ClNO3, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, TOLU, XYLE, OH, HO2.
  • The update to Lana DMS climatology causes differences over the oceans in the following tracers: HNO3, MVK, MACR, PMN, PPN, CH2O, N2O5, DMS, SO2, SO4, SO4s, MSA, and NH3, NH4, NIT, NITs, Br2, BrNO3, MPN, ISOPN, MOBA, RIP, IEPOX, NO2, NO3, HNO2, MTPA, LIMO, MTPO. Some of these tracers are also impacted by the dust changes listed above.
At 500 hPa, list all species that changed by 10% or more: NO, ALK4, ISOP, HNO3, H2O2, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, Br, BrO, HOBr, HBr, BrNO2, BrNO3, MPN, ISOPN, MOBA, HAC, GLYC, MMN, RIP, IEPOX, MAP, NO3, HNO2, BrCl, HOCl, ClNO2, OClO, Cl2, MTPA, LIMO, MTPO, TSOG1, TSOG0, TSOA1, TSOA2, TSOA3, ISOG1, ISOG2, ISOA1, ISOA2, ISOA3, TOLU, XYLE, ASOG1, ASOG2, ASOAN, ASOA1, ASOA2, ASOA3, OH, HO2
Comments on 500 hPa differences: See comments for SURFACE DIFFERENCES above.
In the ZONAL MEAN differences, list all species that changed by 10% or more: ISOP, HNO3, H2O2, MVK, MACR, PMN, PRPE, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, DST1, DST2, DST3, DST4, SALA, SALC, Br2, HOBr, HBr, BrNO3, ISOPN, MOBA, MMN, RIP, NO3, HNO2, Cl, HOCl, ClOO, MTPA, LIMO, MTPO, TSOG1, TSOG2, TSOG3, TSOG0, TSOA1, TSOA2, TSOA3, TSOAO, ISOG1, ISOG2, ISOG3, ISOA1, ISOA2, ASOG1, ASOG2, ISOA3, ASOG3, ASOGAN, ASOA1, ASOA2, ASOA3, OH, HO2
Comments on ZONAL MEAN differences:
  • Differences in BCPO in the stratosphere are due to the fix for black carbon in ucx_mod.
  • For all other differences, see comments for SURFACE DIFFERENCES above.
In the EMISSION RATIO maps, list all species that changed by 10% or more:
  • Biogenic emissions: DMS
  • Dust emissions: DST1, DST2, DST4
Comments on EMISSION RATIO differences:
Additional or summary comments:
  • The change in organic aerosol density for calculating aerosol optical depth was expected to cause a 40% increase in organic carbon AOD. This consistent with the v11-01b AOD plots for OC.
Approval
Requires further investigation: No
Approved by: GCST, Eloise Marais, Tom Breider, Daniel Jacob
Date of approval: 04 Aug 2015

--Lizzie Lundgren (talk) 19:16, 30 July 2015 (UTC)
--Melissa Sulprizio (talk) 22:01, 30 July 2015 (UTC)

v11-01a

Here is the assessment form for 1-month benchmark simulation v11-01a.

Description
New features added into GEOS-Chem:

Features affecting the full-chemistry simulation in this benchmark:

Features not affecting the full-chemistry simulation in this benchmark:

Developer name(s) and institution(s):
Version, resolution, met fields used: v11-01, GEOS-FP (72L), 4x5, July 2013
1-month benchmark finished on: Thurs Jul 02 00:00:12 EDT 2015
Performance statistics:
  • Ran on 8 CPUs of bench@titan-10.as.harvard.edu (2.659 GHz x 8 CPU)
  • Wall time: 7:46:50
  • CPU time / wall time: 6.8812
  • % of ideal performance: 86.01%
Compared to previous benchmark: v10-01-public-release with SOA on
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): Tracer Unit Conversions, Air Quantities (e.g. box height and air mass), RRTMG
Unit test results may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01a.tar.gz
  • NOTE: Unit tests for tagged CO were not performed, since this simulation is not yet 100% compatible with HEMCO.
Plots may be downloaded from: http://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v11-01/v11-01a.tar.gz
Metrics
Global mean OH (from log file): 12.5726451325898 x 105 molec/cm3
Methyl chloroform lifetime: 4.9926 years
Did either of these change by more than 5%? No. The mean OH differs by 0.50%, and the MCF lifetime differs by -0.58%.
At the SURFACE, list all species that changed by 10% or more: NO, ISOP, HNO3, MVK, MACR, PMN, N2O5, NH4, NIT, NITs, OCPO, DST1, DST2, DST3, DST4, Br, BrO, HOBr, ISOPN, MOBA, GLYC, MMN, RIP, IEPOX, BrCl, Cl, ClO, ClNO2, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, ASOA2, ASOA3
Comments on SURFACE differences:
  • All differences are small number differences where concentrations are very low and may be attributed to numerical noise.
    • Especially ISOP and its related species
At 500 hPa, list all species that changed by 10% or more: NO, ISOP, MVK, MACR, PMN, PRPE, NH3, NIT, OCPO, DST3, DST4, Br, ISOPN, MOBA, GLYC, RIP, IEPOX, BrCl, Cl, ClO, ClNO2, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO
Comments on 500 hPa differences:
  • Small differences in NH3 and NIT can be attributed to numerical drift caused by ISORROPIA.
  • All other differences are small number differences where concentrations are very low and therefore can be attributed to numerical noise.
    • Especially ISOP and its related species
In the ZONAL MEAN differences, list all species that changed by 10% or more: NO, ALK4, ISOP, HNO3, MVK, MACR, PMN, PRPE, C3H8, N2O5, SO4s, NH3, NIT, NITs, BCPO, OCPO, DST1, DST2, DST3, DST4, SALC, Br, HBr, BrNO3, ISOPN, MOBA, GLYC, MMN, RIP, IEPOX, OCS, BrCl, CCl4, CH3CCl3, CFC11, H1211, H1301, H24O2, Cl, ClO, ClNO2, ClOO, OClO, Cl2, Cl2O2, MTPA, LIMO, MTPO, ISOA2, TOLU,
Comments on ZONAL MEAN differences:
  • NO, Br, HBr, Cl, ClO, ClOO: Differences for these species are around the South Pole only and reflect small number differences where concentrations are very low.
  • C3H8, N2O5, Br2, BrNO3, HAC, OCS, CCl4, CH3CCl3, CFC11, H1211, H1301, H2402: Differences for these species are in the top few pressure levels only. The small differences occur where concentrations are very low and therefore are attributable to numerical noise.
  • ALK4, PRPE, SO4s, NIT, NITs, BCPO, SALC, TOLU: Differences for these species are only within the stratosphere. The small number differences occur only where concentrations are very low and therefore are attributable to numerical noise.
  • ISOP, HNO3, MVK, MACR, PMN, OCPO, DST1, DST2, DST3, DST4, ISOPN, MOBA, GLYC, MMN, RIP, IEPOX, BrCl, Cl202, Cl2, ClNO2, OClO, Cl2, MTPA, LIMO, MTPO: All differences for these species reflect small number differences where concentrations are very low.
  • Small differences in NH3 and NIT may be attributed to numerical drift caused by ISORROPIA.
  • Some species (NO2, CH4, H2O, OH) show nonzero absolute differences but percent differences less than +/-10%. These are likely caused by the air quantity moisture fixes.
In the EMISSION RATIO maps, list all species that changed by 10% or more: None
Comments on EMISSION RATIO differences:
  • The emission totals for NO changed slightly for several sources: soil and fertilizer (both by -0.000030 Tg N), anthropogenic + biomass burning (by 0.000081 Tg N), and lightning (by 0.005719 Tg N).
-We believe that the small changes in soil NO emissions are due to changes in the atmospheric concentrations associated with the air quantity moisture fixes since these NO emissions are dependent on NOy deposition.
-The small changes in lightning NO emissions appear to arise from the effects of air quantity moisture fixes on variables such as derived cloud top height that affect the lightning parametrization.
-The small changes in anthropogenic + biofuel NO emissions are due to changes in NOx concentrations from the moisture updates feeding back into PARANOX and therefore affecting ship NO emissions. In addition, PARANOX uses air volume and air volume values changed slightly in the new release due to a bug fix in box height.
  • The emission totals for hydrophilic tracer from hydrophobic tracer changed slightly for black carbon (by -0.004145 Tg C) and organic carbon (by -0.012820 Tg C).
Additional or summary comments:
  • The air quantity updates most strongly impact long-lasting tracers such as carbon dioxide for which transport processes dominate. For this reason, the Carbon Working Group has independently evaluated the proposed changes and are incorporating them into the Adjoint model. We therefore recommend that GEOS-Chem users run v11-01 rather than v10-01 for methane and carbon dioxide simulations.
Approval
Requires further investigation: September 3, 2015 update: Version 11-01a dry mixing ratios show a moisture artefact while tracer total mixing ratios [kg/kg] do not show a moisture artefact. There is debate over which mixing ratio, dry or total, should show the moisture artefact.

Legacy versions of GEOS-Chem appear to rely on an implicit assumption of the "same" mixing ratio throughout, including input, output, and transport. Given that total air mass is used for conversions, we assume this "same" mixing ratio is total mixing ratio. Given that (1) legacy versions of GEOS-Chem use the "same" mixing ratio for transport and input/output, and (2) mixing ratios in legacy versions of GEOS-Chem do not show a moisture signature, then it makes sense that we now see a moisture signature in the input/output dry mixing ratio but not the total mixing ratio. This is because the tracer mass distribution is driven by transport not the restart file concentration.

To address this issue, we will change input and output to be total mixing ratio and use total air rather than dry air molecular weight to extract moles from total mixing ratio where necessary. This will make v11-01a consistent with legacy GEOS-Chem while correcting the mixing ratio to mass unit conversion error that was the primary motivation for v11-01a. This change will be incorporated into a future v11-01 version. The Carbon and Transport Working Groups will look into the issue of the moisture signature in dry vs. total mixing ratio and provide a recommendation.

Approved by: GCST
Date of approval: July 7, 2015

--Lizzie Lundgren (talk) 18:00, 3 September 2015 (UTC)

1-year Rn-Pb-Be benchmarks

v11-01i-RnPbBe

Two 1-year Rn-Pb-Be simulations were performed using GEOS-Chem v11-01i. The simulations utilized 4° x 5° GEOS-FP met fields for the year 2013, with a 4-year spinup. For comparison of the Pb-210 and Be-7 budgets to previous versions, please see the following posts on the Rn-Pb-Be simulation wiki page:

  1. Budget of Pb210 from 1-year benchmark simulations
  2. Budget of Be7 from 1-year benchmark simulations

**New in v11-01** We now include a passive tracer to test for mass conservation in the transport algorithm. The new passive tracer revealed that mass is not conserved when the non-local PBL mixing scheme (VDIFF) is turned on. To track this issue, we have completed 1-year Rn-Pb-Be simulations with and without non-local PBL mixing.

You may view the benchmark plots for the simulation by pointing your browser to the following links.

Using the non-local PBL mixing scheme (VDIFF):
http://people.fas.harvard.edu/~geoschem/1yr_benchmarks/v11-01i/RnPbBePasv/RnPbBePasv_VDIFF/output/

Using the full PBL mixing scheme (TURBDAY):
http://people.fas.harvard.edu/~geoschem/1yr_benchmarks/v11-01i/RnPbBePasv/RnPbBePasv_TURBDAY/output/

--Melissa Sulprizio (talk) 17:04, 18 October 2016 (UTC)

v11-01h-RnPbBe

Two 1-year Rn-Pb-Be simulations were performed using GEOS-Chem v11-01h. The simulations utilized 4° x 5° GEOS-FP met fields for the year 2013, with a 4-year spinup. For comparison of the Pb-210 and Be-7 budgets to previous versions, please see the following posts on the Rn-Pb-Be simulation wiki page:

  1. Budget of Pb210 from 1-year benchmark simulations
  2. Budget of Be7 from 1-year benchmark simulations

**New in v11-01** We now include a passive tracer to test for mass conservation in the transport algorithm. The new passive tracer revealed that mass is not conserved when the non-local PBL mixing scheme (VDIFF) is turned on. To track this issue, we have completed 1-year Rn-Pb-Be simulations with and without non-local PBL mixing.

You may view the benchmark plots for the simulation by pointing your browser to the following links.

Using the non-local PBL mixing scheme (VDIFF):
http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01h/RnPbBePasv/RnPbBePasv_VDIFF/output/

Using the full PBL mixing scheme (TURBDAY):
http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01h/RnPbBePasv/RnPbBePasv_TURBDAY/output/

--Melissa Sulprizio (talk) 20:36, 30 September 2016 (UTC)

v11-01f-RnPbBe

Four 1-year Rn-Pb-Be simulations were performed using GEOS-Chem v11-01f. The simulations utilized 4° x 5° GEOS-FP met fields for the year 2013, with a 4-year spinup. For comparison of the Pb-210 and Be-7 budgets to previous versions, please see the following posts on the Rn-Pb-Be simulation wiki page:

  1. Budget of Pb210 from 1-year benchmark simulations
  2. Budget of Be7 from 1-year benchmark simulations

**New in v11-01** We now include a passive tracer to test for mass conservation in the transport algorithm. The new passive tracer revealed that mass is not conserved when the non-local PBL mixing scheme (VDIFF) is turned on. To track this issue, we have completed 1-year Rn-Pb-Be simulations with and without non-local PBL mixing.

You may view the benchmark plots for the simulation by pointing your browser to the following links.

Using GEOS-FP and the non-local PBL mixing scheme (VDIFF):
http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01f/GEOSFP/RnPbBe/RnPbBePasv_VDIFF/output/

Using GEOS-FP and the full PBL mixing scheme (TURBDAY):
http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01f/GEOSFP/RnPbBe/RnPbBePasv_TURBDAY/output/

We also validated MERRA-2 with the Rn-Pb-Be simulation in this version.

Using MERRA-2 the non-local PBL mixing scheme (VDIFF):
http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01f/MERRA2/RnPbBe/RnPbBePasv_VDIFF/output/

Using MERRA-2 the full PBL mixing scheme (TURBDAY):
http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01f/MERRA2/RnPbBe/RnPbBePasv_TURBDAY/output/

--Melissa Sulprizio (talk) 22:45, 7 March 2016 (UTC)

v11-01d-RnPbBe

Two 1-year Rn-Pb-Be simulations were performed using GEOS-Chem v11-01d. The simulations utilized 4° x 5° GEOS-FP met fields for the year 2013, with a 4-year spinup. For comparison of the Pb-210 and Be-7 budgets to previous versions, please see the following posts on the Rn-Pb-Be simulation wiki page:

  1. Budget of Pb210 from 1-year benchmark simulations
  2. Budget of Be7 from 1-year benchmark simulations

**New in v11-01** We now include a passive tracer to test for mass conservation in the transport algorithm. The new passive tracer revealed that mass is not conserved when the non-local PBL mixing scheme (VDIFF) is turned on. To track this issue, we have completed 1-year Rn-Pb-Be simulations with and without non-local PBL mixing.

You may view the benchmark plots for the simulation by pointing your browser to the following links.

NOTE: The original v11-01d benchmark included a quick fix for low Pb tropospheric lifetime against deposition in GEOS-FP and MERRA-2. Due to the high impact on aerosols, the GEOS-Chem Steering Committee rejected the quick fix. We have subsequently removed this fix from v11-01d and performed additional 1-year benchmark simulations with the updated model.

Rn-Pb-Be benchmark results for v11-01d after removal of the quick fix:

Using the non-local PBL mixing scheme (VDIFF):
http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01d/RnPbBe/RnPbBePasv_VDIFF/output/

Using the full PBL mixing scheme (TURBDAY):
http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01d/RnPbBe/RnPbBePasv_TURBDAY/output/

Initial Rn-Pb-Be benchmark plots for v11-01d including the quick fix:

http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01d/RnPbBe/RnPbBe_wQuickFix/output/

--Melissa Sulprizio (talk) 17:41, 4 December 2015 (UTC)

v11-01b-RnPbBe

A 1-year Rn-Pb-Be simulation was performed using GEOS-Chem v11-01b. The simulation utilized 4° x 5° GEOS-FP met fields for the year 2013, with a 4-year spinup. For comparison of the Pb-210 and Be-7 budgets to previous versions, please see the following posts on the Rn-Pb-Be simulation wiki page:

  1. Budget of Pb210 from 1-year benchmark simulations
  2. Budget of Be7 from 1-year benchmark simulations

You may view the benchmark plots for the simulation by pointing your browser to:

http://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v11-01/v11-01b/RnPbBe/output/

Comments about the 1-year benchmark v11-01b-RnPbBe

Daniel Jacob wrote:

Hongyu, please check out the 15-20% decreases in Pb and Be tropospheric lifetimes against deposition due to scavenging of water-soluble aerosol from cold clouds in 11.1b. Be seems to be improved with reference to your canonical 2001 budget but the Pb loading is 25% lower. What do you think?

Hongyu Liu wrote:

The tropospheric 210Pb lifetime against deposition of 6.6 days (G-C/GEOS-FP) is the shortest among G-C versions. Switching from GEOS-5 to GEOS-FP met fields (v9-02r) reduced 210Pb lifetime from 9.3 to 7.7 days. See: http://wiki.seas.harvard.edu/geos-chem/index.php/Rn-Pb-Be_simulation#Budget_of_Pb210.
If v11-01b had been driven by GEOS-5, the 210Pb lifetime may very well be ~8 days.
Wang, Q. et al. [2014] used G-C/GEOS-5 and "find a lifetime of tropospheric 210Pb aerosol against deposition of 8.6 days, as compared to a best estimate of 9 days constrained by observations [Liu et al., 2001]." So it appears that the short 210Pb lifetime (6.6 days) in v11-01b is largely due to switching to GEOS-FP. Wet deposition needs to be re-evaluated and tuned for GEOS-FP.

--Melissa Sulprizio (talk) 13:49, 19 August 2015 (UTC)

1-year Hg benchmarks

A 1-year Hg benchmark (2009, 4x5) was performed by Jenny Fisher for comparing v11-01e against v9-02. A complete set of benchmark plots are available at:

http://ftp.as.harvard.edu/gcgrid/geos-chem/Hg_benchmarks/Hg_benchmark_v11-01c/

Additional information about Hg benchmark simulations can be found on the Mercury wiki page.

--Melissa Sulprizio (talk) 21:58, 1 February 2017 (UTC)