https://wiki.seas.harvard.edu/geos-chem/api.php?action=feedcontributions&user=Psk9&feedformat=atomGeos-chem - User contributions [en]2024-03-29T13:20:44ZUser contributionsMediaWiki 1.24.2https://wiki.seas.harvard.edu/geos-chem/index.php?title=Machine_learning_related_to_GEOS-Chem&diff=41772Machine learning related to GEOS-Chem2019-05-16T20:27:43Z<p>Psk9: </p>
<hr />
<div>All users interested in the use of Machine Learning within the GEOS-Chem community are encouraged to subscribe to the machine learning email list (click on the link in the [[#Contact information|contact information section]] below).<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-valign="top"<br />
!width="300px" bgcolor="#CCCCCC"|Machine Learning in GEOS-Chem support<br />
|width="600px"|<br />
*[http://www.york.ac.uk/chemistry/staff/academic/d-g/evansm/ Mat Evans]<br />
*[https://sciences.gsfc.nasa.gov/sed/bio/christoph.a.keller Christoph Keller]<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|GEOS-Chem Machine Learning email list<br />
|<tt>geos-chem-ml [at] g.harvard.edu</tt><br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|To subscribe to email list<br />
|Either<br />
*Send an email to <tt>geos-chem-ml+subscribe [at] g.harvard.edu</tt><br />
Or<br />
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-ml GEOS-Chem Machine Learning]<br />
*Click on '''Subscribe to this group'''<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|To unsubscribe from email list<br />
|Either<br />
*Send an email to <tt>geos-chem-ml+unsubscribe [at] g.harvard.edu</tt><br />
Or<br />
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-ml GEOS-Chem Machine Learning]<br />
*Click on the '''My Settings''' button<br />
*Click on '''Leave this group'''<br />
<br />
|}<br />
<br />
<br />
== GEOS-Chem Machine Learning Publications ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!width="150px"|Contact Persons<br />
!width="600px"|Paper<br />
!width="100px"|Date Added<br />
|-<br />
|[mailto:christoph.a.keller@nasa.gov Christoph Keller] <br> [mailto:mat.evans@york.ac.uk Mat Evans]<br />
|[https://www.geosci-model-dev.net/12/1209/2019/gmd-12-1209-2019.html Application of random forest regression to the calculation of gas-phase chemistry within the GEOS-Chem chemistry model v10]<br />
|14th May 2019<br />
|-<br />
|[mailto:samsilva@mit.edu Sam Silva] <br> [mailto:heald@mit.edu Colette Heald]<br />
|[https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2018GL081049 A Deep Learning Parameterization for Ozone Dry Deposition Velocities]<br />
|14th May 2019<br />
|-<br />
|[mailto:tomas.sherwen@york.ac.uk Tomas Sherwen] <br> [mailto:mat.evans@york.ac.uk Mat Evans]<br />
|[https://www.earth-syst-sci-data-discuss.net/essd-2019-40/ A machine learning based global sea-surface iodide distribution]<br />
|14th May 2019<br />
|}<br />
<br />
<br />
== Current GEOS-Chem Machine Learning Projects ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!width="200px"|User Group <br />
!width="600px"|Description <br />
!width="150px"|Contact Person<br />
!width="100px"|Date Added<br />
|-<br />
|University of York <br />
|Post processing bias corrector <br />
|[mailto:pi517@york.ac.uk Peter Ivatt]<br>[mailto:mat.evans@york.ac.uk Mat Evans]<br />
|14th May 2019<br />
|-<br />
|Duke University<br />
|Ozone metrics predictor<br />
|[mailto:psk9@duke.edu Prasad Kasibhatla]<br />
|14th May 2019<br />
|-<br />
|University of York <br />
|Spatial and temporal concentration prediction from sparse observations at the ocean surface<br />
|[mailto:tomas.sherwen@york.ac.uk Tomás Sherwen]<br />
|14th May 2019<br />
|-<br />
|NASA GMAO<br />
|GEOS-Chem emulator within the GEOS model<br />
|[mailto:christoph.a.keller@nasa.gov Christoph Keller]<br />
|16th May 2019<br />
|}<br />
<br />
== Useful resources ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!width="300px"|Resource<br />
!width="600px"|Description <br />
|-<br />
|[https://en.wikipedia.org/wiki/Machine_learning Wikipedia Page]<br />
|Default Wikipedia ML launch page<br />
|-<br />
|[https://www.tensorflow.org Google Tensor Flow]<br />
|Google's Machine Learning package<br />
|-<br />
|[https://pytorch.org/ PyTorch]<br />
|Open-source deep learning platform<br />
|-<br />
|[https://scikit-learn.org/stable/ Scikit-Learn]<br />
|Scikit-Learn package for machine learning in Python<br />
|-<br />
|[https://xgboost.readthedocs.io/en/latest/ XGboost]<br />
| Machine learning algorithms implemented under the Gradient Boosting framework in Python<br />
|-<br />
|[https://lightgbm.readthedocs.io/en/latest/ GBMLight]<br />
| Microsofts' distributed high-performance gradient boosting implementation<br />
|-<br />
|[https://rapids.ai/ RAPIDS]<br />
| NVIDIA's software package for GPU-accelerated data analytics and machine learning<br />
|}<br />
<br />
== Upcoming conferences / workshops ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!width="300px"|Conference<br />
!width="600px"|Date<br />
|-<br />
|[https://www.rmets.org/event/atmospheric-science-conference-2019 Machine Learning in Earth Systems workshop at NCAS'/RMetS' Atmospheric Science Conference 2019]<br />
|2-3rd July 2019<br />
|-<br />
|[http://users.ox.ac.uk/~phys0895/mlwc2019/index.html Machine Learning for Weather and Climate Modelling 2019]<br />
|2-5th Sept 2019<br />
|-<br />
|[https://www2.acom.ucar.edu/workshop/fascinate-2019 Frontiers of Atmospheric Science and Chemistry: Integration of Novel Applications and Technological Endeavors (FASCINATE)]<br />
|9-11th Sept 2019<br />
|-<br />
|[https://meetings.agu.org/fall-meeting-2019/ AGU Fall 2019]<br />
|9-13th Dec 2019<br />
|}</div>Psk9https://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_v9-01-03_benchmark_history&diff=10561GEOS-Chem v9-01-03 benchmark history2012-05-18T20:09:17Z<p>Psk9: /* v9-01-03l */</p>
<hr />
<div>On this page we have posted complete information about all benchmark simulations (both 1-month and 1-year) for [[GEOS-Chem v9-01-03]].<br />
<br />
== 1-year benchmarks ==<br />
<br />
=== v9-01-03e ===<br />
<br />
==== Run0 ====<br />
<br />
Three GEOS-Chem model versions were compared to each other:<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|- bgcolor="#CCCCCC"<br />
!Color <br />
!Quantity Plotted<br />
!Met Type<br />
!Anthro<br>emissions<br />
!Biofuel<br>emissions<br />
!Biomass<br>emissions<br />
!Wet deposition<br />
!Linoz<br />
!Annual Mean OH<br>[10<sup>5</sup> molec/cm3]<br />
<br />
|-align="center"<br />
|Red<br />
|[[GEOS-Chem v9-01-02 benchmark history#Run0|v9-01-02-Run0]]<br />
|GEOS-5, 4x5<br />
|Same as [[GEOS-Chem_v9-01-01_benchmark_history#Run0|v9-01-01-Run0]]<br>'''+ [[Carbon_Gases_and_Organics_Working_Group#GEIA_anthropogenic_scaling_factors|Fix for GEIA emissions scaling factor]]<br> + [[Anthropogenic_emissions#Streets_2000|Imposed seasonality on Streets 2000 NH3 emissions]]<br> + [[Ship_emissions#Bug_in_ship_NOx_emissions|Bug fix in ship NOx emissions]]'''<br />
|Same as [[GEOS-Chem_v9-01-01_benchmark_history#Run0|v9-01-01-Run0]] '''+ [[Anthropogenic_emissions#Bug_fix_for_Streets_biofuel_emissions|Bug fix for Streets biofuel emissions]]<br>'''<br />
|Same as [[GEOS-Chem_v9-01-01_benchmark_history#Run0|v9-01-01-Run0]]<br>([[Biomass_burning_emissions#GFED2|GFED2 monthly inventory]])<br />
|Same as [[GEOS-Chem_v9-01-01_benchmark_history#Run0|v9-01-01-Run0]]<br> (Original algorithm described in [http://acmg.seas.harvard.edu/geos/wiki_docs/deposition/wetdep.jacob_etal_2000.pdf Jacob et al <nowiki>[2000]</nowiki>]<br>+ [[Wet_deposition#Allow_both_washout_and_rainout_when_precipitation_forms|Allow both washout and rainout when precip. forms]]<br> + [[Wet_deposition#Updates_for_MERRA_met_fields|Updates for MERRA met fields]])<br />
|ON<br />
|12.233<br />
<br />
|-align="center"<br />
|Green<br />
|[[GEOS-Chem v9-01-02 benchmark history#Run1|v9-01-02-Run1]]<br />
|GEOS-5, 4x5<br />
|'''+ [[Implementation_of_RETRO_Anthropogenic_Emissions|RETRO anthropogenic VOC emissions]]<br />
|" "<br />
|'''+ [[Biomass_burning_emissions#GFED3|GFED3 monthly inventory]]'''<br />
|" "<br />
|ON<br />
|12.332<br />
<br />
|-align="center"<br />
|Blue<br />
|[[GEOS-Chem v9-01-03 benchmark history#Run0|v9-01-03e-Run0]]<br />
|GEOS-5, 4x5<br />
|" "<br />
|" "<br />
|" "<br />
|'''+ Improved [[Wet_deposition#Add_scavenging_by_snow|snow scavenging]] and [[Wet deposition#Updates for aerosol scavenging efficiency|washout parameterization]]<br />
|ON<br />
|11.935<br />
<br />
|-align="center"<br />
|Black <br />
|Observations<br />
|&nbsp; <br />
|&nbsp; <br />
|&nbsp;<br />
|&nbsp;<br />
|&nbsp;<br />
|&nbsp;<br />
!&nbsp;<br />
|}<br />
<br />
<br />
The output plots for Run1 (both PostScript and PDF format) may be downloaded from:<br />
<br />
ftp ftp.as.harvard.edu<br />
cd gcgrid/geos-chem/1yr_benchmarks/v9-01-03/v9-01-03e/geos5/2005/Run0/output/ps<br />
mget *<br />
cd gcgrid/geos-chem/1yr_benchmarks/v9-01-03/v9-01-03e/geos5/2005/Run0/output/pdf<br />
mget *<br />
<br />
You may also view the PDF files online by pointing your browser to<br />
<br />
ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v9-01-03/v9-01-03e/geos5/2005/Run0/output/pdf/<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 13:19, 1 February 2012 (EST)<br />
<br />
==== Rn-Pb-Be simulation ====<br />
<br />
We also conducted a 1-year [[Rn-Pb-Be simulation]] with GEOS-Chem v9-01-03e. Please follow the links below to see the budget of Pb210 and Be7 from 1-year Rn-Pb-Be simulations for v9-01-03e and previous versions:<br />
<br />
#[[Rn-Pb-Be simulation#Budget of Pb210 from 1-year benchmark simulations|Budget of Pb210 from 1-year benchmark simulations]]<br />
#[[Rn-Pb-Be simulation#Budget of Be7 from 1-year benchmark simulations|Budget of Be7 from 1-year benchmark simulations]]<br />
<br />
Plots comparing modeled Rn222, Pb210, and Be7 to [[GEOS-Chem v9-01-02]] are now available. The plotting programs were provided by [mailto:hongyu.liu-1@nasa.gov Hongyu Liu]. For more information on the plots, see [http://acmg.seas.harvard.edu/publications/liu2001.pdf Liu et al. <nowiki>[2001]</nowiki>].<br />
<br />
You may view the PDF files online by pointing your browser to:<br />
<br />
<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v9-01-03/v9-01-03e/geos5/2005/RnPbBe/output/pdf/</tt><br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:48, 24 January 2012 (EST)<br />
<br />
== 1-month benchmarks ==<br />
<br />
=== v9-01-03l ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03l'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Biomass burning emissions#GFED3 daily and 3-hourly emissions|Daily and 3-hourly GFED3 biomass emissions]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Prasad Kasibhatla (Duke) <br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Fri May 4 19:40:32 EDT 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-11-c.as.harvard.edu (2.660 GHz x 8 CPU) <br />
*Wall time: 1:43<br />
*Scalability: 7.6201<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03k|v9-01-03k]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, '''Biomass Emiss''', Photolysis, Chemistry, Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03l/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1174291218146 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7610 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|Various species at discrete locations<br />
|-<br />
|Comments on SURFACE differences: <br />
|Related to change in code to regrid on the fly from native GFED3 resolution to model grid<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|A few species at a few locations<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Some related to changes in surface; a bit puzzled by changes to a few species like NH3, NIT, and ISOP (one grid box over the Amazon), but likely related to changes to chemistry at surface caused by regridding change (ISOP) or in regions with very low concentratiomns (eg NIT) <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more: <br />
|ISOP, MVK, MACR, N2O5 at isolated latitudes, but more widespread changes in NIT and NH3<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|I think the changes in ISOP, MVK, etc are related to changes in chemistry caused by changes in regridding, but am a bit puzzled by NIT and NH3 changes.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|Some species at discrete locations<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|Due to changes associated with regridding on the fly from native GFED3 resolution<br />
|-<br />
|Additional or summary comments:<br />
|Note: Special benchmarks were also requested for (1) 3-hourly and (2) daily GFED3 biomass burning emissions. The benchmark plots for these simulations may be viewed at:<br />
#3-hourly GFED3: <tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03l.3h_GFED3/</tt><br />
#Daily GFED3: <tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03l.daily_GFED3/</tt><br />
Differences are consistent with Daily and 3-hourly variation in emisisons<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
!<br />
|-<br />
|Requires further investigation:<br />
No<br />
|- <br />
|Approved:<br />
Yes<br />
|-<br />
|Date of approval:<br />
18 May, 2012<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 17:33, 9 May 2012 (EDT)<br />
<br />
=== v9-01-03k ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03k'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Emissions overview#MAP_A2A regridding algorithm|Replace existing regridding routines with the MAP_A2A regridding package]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Matt Cooper (Dalhousie)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Wed Apr 25 14:48:08 EDT 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-05-c.as.harvard.edu (2.793 GHz x 16 CPU) <br />
*Wall time: 1:27<br />
*Scalability: 7.6049<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03j|v9-01-03j]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): '''We expect to see no changes from v9-01-03j'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03k/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1180503320529 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7607 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|NOx, PAN, ALK4, ISOP, HNO3, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, C3H8, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, OH<br />
|-<br />
|Comments on SURFACE differences: <br />
|For most species, small numerical noise where concentrations are low cause large percent differences. Absolute differences are generally small. Other species (ie HNO3, NOx) with large differences generally have a grid box with positive change next to box with similar negative change. This is due to slight shifts in location of some emissions under new regrid algorithm.<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ISOP, MEK, RCHO, MVK, MACR, PMN, PRPE, N2O5, DMS, SO2, SO4, NH3, NIT, BCPO, OCPO<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Small numerical noise where concentrations are low cause large percent differences. Absolute differences are generally small.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more: <br />
|ALK4, ISOP, MVK, MACR, PRPE, N2O5, NH3,NIT, OCPO<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Small numerical noise where concentrations are low cause large percent differences. Absolute differences are generally small.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|ACET, ALD2, ALK4, BC, C3H8, CH2O, ISOP, MEK, NH3, NOx, OC, PRPE, SO2, SO4<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|Small numerical noise where concentrations are low cause large percent differences. Absolute differences are generally small.<br />
|-<br />
|Additional or summary comments:<br />
|<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
!<br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|27 April 2012<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 14:45, 26 April 2012 (EDT)<br />
<br />
=== v9-01-03j ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03j'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Leaf area indices in GEOS-Chem#Implementation of an updated LAI code|Implementation of updated LAI code]]<br />
*[[Grid-independent_GEOS-Chem#Restructuring_of_GEOS-Chem_for_grid-independent_functionality|Grid-independent GEOS-Chem updates #2: Preliminary interface to link driving GCM]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''Updated LAI:'' [[GEOS-Chem Support Team]]<br />
*''Grid-independent GEOS-Chem:'' [[GEOS-Chem Support Team]]<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Fri Apr 13 15:02:26 EDT 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-10-c.as.harvard.edu (2.659 GHz x 8 CPU) <br />
*Wall time: 1:42<br />
*Scalability: 7.6407<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03i|v9-01-03i]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, '''Dry Dep''', Wet Dep, Stratosphere, Anthro Emiss, '''Biogenic Emiss''', Biomass Emiss, Photolysis, Chemistry, Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03j/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1149651381533 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7612 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|ISOP, MVK, MACR<br />
|-<br />
|Comments on SURFACE differences: <br />
|Differences are seen in ISOP in locations where concentrations are already very low (i.e. over oceans). MVK and MACR differences are presumably tied ot to the differences in ISOP. [[Leaf area indices in GEOS-Chem#Using Olson 1992 land map|As described in this wiki post]], we attribute these changes to the numerical differences caused by regridding leaf area index data from 0.5&deg; x 0.5&deg; native resolution (instead of from 1&deg; x 1&deg;, as was done in the past).<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ISOP, MVK, MACR, NH3, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Differences are seen in ISOP in locations where concentrations are already very low (i.e. over oceans). MVK and MACR differences are presumably tied to to the differences in ISOP. [[Leaf area indices in GEOS-Chem#Using Olson 1992 land map|As described in this wiki post]], we attribute these changes to the numerical differences caused by regridding leaf area index data from 0.5&deg; x 0.5&deg; native resolution (instead of from 1&deg; x 1&deg;, as was done in the past).<br />
<br />
Differences in NH3 and NIT are attributed to the [[ISORROPIA_II#Persistence_of_problem|Numerical noise issue in ISORROPIA II]].<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|ISOP, NH3, NIT <br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|ISOP shows % differences of about ~5% in places where concentrations are already very low. [[Leaf area indices in GEOS-Chem#Using Olson 1992 land map|As described in this wiki post]], we attribute these changes to the numerical differences caused by regridding leaf area index data from 0.5&deg; x 0.5&deg; native resolution (instead of from 1&deg; x 1&deg;, as was done in the past).<br />
<br />
Differences in NH3 and NIT are attributed to the [[ISORROPIA_II#Persistence_of_problem|Numerical noise issue in ISORROPIA II]].<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|Biogenic ACET, Biogenic ISOP, Biogenic PRPE<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|All of the above-mentioned species show differences, especially near coastlines. All of these species are computed by the [[MEGAN biogenic emissions]] module, which now takes in the leaf area indices regridded from 0.5&deg; x 0.5&deg;, [[Leaf area indices in GEOS-Chem#Using Olson 1992 land map|As described in this wiki post]]. We attribute the differences in these species to the numerical differences in the leaf area index data.<br />
|-<br />
|Additional or summary comments:<br />
|The updates added to v9-01-03j were made to primarily assist development of the [[Grid-independent GEOS-Chem]]. We needed to rewrite the leaf area index module in order to (1) remove obsolete ASCII data files that were prohibiting the grid-independent model from functioning efficiently, and (2) compute leaf area indices consistently by regridding them from the native resolution (in this case, 0.5&deg; x 0.5&deg;) instead of using leaf area index data at several different resolutions. Also, we have merged into the standard repository several updates from Mike Long that are necessary in order to have GEOS-Chem driven by the NASA/GEOS-5 GCM.<br />
<br />
We performed benchmark v9-01-03j with the [[Olson land map#Olson 1992 land map|Olson 1992 land map]] (which is the default in GEOS-Chem), and the [[MODIS leaf area indices]], both at 0.5&deg; x 0.5&deg; resolution. The updated LAI code introduced into v9-01-03j will eventually allow us to use higher resolution versions of both the Olson land map and the MODIS leaf area indices. This will be an important step that will facilitate GEOS-Chem nested-grid simulations 0.25&deg; x 0.25&deg;.<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
!<br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|17 Apr 2012<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 11:06, 17 April 2012 (EDT)<br />
<br />
=== v9-01-03i ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03i'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Grid-independent GEOS-Chem#Modifications to remove legacy code that hinders grid-indpendent functionality|Grid-independent GEOS-Chem updates #1: Fixes to facilitate implementation of grid-independent code]]<br />
*[[Implementation of RETRO Anthropogenic Emissions#RETRO anthropogenic ethane emissions are too low|Replace RETRO C2H6 emissions with emissions from offline C2H6 simulation]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''Grid-independent GEOS-Chem:'' [[GEOS-Chem Support Team]]<br />
*''Ethane:'' [[GEOS-Chem Support Team]]<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Thu Mar 22 18:19:43 EDT 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-11-c.as.harvard.edu (2.660 GHz x 8 CPU) <br />
*Wall time: 1:42<br />
*Scalability: 7.6384<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03h|v9-01-03h]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, '''Anthro Emiss''', Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03i/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1142905403284 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7616 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|PAN, ALD2, C2H6<br />
|-<br />
|Comments on SURFACE differences: <br />
|<br />
Concentrations of C2H6 increase 10-100% globally, except in eastern North America and coastal China. Typically, regional emission inventories overwrite the global emissions inventories; however, in this update, the C2H6 anthropogenic emissions overwrite has been removed for [[Anthropogenic emissions#EPA.2FNEI05|EPA/NEI2005]], [[Anthropogenic emissions#Streets 2006|Streets]], and [[Anthropogenic emissions#EMEP|EMEP]] because anthropogenic emissions of C2H6 were found to be [[Anthropogenic emissions#Anthropogenic ethane emissions are too low|too low in these regional inventories]]. Aside from decreases over eastern North America and coastal China, the offline C2H6 emissions improve concentrations over the rest of the North American and Asian regions.<br />
<br />
Smaller increases in PAN (~10%) and ALD2 (10-60%) are expected with an increase in C2H6, as C2H6 is a source of these species.<br />
<br />
''Note: Differences in NIT are numerical noise caused by [[ISORROPIA II#Optimization and.2For parallelization issues in ISORROPIA II|ISORROPIA]].''<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ALD2, C2H6<br />
|-<br />
|Comments on 500 hPa differences:<br />
|<br />
The changes at the surface propagate into the free troposphere for ALD2 and C2H6.<br />
<br />
''Note: Differences in NH3 and NIT are numerical noise caused by ISORROPIA.''<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|PAN, ALD2, C2H6<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|<br />
Patterns are consistent with the surface changes described above.<br />
<br />
''Note: Differences in NH3 and NIT are numerical noise caused by ISORROPIA.''<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|C2H6<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|There are widespread increases in anthropogenic emissions of C2H6 by as much as 100%. Decreases of up to 50% occur in some regions, primarily in regions where C2H6 anthropogenic emissions are low in the first place. Overall, this is an improvement from using RETRO C2H6 anthropogenic emissions, which were found to be too low.<br />
|-<br />
|Additional or summary comments:<br />
|<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
!<br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes (--[[User:Melissa Payer|Melissa Payer]] 12:22, 23 March 2012 (EDT))<br />
|-<br />
|Date of approval:<br />
|26 March 2012<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 17:49, 20 March 2012 (EDT)<br />
<br />
=== v9-01-03h ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03h'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Mercury#Hg.28II.29_gas-particle_partitioning|Hg(II) gas-aerosol partitioning]]<br />
*[[CO2_simulation#Nested-grid_CO2_simulation|Nested-grid CO2]]<br />
*[[Sources_and_Sinks_Working_Group#Available_Historical_and_Future_Emissions|Historical emission inventories of SO2, NOx, BC, and POA]]<br />
*[[CH4_simulation#Update_methane_emissions_and_add_capability_for_North_America_nested_grid|CH4 simulation updates]]<br />
*[[Overview of GMAO met data products#Removal of support for GEOS-3|Remove support for GEOS-3 meteorology]]<br />
*[[GEOS-Chem v9-01-03#Bug fix in streets_anthro_mod.F for offline simulations|Bug fix in streets_anthro_mod.F for offline simulations]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''Hg(II) partitioning:'' Helen Amos (Harvard)<br />
*''Nested-grid CO2'': Yuxuan Wang (Tsinghua)<br />
*''Historical emission inventories:'' Eric Leibensperger (MIT)<br />
*''CH4 simulation updates:'' Kevin Wecht (Harvard)<br />
*''Remove support for GEOS-3:'' [[GEOS-Chem Support Team]]<br />
*''Fix in streets_anthro_mod.F:'' Fabien Paulot<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Thu Mar 8 19:02:33 EST 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU) <br />
*Wall time: 1:40<br />
*Scalability: 7.6326<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03g|v9-01-03g]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): '''We expect to see no changes from v9-01-03g'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03h/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1255094316462 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7576 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|NIT<br />
|-<br />
|Comments on SURFACE differences: <br />
|Small numerical noise where concentrations are low cause large % differences. This is due to [[ISORROPIA_II#Optimization_and.2For_parallelization_issues_in_ISORROPIA_II|ISORROPIA]].<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Small numerical noise where concentrations are low cause large % differences. This is due to ISORROPIA.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NH3, NIT <br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Small numerical noise where concentrations are low cause large % differences. This is due to ISORROPIA.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None.<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|<br />
|-<br />
|Additional or summary comments:<br />
|To eliminate the effect from ISORROPIA, we re-ran 1-month benchmarks for v9-01-02g and v9-01-02h with ISORROPIA turned off. We have created [ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03h/v9-01-03h-2.freq_distribution.pdf this frequency distribution histogram plot]. As you can see, both benchmarks have identical results (i.e. 100% of all grid boxes in the central bar of the histogram).<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
!<br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|09 March 2012<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 10:36, 9 March 2012 (EST)<br />
<br />
=== v9-01-03g ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03g'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[GEOS-Chem v9-01-02#Fixes in emep_mod.f|Bug fix in emep_mod.F for offline simulations]]<br />
*[[GEOS-Chem_v9-01-02#Fix_for_offline_simulations_in_nei2005_anthro_mod.f|Bug fix in nei2005_anthro_mod.F for offline simulations]]<br />
*[[Wet deposition#Anomalous PRECTOT values on 22 July 2010|Bug fix to prevent crash in wetdep when encountering anomalously low PRECTOT values]]<br />
*[[Rn-Pb-Be_simulation#Missing_drydep_diagnostics_caused_by_tracer_name_error|Minor fix in Rn-Pb-Be simulation to prevent missing drydep diagnostics]]<br />
*[[GEOS-Chem v9-01-03#Correct out-of-bounds error in offline aerosol simulation|Correct out-of-bounds error in offline aerosol simulation]]<br />
*[[GEOS-Chem v9-01-03#Bug fixes in diag3.F|Bug fixes in diag3.F]]<br />
*[[GEOS-Chem v9-01-03#Bug fixes for nested-grid simulation|Bug fixes for nested-grid simulation]]<br />
*[[Mercury#Bug fix for reading Hg emissions|Bug fix for reading Hg emissions]]<br />
*[[Lightning_NOx_emissions#OTD.2FLIS_redistribution_for_MERRA_2x2.5|Add scaling of lightning NOx for 2x2.5 MERRA simulations]]<br />
*[[GEOS-5.7.2 implementation details#Initial source code modifications for GEOS-5.7.2|Initial source code modifications for GEOS-5.7.2]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''emep_mod.F fix:'' [[GEOS-Chem Support Team]]<br />
*''nei2005_anthro_mod.F fix:'' GEOS-Chem Support Team<br />
*''PRECTOT fix:'' GEOS-Chem Support Team<br />
*''Rn-Pb-Be drydep diagnostic fix'': GEOS-Chem Support Team<br />
*''Offline aerosol fix:'' GEOS-Chem Support Team<br />
*''diag3.F fixes:'' Mat Evans (Leeds) and GEOS-Chem Support Team<br />
*''Nested-grid bug fixes:'' Dylan Millet (U. Minnesota)<br />
*''Hg emissions fix:'' Jenny Fisher (Harvard)<br />
*''MERRA 2x2.5 lightning NOx:'' Lee Murray (Harvard) and Matt Cooper (Dalhousie)<br />
*''GEOS-5.7.2:'' GEOS-Chem Support Team<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Mon Feb 27 15:00:20 EST 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-03-c.as.harvard.edu (2.659 GHz x 8 CPU) <br />
*Wall time: 1:39<br />
*Scalability: 7.6499<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03f|v9-01-03f]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): '''We expect to see no changes from v9-01-03f'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-03g/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1253265985999 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7576 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|NIT<br />
|-<br />
|Comments on SURFACE differences: <br />
|Small numerical noise where concentrations are low cause large % differences. This is due to [[ISORROPIA_II#Optimization_and.2For_parallelization_issues_in_ISORROPIA_II|ISORROPIA]].<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Small numerical noise where concentrations are low cause large % differences. This is due to ISORROPIA.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Small numerical noise where concentrations are low cause large % differences. This is due to ISORROPIA. <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None.<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|<br />
|-<br />
|Additional or summary comments:<br />
|To eliminate the effect from ISORROPIA, we re-ran 1-month benchmarks for v9-01-02f and v9-01-02g with ISORROPIA turned off. We have created [ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03g/v9-01-03g-2.freq_distribution.pdf this frequency distribution histogram plot]. As you can see, both benchmarks have identical results (i.e. 100% of all grid boxes in the central bar of the histogram). <br />
<br />
<br />
NOTE: The kludge implemented to [[Wet_deposition#Anomalous PRECTOT values on 22 July 2010|prevent crashes in wetdep when encountering anomalously low PRECTOT values]] causes very small (mostly on the order of 0.0001 ppbv) changes in tracer concentration, as seen in [ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03g/v9-01-03g-2.differences.dyn_range.pdf this dynamic range difference plot] with ISORROPIA turned off. The kludge is still an improvement to the code because the fraction of the precipitating box should always be between 0 and 1.<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|27 Feb 2012<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:36, 27 February 2012 (EST)<br />
<br />
=== v9-01-03f ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03f'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Ship emissions#PARANOX ship plume model|PARANOX ship plume emissions]]<br />
*[[Nested_Model_Working_Group#Fixes_to_Streets_emissions_for_model_years_2005_and_earlier|Bug fixes for David Streets emissions for years 2005 and earlier]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''PARANOX:'' Geert Vinken (Eindhoven)<br />
*''Streets bug fixes:'' Jenny Fisher (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Wed Feb 15 15:30:13 EST 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-10-c.as.harvard.edu (2.659 GHz x 8 CPU) <br />
*Wall time: 1:40<br />
*Scalability: 7.6161<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03e_2|v9-01-03e]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, '''Anthro Emiss''', Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): <br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-03f/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1254879976765 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7576 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|NOx, Ox, PAN, ALK4, ISOP, HNO3, H2O2, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2,PRPE, C3H8, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, OH<br />
|-<br />
|Comments on SURFACE differences: <br />
|In original model, ship NOx was released as 10*O3 and 1*HNO3 molecules (continuously, day and night). Now we release a fraction of the NOx, and O3 and HNO3 produced. This explains large increase in NOx, as no ship NOx was present before this update. Other species are influenced by changes in O3 (and consequently OH). <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NOx, ISOP, MVK, MACR, PMN, PRPE, N2O5, HNO4, DMS, SO2, MSA, NH3 (noisy), NIT (noisy), NITs <br />
|-<br />
|Comments on 500 hPa differences:<br />
| <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NOx, PAN, ISOP, HNO3, H2O2, RCHO, MVK, MACR, PMN, PPN, PRPE, CH2O, N2O5, HNO4, MP, DMS, MSA, NH3, NIT (noisy), NITs, OH<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Most of the effects are concentrated near the surface and in the lat range 0..60, where most of the ship emissions are located. <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|NOx<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|Instead of emitting no ship NOx, we now release a fraction of the ship NOx (+O3 and HNO3 produced).<br />
|-<br />
|Additional or summary comments:<br />
|Streets bugfix only influences model runs before 2000 or nested Asia simulations (see [[Nested_Model_Working_Group#Fixes_to_Streets_emissions_for_model_years_2005_and_earlier|Bug fixes for David Streets emissions for years 2005 and earlier]]) <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|17 Feb 2012<br />
|}<br />
<br />
--[[User:Geert Vinken|Geert Vinken]] 13:46, 17 February 2012 (CET)<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:35, 15 February 2012 (EST)<br />
<br />
=== v9-01-03e ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03e'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*Improved [[Wet_deposition#Add_scavenging_by_snow|snow scavenging]] and [[Wet deposition#Updates for aerosol scavenging efficiency|washout parameterization]]<br />
*[[GEOS-Chem v9-01-03#Structural changes to clarify science behind washout|Structural changes to clarify science behind washout]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''Scavenging improvements:'' Qiaoqiao Wang (Harvard) <br />
*''Washout structural update:'' Helen Amos (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Fri Jan 20 13:26:06 EST 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-08-c.as.harvard.edu (2.926 GHz x 8 CPU) <br />
*Wall time: 1:13<br />
*Scalability: 7.7027<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03d|v9-01-03d]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, '''Wet Dep''', Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): <br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-03e/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.0850715760517 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7757 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|NOx, PAN, ISOP, HNO3, H2O2, MVK, PPN, PRPE, N2O5, HNO4,SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, BCPO, OCPI, OCPO, DST1, DST2, DTS3, DST4, SALA, SALC<br />
|-<br />
|Comments on SURFACE differences: <br />
|The differences are mainly due to the changes in below-cloud scavenging for aerosols. The below-cloud scavenging is very efficient for coarse sea salt and coarse dust, but not for other aerosols. <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NOx, ALK4, ISOP, HNO3, MVK, MACR, PMN, PRPE, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, BCPO, OCPI, OCPO, DST1, DST2, DTS3, DST4, SALA, SALC<br />
|-<br />
|Comments on 500 hPa differences:<br />
|The significant decreases in DUST, BCPO and HNO3 are because of the in-cloud scavenging by snow. <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NOx, ALK4, ISOP, HNO3, H2O2, MVK, MACR, PMN, PRPE, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, BCPO, OCPI, OCPO, DST1, DST2, DTS3, DST4, SALA, SALC, OH <br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Changes in below-cloud scavenging reduces concentrations of coarse dust and coarse sea salt but increases other aerosol concentrations. Changes in in-cloud scavenging decrease concentrations of BCPO, dust and HNO3 especially at high altitudes. As a result, dust concentrations are decreased at all altitudes. BCPO concentrations tend to decrease at high altitude but increase at low altitude. Concentrations of other aerosols tend to increase at high altitude especially over the tropics and subtropics. This is because we suppress the in-cloud scavenging at low temperature during convective updrafts so as to be consistent with the parameterizations in large-scale precipitation. <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|No<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|<br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|NO<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|02 Feb 2012<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:15, 23 January 2012 (EST)<br />
<br />
=== v9-01-03d ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03d'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*Improved sea salt [[Sea salt aerosols#SST dependent sea salt emissions|emission]] & [[Sea salt aerosols#Updates to sea salt dry deposition|deposition]]<br />
*[[Dry deposition#Update dry deposition to use local surface pressure|Update dry deposition to use local surface pressure]]<br />
*[[Mineral dust aerosols#Sub-micron dust mass partitioning change|Dust submicron size distribution for optics]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''Sea salt improvements:'' Lyatt Jaegl&eacute; (U. Washington)<br />
*''Dry deposition:'' Lyatt Jaegl&eacute; (U. Washington) and [[GEOS-Chem Support Team]]<br />
*''Dust submicron size distribution:'' David Ridley (Colo. State)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Tue Jan 10 19:18:47 EST 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-12-c.as.harvard.edu (2.670 GHz x 8 CPU) <br />
*Wall time: 1:32<br />
*Scalability: 7.6956<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03c|v9-01-03c]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, '''Dry Dep''', Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): '''Sea salt emissions & deposition''', '''Dust AOD'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-03d/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.3024776896910 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7075 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
| SALA, SALC, N2O5, HNO3, NIT, NITs, NH4, NH3, SO4s, HNO4, NOx, PAN<br />
|-<br />
|Comments on SURFACE differences: <br />
| Concentrations of sea salt aerosols (SALA and SALC) increase in the tropics by ~50-100% and decrease at mid-high latitudes by 50-100% as expected from the implementation of the SST dependent sea salt source function.<br />
The impact on other species is largest for nitrogen and sulfur species that directly interact with sea salt. While the levels for some of these species change by factors of 1.5-2 over the tropical and high latitude oceans (HNO3, NIT, NITs, SO4s, NH3, NH4), their concentrations are very small in these remote regions, so the absolute changes are small. For example, HNO3 increases by more than a factor of 2 over the remote southern ocean, and decreases by a factor of 2 over the tropics. But the absolute changes are a few pptv at the surface.<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
| SALA, SALC, SO4s, NH3, NIT, NITs<br />
|-<br />
|Comments on 500 hPa differences:<br />
| <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
| SALA, SALC, HNO3, N2O5, HNO4, SO4s, NH4, NIT, NITs<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
| Most of the effects are concentrated near the surface, where the sea salt burden is highest.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
| SALA, SALC<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| As expected from the inclusion of a SST dependence in the sea salt source function, sea salt emissions for accumulation mode sea salt aerosols (SALA) increase by 30-80% in warm tropical regions, and decrease by ~50% over high-latitudes. Overall SALA emissions decrease by 23%. Global emission of coarse mode sea salt aerosols (SALC) increase by 70%, with the largest increases in the tropics. This is driven by both the SST dependence but also the expansion of the size distribution of sea salt from 0.5-4 to 0.5-8 microns.<br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|12 Jan 2012<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 11:44, 11 January 2012 (EST)<br />
<br />
=== v9-01-03c ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03c'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Dry deposition#OVOCs dry deposition|OVOC dry deposition updates]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Jingqiu Mao (NOAA/GFDL) <br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Fri Dec 16 00:16:12 EST 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-11-c.as.harvard.edu (2.660 GHz x 8 CPU) <br />
*Wall time: 1:58<br />
*Scalability: 6.2283<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03b|v9-01-03b]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, '''Dry Dep''', Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-03c/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.3104192214225 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7056 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|PAN, ISOP, ALD2, RCHO, MVK, MACR, PMN, PPN, PRPE, CH2O, N2O5, MP, DMS <br />
|-<br />
|Comments on SURFACE differences: <br />
|The biggest difference were found for MVK and MACR, as they were not deposited in previous versions. The difference in HCHO is about 10%. The differences in organic nitrates are expected due to the supply of OVOCs. <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ISOP, ALD2, RCHO, MVK, MACR, PMN, PRPE, N2O5, DMS, NH3, NIT <br />
|-<br />
|Comments on 500 hPa differences:<br />
| Expected.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|MVK,MACR,PMN,NH3,NIT <br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
| Expected.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
| None<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| <br />
|-<br />
|Additional or summary comments:<br />
|The small increase in global mean OH is likely due to the small increase of NOx (similar pattern in the difference plots).<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes (Jingqiu Mao)<br />
|-<br />
|Date of approval:<br />
|12-19-2011<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 10:46, 19 December 2011 (EST)<br />
<br />
=== v9-01-03b ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03b'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Acetone|Improved acetone simulation]]<br />
*Complete shift of biogenic VOC emissions from GEIA to [[MEGAN biogenic emissions|MEGAN]]; [[Biogenic emissions#Retirement of obsolete GEIA_biogenic emissions|retire GEIA ]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''Acetone:'' Emily Fischer (Harvard)<br />
*''Retirement of GEIA:'' Dylan Millet (U. Minnesota)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Tue Dec 13 12:20:47 EST 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-10-c.as.harvard.edu (2.659 GHz x 8 CPU) <br />
*Wall time: 1:39<br />
*Scalability: 7.2830<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03a|v9-01-03a]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, '''Biogenic Emiss''', Biomass Emiss, Photolysis, Chemistry, Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-03b/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.2811407896285 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7161 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|PAN, ACET, R4N2 <br />
|-<br />
|Comments on SURFACE differences:<br />
|ACET generally decreases 10-50%, strongest decreases over the oceans due to elimination of the (incorrect) ocean source. Over continental regions, the largest changes are away from terrestrial acetone sources. There are smaller relative changes over the main continental emission regions. PAN decreases by 10-25% over most of the NH oceans, but the absolute differences are very small due to low surface PAN mixing ratios in these regions (< 30 pptv). Weak decreases for R4N2 in a couple spots. <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ACET, R4N2 <br />
|-<br />
|Comments on 500 hPa differences:<br />
|ACET decreases of 10-25% over many regions at 500hPa. Weak decreases for R4N2 in a couple spots. <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|ACET, PAN<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Changes exceeding 10% for ACET and PAN, consistent with the above. <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|ACET <br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|Changes as expected based on emission updates. <br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes (--[[User:Dbm|Dbm]] 11:17, 14 December 2011 (EST))<br>Yes (--[[User:Emily Fischer] 3:32, 14 December 2011 (EST))<br />
|-<br />
|Date of approval:<br />
|12-14-2011<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 13:42, 13 December 2011 (EST)<br>--[[User:Bmy|Bob Y.]] 17:06, 14 December 2011 (EST)<br />
<br />
=== v9-01-03a ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03a'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Chemistry_Issues#GLCO3.2C_GLPAN_bug_in_standard_mechanism|Fix for GLCO3/GLPAN bug in standard chemistry mechanism]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Fabien Paulot (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Wed Dec 7 16:06:38 EST 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-04-c.as.harvard.edu (2.925 GHz x 8 CPU) <br />
*Wall time: 0:57<br />
*Scalability: 7.4849<br />
|-<br />
|Compared to previous benchmark:<br />
|[[GEOS-Chem v9-01-02 benchmark history#v9-01-02s|v9-01-02s]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, '''Chemistry''', Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-03a/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.2473124589166 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7300 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|PAN (downwind of South America), ALK4 over oceanic basins, ISOP downwind of South America, MEK tropics, MVK, MACR (downwind of South America), PMN, PPN, PRPE, N2O5, DMS<br />
|-<br />
|Comments on SURFACE differences:<br />
|Sort of makes sense. Changes are in regions that are NOx starved (South America) or cold (the loss from GLPAN will be greatest). Changes are small overall and almost always negative. The changes for DMS are relatively large (10-20% decrease)<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ALK4, ISOP, MEK, MVK, MACR, PRPE (large changes in polar regions > 20%), DMS<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Changes are generally bigger than at the surface (temperature dependence of GLPAN)<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|ISOP (but at high altitude and in polar regions), ALK4 in polar regions, MEK, MVK, MACR, PMN, PRPE<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Small changes overall (in an absolute sense). DMS has the largest change.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|none <br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| <br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|Approved 08 Dec 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 11:21, 8 December 2011 (EST)<br>--[[User:Melissa Payer|Melissa Payer]] 13:48, 13 December 2011 (EST)</div>Psk9https://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_v9-01-03_benchmark_history&diff=10560GEOS-Chem v9-01-03 benchmark history2012-05-18T20:07:43Z<p>Psk9: /* v9-01-03l */</p>
<hr />
<div>On this page we have posted complete information about all benchmark simulations (both 1-month and 1-year) for [[GEOS-Chem v9-01-03]].<br />
<br />
== 1-year benchmarks ==<br />
<br />
=== v9-01-03e ===<br />
<br />
==== Run0 ====<br />
<br />
Three GEOS-Chem model versions were compared to each other:<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|- bgcolor="#CCCCCC"<br />
!Color <br />
!Quantity Plotted<br />
!Met Type<br />
!Anthro<br>emissions<br />
!Biofuel<br>emissions<br />
!Biomass<br>emissions<br />
!Wet deposition<br />
!Linoz<br />
!Annual Mean OH<br>[10<sup>5</sup> molec/cm3]<br />
<br />
|-align="center"<br />
|Red<br />
|[[GEOS-Chem v9-01-02 benchmark history#Run0|v9-01-02-Run0]]<br />
|GEOS-5, 4x5<br />
|Same as [[GEOS-Chem_v9-01-01_benchmark_history#Run0|v9-01-01-Run0]]<br>'''+ [[Carbon_Gases_and_Organics_Working_Group#GEIA_anthropogenic_scaling_factors|Fix for GEIA emissions scaling factor]]<br> + [[Anthropogenic_emissions#Streets_2000|Imposed seasonality on Streets 2000 NH3 emissions]]<br> + [[Ship_emissions#Bug_in_ship_NOx_emissions|Bug fix in ship NOx emissions]]'''<br />
|Same as [[GEOS-Chem_v9-01-01_benchmark_history#Run0|v9-01-01-Run0]] '''+ [[Anthropogenic_emissions#Bug_fix_for_Streets_biofuel_emissions|Bug fix for Streets biofuel emissions]]<br>'''<br />
|Same as [[GEOS-Chem_v9-01-01_benchmark_history#Run0|v9-01-01-Run0]]<br>([[Biomass_burning_emissions#GFED2|GFED2 monthly inventory]])<br />
|Same as [[GEOS-Chem_v9-01-01_benchmark_history#Run0|v9-01-01-Run0]]<br> (Original algorithm described in [http://acmg.seas.harvard.edu/geos/wiki_docs/deposition/wetdep.jacob_etal_2000.pdf Jacob et al <nowiki>[2000]</nowiki>]<br>+ [[Wet_deposition#Allow_both_washout_and_rainout_when_precipitation_forms|Allow both washout and rainout when precip. forms]]<br> + [[Wet_deposition#Updates_for_MERRA_met_fields|Updates for MERRA met fields]])<br />
|ON<br />
|12.233<br />
<br />
|-align="center"<br />
|Green<br />
|[[GEOS-Chem v9-01-02 benchmark history#Run1|v9-01-02-Run1]]<br />
|GEOS-5, 4x5<br />
|'''+ [[Implementation_of_RETRO_Anthropogenic_Emissions|RETRO anthropogenic VOC emissions]]<br />
|" "<br />
|'''+ [[Biomass_burning_emissions#GFED3|GFED3 monthly inventory]]'''<br />
|" "<br />
|ON<br />
|12.332<br />
<br />
|-align="center"<br />
|Blue<br />
|[[GEOS-Chem v9-01-03 benchmark history#Run0|v9-01-03e-Run0]]<br />
|GEOS-5, 4x5<br />
|" "<br />
|" "<br />
|" "<br />
|'''+ Improved [[Wet_deposition#Add_scavenging_by_snow|snow scavenging]] and [[Wet deposition#Updates for aerosol scavenging efficiency|washout parameterization]]<br />
|ON<br />
|11.935<br />
<br />
|-align="center"<br />
|Black <br />
|Observations<br />
|&nbsp; <br />
|&nbsp; <br />
|&nbsp;<br />
|&nbsp;<br />
|&nbsp;<br />
|&nbsp;<br />
!&nbsp;<br />
|}<br />
<br />
<br />
The output plots for Run1 (both PostScript and PDF format) may be downloaded from:<br />
<br />
ftp ftp.as.harvard.edu<br />
cd gcgrid/geos-chem/1yr_benchmarks/v9-01-03/v9-01-03e/geos5/2005/Run0/output/ps<br />
mget *<br />
cd gcgrid/geos-chem/1yr_benchmarks/v9-01-03/v9-01-03e/geos5/2005/Run0/output/pdf<br />
mget *<br />
<br />
You may also view the PDF files online by pointing your browser to<br />
<br />
ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v9-01-03/v9-01-03e/geos5/2005/Run0/output/pdf/<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 13:19, 1 February 2012 (EST)<br />
<br />
==== Rn-Pb-Be simulation ====<br />
<br />
We also conducted a 1-year [[Rn-Pb-Be simulation]] with GEOS-Chem v9-01-03e. Please follow the links below to see the budget of Pb210 and Be7 from 1-year Rn-Pb-Be simulations for v9-01-03e and previous versions:<br />
<br />
#[[Rn-Pb-Be simulation#Budget of Pb210 from 1-year benchmark simulations|Budget of Pb210 from 1-year benchmark simulations]]<br />
#[[Rn-Pb-Be simulation#Budget of Be7 from 1-year benchmark simulations|Budget of Be7 from 1-year benchmark simulations]]<br />
<br />
Plots comparing modeled Rn222, Pb210, and Be7 to [[GEOS-Chem v9-01-02]] are now available. The plotting programs were provided by [mailto:hongyu.liu-1@nasa.gov Hongyu Liu]. For more information on the plots, see [http://acmg.seas.harvard.edu/publications/liu2001.pdf Liu et al. <nowiki>[2001]</nowiki>].<br />
<br />
You may view the PDF files online by pointing your browser to:<br />
<br />
<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v9-01-03/v9-01-03e/geos5/2005/RnPbBe/output/pdf/</tt><br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:48, 24 January 2012 (EST)<br />
<br />
== 1-month benchmarks ==<br />
<br />
=== v9-01-03l ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03l'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Biomass burning emissions#GFED3 daily and 3-hourly emissions|Daily and 3-hourly GFED3 biomass emissions]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Prasad Kasibhatla (Duke) <br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Fri May 4 19:40:32 EDT 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-11-c.as.harvard.edu (2.660 GHz x 8 CPU) <br />
*Wall time: 1:43<br />
*Scalability: 7.6201<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03k|v9-01-03k]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, '''Biomass Emiss''', Photolysis, Chemistry, Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03l/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1174291218146 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7610 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|Various species at discrete locations<br />
|-<br />
|Comments on SURFACE differences: <br />
|Related to change in code to regrid on the fly from native GFED3 resolution to model grid<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|A few species at a few locations<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Some related to changes in surface; a bit puzzled by changes to a few species like NH3, NIT, and ISOP (one grid box over the Amazon), but<br />
likely related to change changes to chemistry at surface caused by regridding change (ISOP) or in regions with very low concentratiomns (eg NIT) <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more: <br />
|ISOP, MVK, MACR, N2O5 at isolated latitudes, but more widespread changes in NIT and NH3<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|I think the changes in ISOP, MVK, etc are related to changes in chemistry caused by changes in regridding, but am a but puzzled by NIT and NH3 changes.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|Some species at discrete locations<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|Due to changes associated with regridding on the fly from native GFED3 resolution<br />
|-<br />
|Additional or summary comments:<br />
|Note: Special benchmarks were also requested for (1) 3-hourly and (2) daily GFED3 biomass burning emissions. The benchmark plots for these simulations may be viewed at:<br />
#3-hourly GFED3: <tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03l.3h_GFED3/</tt><br />
#Daily GFED3: <tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03l.daily_GFED3/</tt><br />
Differences are consistent with Daily and 3-hourly variation in emisisons<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
!<br />
|-<br />
|Requires further investigation:<br />
No<br />
|- <br />
|Approved:<br />
Yes<br />
|-<br />
|Date of approval:<br />
18 May, 2012<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 17:33, 9 May 2012 (EDT)<br />
<br />
=== v9-01-03k ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03k'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Emissions overview#MAP_A2A regridding algorithm|Replace existing regridding routines with the MAP_A2A regridding package]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Matt Cooper (Dalhousie)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Wed Apr 25 14:48:08 EDT 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-05-c.as.harvard.edu (2.793 GHz x 16 CPU) <br />
*Wall time: 1:27<br />
*Scalability: 7.6049<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03j|v9-01-03j]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): '''We expect to see no changes from v9-01-03j'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03k/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1180503320529 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7607 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|NOx, PAN, ALK4, ISOP, HNO3, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2, PRPE, C3H8, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, NITs, BCPI, OCPI, BCPO, OCPO, OH<br />
|-<br />
|Comments on SURFACE differences: <br />
|For most species, small numerical noise where concentrations are low cause large percent differences. Absolute differences are generally small. Other species (ie HNO3, NOx) with large differences generally have a grid box with positive change next to box with similar negative change. This is due to slight shifts in location of some emissions under new regrid algorithm.<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ISOP, MEK, RCHO, MVK, MACR, PMN, PRPE, N2O5, DMS, SO2, SO4, NH3, NIT, BCPO, OCPO<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Small numerical noise where concentrations are low cause large percent differences. Absolute differences are generally small.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more: <br />
|ALK4, ISOP, MVK, MACR, PRPE, N2O5, NH3,NIT, OCPO<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Small numerical noise where concentrations are low cause large percent differences. Absolute differences are generally small.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|ACET, ALD2, ALK4, BC, C3H8, CH2O, ISOP, MEK, NH3, NOx, OC, PRPE, SO2, SO4<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|Small numerical noise where concentrations are low cause large percent differences. Absolute differences are generally small.<br />
|-<br />
|Additional or summary comments:<br />
|<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
!<br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|27 April 2012<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 14:45, 26 April 2012 (EDT)<br />
<br />
=== v9-01-03j ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03j'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Leaf area indices in GEOS-Chem#Implementation of an updated LAI code|Implementation of updated LAI code]]<br />
*[[Grid-independent_GEOS-Chem#Restructuring_of_GEOS-Chem_for_grid-independent_functionality|Grid-independent GEOS-Chem updates #2: Preliminary interface to link driving GCM]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''Updated LAI:'' [[GEOS-Chem Support Team]]<br />
*''Grid-independent GEOS-Chem:'' [[GEOS-Chem Support Team]]<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Fri Apr 13 15:02:26 EDT 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-10-c.as.harvard.edu (2.659 GHz x 8 CPU) <br />
*Wall time: 1:42<br />
*Scalability: 7.6407<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03i|v9-01-03i]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, '''Dry Dep''', Wet Dep, Stratosphere, Anthro Emiss, '''Biogenic Emiss''', Biomass Emiss, Photolysis, Chemistry, Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03j/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1149651381533 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7612 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|ISOP, MVK, MACR<br />
|-<br />
|Comments on SURFACE differences: <br />
|Differences are seen in ISOP in locations where concentrations are already very low (i.e. over oceans). MVK and MACR differences are presumably tied ot to the differences in ISOP. [[Leaf area indices in GEOS-Chem#Using Olson 1992 land map|As described in this wiki post]], we attribute these changes to the numerical differences caused by regridding leaf area index data from 0.5&deg; x 0.5&deg; native resolution (instead of from 1&deg; x 1&deg;, as was done in the past).<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ISOP, MVK, MACR, NH3, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Differences are seen in ISOP in locations where concentrations are already very low (i.e. over oceans). MVK and MACR differences are presumably tied to to the differences in ISOP. [[Leaf area indices in GEOS-Chem#Using Olson 1992 land map|As described in this wiki post]], we attribute these changes to the numerical differences caused by regridding leaf area index data from 0.5&deg; x 0.5&deg; native resolution (instead of from 1&deg; x 1&deg;, as was done in the past).<br />
<br />
Differences in NH3 and NIT are attributed to the [[ISORROPIA_II#Persistence_of_problem|Numerical noise issue in ISORROPIA II]].<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|ISOP, NH3, NIT <br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|ISOP shows % differences of about ~5% in places where concentrations are already very low. [[Leaf area indices in GEOS-Chem#Using Olson 1992 land map|As described in this wiki post]], we attribute these changes to the numerical differences caused by regridding leaf area index data from 0.5&deg; x 0.5&deg; native resolution (instead of from 1&deg; x 1&deg;, as was done in the past).<br />
<br />
Differences in NH3 and NIT are attributed to the [[ISORROPIA_II#Persistence_of_problem|Numerical noise issue in ISORROPIA II]].<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|Biogenic ACET, Biogenic ISOP, Biogenic PRPE<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|All of the above-mentioned species show differences, especially near coastlines. All of these species are computed by the [[MEGAN biogenic emissions]] module, which now takes in the leaf area indices regridded from 0.5&deg; x 0.5&deg;, [[Leaf area indices in GEOS-Chem#Using Olson 1992 land map|As described in this wiki post]]. We attribute the differences in these species to the numerical differences in the leaf area index data.<br />
|-<br />
|Additional or summary comments:<br />
|The updates added to v9-01-03j were made to primarily assist development of the [[Grid-independent GEOS-Chem]]. We needed to rewrite the leaf area index module in order to (1) remove obsolete ASCII data files that were prohibiting the grid-independent model from functioning efficiently, and (2) compute leaf area indices consistently by regridding them from the native resolution (in this case, 0.5&deg; x 0.5&deg;) instead of using leaf area index data at several different resolutions. Also, we have merged into the standard repository several updates from Mike Long that are necessary in order to have GEOS-Chem driven by the NASA/GEOS-5 GCM.<br />
<br />
We performed benchmark v9-01-03j with the [[Olson land map#Olson 1992 land map|Olson 1992 land map]] (which is the default in GEOS-Chem), and the [[MODIS leaf area indices]], both at 0.5&deg; x 0.5&deg; resolution. The updated LAI code introduced into v9-01-03j will eventually allow us to use higher resolution versions of both the Olson land map and the MODIS leaf area indices. This will be an important step that will facilitate GEOS-Chem nested-grid simulations 0.25&deg; x 0.25&deg;.<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
!<br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|17 Apr 2012<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 11:06, 17 April 2012 (EDT)<br />
<br />
=== v9-01-03i ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03i'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Grid-independent GEOS-Chem#Modifications to remove legacy code that hinders grid-indpendent functionality|Grid-independent GEOS-Chem updates #1: Fixes to facilitate implementation of grid-independent code]]<br />
*[[Implementation of RETRO Anthropogenic Emissions#RETRO anthropogenic ethane emissions are too low|Replace RETRO C2H6 emissions with emissions from offline C2H6 simulation]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''Grid-independent GEOS-Chem:'' [[GEOS-Chem Support Team]]<br />
*''Ethane:'' [[GEOS-Chem Support Team]]<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Thu Mar 22 18:19:43 EDT 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-11-c.as.harvard.edu (2.660 GHz x 8 CPU) <br />
*Wall time: 1:42<br />
*Scalability: 7.6384<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03h|v9-01-03h]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, '''Anthro Emiss''', Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03i/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1142905403284 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7616 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|PAN, ALD2, C2H6<br />
|-<br />
|Comments on SURFACE differences: <br />
|<br />
Concentrations of C2H6 increase 10-100% globally, except in eastern North America and coastal China. Typically, regional emission inventories overwrite the global emissions inventories; however, in this update, the C2H6 anthropogenic emissions overwrite has been removed for [[Anthropogenic emissions#EPA.2FNEI05|EPA/NEI2005]], [[Anthropogenic emissions#Streets 2006|Streets]], and [[Anthropogenic emissions#EMEP|EMEP]] because anthropogenic emissions of C2H6 were found to be [[Anthropogenic emissions#Anthropogenic ethane emissions are too low|too low in these regional inventories]]. Aside from decreases over eastern North America and coastal China, the offline C2H6 emissions improve concentrations over the rest of the North American and Asian regions.<br />
<br />
Smaller increases in PAN (~10%) and ALD2 (10-60%) are expected with an increase in C2H6, as C2H6 is a source of these species.<br />
<br />
''Note: Differences in NIT are numerical noise caused by [[ISORROPIA II#Optimization and.2For parallelization issues in ISORROPIA II|ISORROPIA]].''<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ALD2, C2H6<br />
|-<br />
|Comments on 500 hPa differences:<br />
|<br />
The changes at the surface propagate into the free troposphere for ALD2 and C2H6.<br />
<br />
''Note: Differences in NH3 and NIT are numerical noise caused by ISORROPIA.''<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|PAN, ALD2, C2H6<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|<br />
Patterns are consistent with the surface changes described above.<br />
<br />
''Note: Differences in NH3 and NIT are numerical noise caused by ISORROPIA.''<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|C2H6<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|There are widespread increases in anthropogenic emissions of C2H6 by as much as 100%. Decreases of up to 50% occur in some regions, primarily in regions where C2H6 anthropogenic emissions are low in the first place. Overall, this is an improvement from using RETRO C2H6 anthropogenic emissions, which were found to be too low.<br />
|-<br />
|Additional or summary comments:<br />
|<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
!<br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes (--[[User:Melissa Payer|Melissa Payer]] 12:22, 23 March 2012 (EDT))<br />
|-<br />
|Date of approval:<br />
|26 March 2012<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 17:49, 20 March 2012 (EDT)<br />
<br />
=== v9-01-03h ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03h'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Mercury#Hg.28II.29_gas-particle_partitioning|Hg(II) gas-aerosol partitioning]]<br />
*[[CO2_simulation#Nested-grid_CO2_simulation|Nested-grid CO2]]<br />
*[[Sources_and_Sinks_Working_Group#Available_Historical_and_Future_Emissions|Historical emission inventories of SO2, NOx, BC, and POA]]<br />
*[[CH4_simulation#Update_methane_emissions_and_add_capability_for_North_America_nested_grid|CH4 simulation updates]]<br />
*[[Overview of GMAO met data products#Removal of support for GEOS-3|Remove support for GEOS-3 meteorology]]<br />
*[[GEOS-Chem v9-01-03#Bug fix in streets_anthro_mod.F for offline simulations|Bug fix in streets_anthro_mod.F for offline simulations]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''Hg(II) partitioning:'' Helen Amos (Harvard)<br />
*''Nested-grid CO2'': Yuxuan Wang (Tsinghua)<br />
*''Historical emission inventories:'' Eric Leibensperger (MIT)<br />
*''CH4 simulation updates:'' Kevin Wecht (Harvard)<br />
*''Remove support for GEOS-3:'' [[GEOS-Chem Support Team]]<br />
*''Fix in streets_anthro_mod.F:'' Fabien Paulot<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Thu Mar 8 19:02:33 EST 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU) <br />
*Wall time: 1:40<br />
*Scalability: 7.6326<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03g|v9-01-03g]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): '''We expect to see no changes from v9-01-03g'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03h/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1255094316462 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7576 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|NIT<br />
|-<br />
|Comments on SURFACE differences: <br />
|Small numerical noise where concentrations are low cause large % differences. This is due to [[ISORROPIA_II#Optimization_and.2For_parallelization_issues_in_ISORROPIA_II|ISORROPIA]].<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Small numerical noise where concentrations are low cause large % differences. This is due to ISORROPIA.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NH3, NIT <br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Small numerical noise where concentrations are low cause large % differences. This is due to ISORROPIA.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None.<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|<br />
|-<br />
|Additional or summary comments:<br />
|To eliminate the effect from ISORROPIA, we re-ran 1-month benchmarks for v9-01-02g and v9-01-02h with ISORROPIA turned off. We have created [ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03h/v9-01-03h-2.freq_distribution.pdf this frequency distribution histogram plot]. As you can see, both benchmarks have identical results (i.e. 100% of all grid boxes in the central bar of the histogram).<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
!<br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|09 March 2012<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 10:36, 9 March 2012 (EST)<br />
<br />
=== v9-01-03g ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03g'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[GEOS-Chem v9-01-02#Fixes in emep_mod.f|Bug fix in emep_mod.F for offline simulations]]<br />
*[[GEOS-Chem_v9-01-02#Fix_for_offline_simulations_in_nei2005_anthro_mod.f|Bug fix in nei2005_anthro_mod.F for offline simulations]]<br />
*[[Wet deposition#Anomalous PRECTOT values on 22 July 2010|Bug fix to prevent crash in wetdep when encountering anomalously low PRECTOT values]]<br />
*[[Rn-Pb-Be_simulation#Missing_drydep_diagnostics_caused_by_tracer_name_error|Minor fix in Rn-Pb-Be simulation to prevent missing drydep diagnostics]]<br />
*[[GEOS-Chem v9-01-03#Correct out-of-bounds error in offline aerosol simulation|Correct out-of-bounds error in offline aerosol simulation]]<br />
*[[GEOS-Chem v9-01-03#Bug fixes in diag3.F|Bug fixes in diag3.F]]<br />
*[[GEOS-Chem v9-01-03#Bug fixes for nested-grid simulation|Bug fixes for nested-grid simulation]]<br />
*[[Mercury#Bug fix for reading Hg emissions|Bug fix for reading Hg emissions]]<br />
*[[Lightning_NOx_emissions#OTD.2FLIS_redistribution_for_MERRA_2x2.5|Add scaling of lightning NOx for 2x2.5 MERRA simulations]]<br />
*[[GEOS-5.7.2 implementation details#Initial source code modifications for GEOS-5.7.2|Initial source code modifications for GEOS-5.7.2]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''emep_mod.F fix:'' [[GEOS-Chem Support Team]]<br />
*''nei2005_anthro_mod.F fix:'' GEOS-Chem Support Team<br />
*''PRECTOT fix:'' GEOS-Chem Support Team<br />
*''Rn-Pb-Be drydep diagnostic fix'': GEOS-Chem Support Team<br />
*''Offline aerosol fix:'' GEOS-Chem Support Team<br />
*''diag3.F fixes:'' Mat Evans (Leeds) and GEOS-Chem Support Team<br />
*''Nested-grid bug fixes:'' Dylan Millet (U. Minnesota)<br />
*''Hg emissions fix:'' Jenny Fisher (Harvard)<br />
*''MERRA 2x2.5 lightning NOx:'' Lee Murray (Harvard) and Matt Cooper (Dalhousie)<br />
*''GEOS-5.7.2:'' GEOS-Chem Support Team<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Mon Feb 27 15:00:20 EST 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-03-c.as.harvard.edu (2.659 GHz x 8 CPU) <br />
*Wall time: 1:39<br />
*Scalability: 7.6499<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03f|v9-01-03f]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): '''We expect to see no changes from v9-01-03f'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-03g/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1253265985999 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7576 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|NIT<br />
|-<br />
|Comments on SURFACE differences: <br />
|Small numerical noise where concentrations are low cause large % differences. This is due to [[ISORROPIA_II#Optimization_and.2For_parallelization_issues_in_ISORROPIA_II|ISORROPIA]].<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Small numerical noise where concentrations are low cause large % differences. This is due to ISORROPIA.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Small numerical noise where concentrations are low cause large % differences. This is due to ISORROPIA. <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None.<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|<br />
|-<br />
|Additional or summary comments:<br />
|To eliminate the effect from ISORROPIA, we re-ran 1-month benchmarks for v9-01-02f and v9-01-02g with ISORROPIA turned off. We have created [ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03g/v9-01-03g-2.freq_distribution.pdf this frequency distribution histogram plot]. As you can see, both benchmarks have identical results (i.e. 100% of all grid boxes in the central bar of the histogram). <br />
<br />
<br />
NOTE: The kludge implemented to [[Wet_deposition#Anomalous PRECTOT values on 22 July 2010|prevent crashes in wetdep when encountering anomalously low PRECTOT values]] causes very small (mostly on the order of 0.0001 ppbv) changes in tracer concentration, as seen in [ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-03g/v9-01-03g-2.differences.dyn_range.pdf this dynamic range difference plot] with ISORROPIA turned off. The kludge is still an improvement to the code because the fraction of the precipitating box should always be between 0 and 1.<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|27 Feb 2012<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:36, 27 February 2012 (EST)<br />
<br />
=== v9-01-03f ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03f'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Ship emissions#PARANOX ship plume model|PARANOX ship plume emissions]]<br />
*[[Nested_Model_Working_Group#Fixes_to_Streets_emissions_for_model_years_2005_and_earlier|Bug fixes for David Streets emissions for years 2005 and earlier]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''PARANOX:'' Geert Vinken (Eindhoven)<br />
*''Streets bug fixes:'' Jenny Fisher (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Wed Feb 15 15:30:13 EST 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-10-c.as.harvard.edu (2.659 GHz x 8 CPU) <br />
*Wall time: 1:40<br />
*Scalability: 7.6161<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03e_2|v9-01-03e]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, '''Anthro Emiss''', Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): <br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-03f/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1254879976765 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7576 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|NOx, Ox, PAN, ALK4, ISOP, HNO3, H2O2, MEK, ALD2, RCHO, MVK, MACR, PMN, PPN, R4N2,PRPE, C3H8, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, OH<br />
|-<br />
|Comments on SURFACE differences: <br />
|In original model, ship NOx was released as 10*O3 and 1*HNO3 molecules (continuously, day and night). Now we release a fraction of the NOx, and O3 and HNO3 produced. This explains large increase in NOx, as no ship NOx was present before this update. Other species are influenced by changes in O3 (and consequently OH). <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NOx, ISOP, MVK, MACR, PMN, PRPE, N2O5, HNO4, DMS, SO2, MSA, NH3 (noisy), NIT (noisy), NITs <br />
|-<br />
|Comments on 500 hPa differences:<br />
| <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NOx, PAN, ISOP, HNO3, H2O2, RCHO, MVK, MACR, PMN, PPN, PRPE, CH2O, N2O5, HNO4, MP, DMS, MSA, NH3, NIT (noisy), NITs, OH<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Most of the effects are concentrated near the surface and in the lat range 0..60, where most of the ship emissions are located. <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|NOx<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|Instead of emitting no ship NOx, we now release a fraction of the ship NOx (+O3 and HNO3 produced).<br />
|-<br />
|Additional or summary comments:<br />
|Streets bugfix only influences model runs before 2000 or nested Asia simulations (see [[Nested_Model_Working_Group#Fixes_to_Streets_emissions_for_model_years_2005_and_earlier|Bug fixes for David Streets emissions for years 2005 and earlier]]) <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|17 Feb 2012<br />
|}<br />
<br />
--[[User:Geert Vinken|Geert Vinken]] 13:46, 17 February 2012 (CET)<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:35, 15 February 2012 (EST)<br />
<br />
=== v9-01-03e ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03e'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*Improved [[Wet_deposition#Add_scavenging_by_snow|snow scavenging]] and [[Wet deposition#Updates for aerosol scavenging efficiency|washout parameterization]]<br />
*[[GEOS-Chem v9-01-03#Structural changes to clarify science behind washout|Structural changes to clarify science behind washout]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''Scavenging improvements:'' Qiaoqiao Wang (Harvard) <br />
*''Washout structural update:'' Helen Amos (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Fri Jan 20 13:26:06 EST 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-08-c.as.harvard.edu (2.926 GHz x 8 CPU) <br />
*Wall time: 1:13<br />
*Scalability: 7.7027<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03d|v9-01-03d]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, '''Wet Dep''', Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): <br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-03e/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.0850715760517 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7757 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|NOx, PAN, ISOP, HNO3, H2O2, MVK, PPN, PRPE, N2O5, HNO4,SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, BCPO, OCPI, OCPO, DST1, DST2, DTS3, DST4, SALA, SALC<br />
|-<br />
|Comments on SURFACE differences: <br />
|The differences are mainly due to the changes in below-cloud scavenging for aerosols. The below-cloud scavenging is very efficient for coarse sea salt and coarse dust, but not for other aerosols. <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NOx, ALK4, ISOP, HNO3, MVK, MACR, PMN, PRPE, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, BCPO, OCPI, OCPO, DST1, DST2, DTS3, DST4, SALA, SALC<br />
|-<br />
|Comments on 500 hPa differences:<br />
|The significant decreases in DUST, BCPO and HNO3 are because of the in-cloud scavenging by snow. <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NOx, ALK4, ISOP, HNO3, H2O2, MVK, MACR, PMN, PRPE, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, MSA, NH3, NH4, NIT, NITs, BCPI, BCPO, OCPI, OCPO, DST1, DST2, DTS3, DST4, SALA, SALC, OH <br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Changes in below-cloud scavenging reduces concentrations of coarse dust and coarse sea salt but increases other aerosol concentrations. Changes in in-cloud scavenging decrease concentrations of BCPO, dust and HNO3 especially at high altitudes. As a result, dust concentrations are decreased at all altitudes. BCPO concentrations tend to decrease at high altitude but increase at low altitude. Concentrations of other aerosols tend to increase at high altitude especially over the tropics and subtropics. This is because we suppress the in-cloud scavenging at low temperature during convective updrafts so as to be consistent with the parameterizations in large-scale precipitation. <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|No<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|<br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|NO<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|02 Feb 2012<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 16:15, 23 January 2012 (EST)<br />
<br />
=== v9-01-03d ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03d'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*Improved sea salt [[Sea salt aerosols#SST dependent sea salt emissions|emission]] & [[Sea salt aerosols#Updates to sea salt dry deposition|deposition]]<br />
*[[Dry deposition#Update dry deposition to use local surface pressure|Update dry deposition to use local surface pressure]]<br />
*[[Mineral dust aerosols#Sub-micron dust mass partitioning change|Dust submicron size distribution for optics]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''Sea salt improvements:'' Lyatt Jaegl&eacute; (U. Washington)<br />
*''Dry deposition:'' Lyatt Jaegl&eacute; (U. Washington) and [[GEOS-Chem Support Team]]<br />
*''Dust submicron size distribution:'' David Ridley (Colo. State)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Tue Jan 10 19:18:47 EST 2012<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-12-c.as.harvard.edu (2.670 GHz x 8 CPU) <br />
*Wall time: 1:32<br />
*Scalability: 7.6956<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03c|v9-01-03c]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, '''Dry Dep''', Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify): '''Sea salt emissions & deposition''', '''Dust AOD'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-03d/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.3024776896910 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7075 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
| SALA, SALC, N2O5, HNO3, NIT, NITs, NH4, NH3, SO4s, HNO4, NOx, PAN<br />
|-<br />
|Comments on SURFACE differences: <br />
| Concentrations of sea salt aerosols (SALA and SALC) increase in the tropics by ~50-100% and decrease at mid-high latitudes by 50-100% as expected from the implementation of the SST dependent sea salt source function.<br />
The impact on other species is largest for nitrogen and sulfur species that directly interact with sea salt. While the levels for some of these species change by factors of 1.5-2 over the tropical and high latitude oceans (HNO3, NIT, NITs, SO4s, NH3, NH4), their concentrations are very small in these remote regions, so the absolute changes are small. For example, HNO3 increases by more than a factor of 2 over the remote southern ocean, and decreases by a factor of 2 over the tropics. But the absolute changes are a few pptv at the surface.<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
| SALA, SALC, SO4s, NH3, NIT, NITs<br />
|-<br />
|Comments on 500 hPa differences:<br />
| <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
| SALA, SALC, HNO3, N2O5, HNO4, SO4s, NH4, NIT, NITs<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
| Most of the effects are concentrated near the surface, where the sea salt burden is highest.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
| SALA, SALC<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| As expected from the inclusion of a SST dependence in the sea salt source function, sea salt emissions for accumulation mode sea salt aerosols (SALA) increase by 30-80% in warm tropical regions, and decrease by ~50% over high-latitudes. Overall SALA emissions decrease by 23%. Global emission of coarse mode sea salt aerosols (SALC) increase by 70%, with the largest increases in the tropics. This is driven by both the SST dependence but also the expansion of the size distribution of sea salt from 0.5-4 to 0.5-8 microns.<br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|12 Jan 2012<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 11:44, 11 January 2012 (EST)<br />
<br />
=== v9-01-03c ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03c'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Dry deposition#OVOCs dry deposition|OVOC dry deposition updates]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Jingqiu Mao (NOAA/GFDL) <br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Fri Dec 16 00:16:12 EST 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-11-c.as.harvard.edu (2.660 GHz x 8 CPU) <br />
*Wall time: 1:58<br />
*Scalability: 6.2283<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03b|v9-01-03b]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, '''Dry Dep''', Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-03c/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.3104192214225 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7056 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|PAN, ISOP, ALD2, RCHO, MVK, MACR, PMN, PPN, PRPE, CH2O, N2O5, MP, DMS <br />
|-<br />
|Comments on SURFACE differences: <br />
|The biggest difference were found for MVK and MACR, as they were not deposited in previous versions. The difference in HCHO is about 10%. The differences in organic nitrates are expected due to the supply of OVOCs. <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ISOP, ALD2, RCHO, MVK, MACR, PMN, PRPE, N2O5, DMS, NH3, NIT <br />
|-<br />
|Comments on 500 hPa differences:<br />
| Expected.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|MVK,MACR,PMN,NH3,NIT <br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
| Expected.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
| None<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| <br />
|-<br />
|Additional or summary comments:<br />
|The small increase in global mean OH is likely due to the small increase of NOx (similar pattern in the difference plots).<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes (Jingqiu Mao)<br />
|-<br />
|Date of approval:<br />
|12-19-2011<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 10:46, 19 December 2011 (EST)<br />
<br />
=== v9-01-03b ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03b'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Acetone|Improved acetone simulation]]<br />
*Complete shift of biogenic VOC emissions from GEIA to [[MEGAN biogenic emissions|MEGAN]]; [[Biogenic emissions#Retirement of obsolete GEIA_biogenic emissions|retire GEIA ]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''Acetone:'' Emily Fischer (Harvard)<br />
*''Retirement of GEIA:'' Dylan Millet (U. Minnesota)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Tue Dec 13 12:20:47 EST 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-10-c.as.harvard.edu (2.659 GHz x 8 CPU) <br />
*Wall time: 1:39<br />
*Scalability: 7.2830<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-03a|v9-01-03a]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, '''Biogenic Emiss''', Biomass Emiss, Photolysis, Chemistry, Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-03b/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.2811407896285 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7161 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|PAN, ACET, R4N2 <br />
|-<br />
|Comments on SURFACE differences:<br />
|ACET generally decreases 10-50%, strongest decreases over the oceans due to elimination of the (incorrect) ocean source. Over continental regions, the largest changes are away from terrestrial acetone sources. There are smaller relative changes over the main continental emission regions. PAN decreases by 10-25% over most of the NH oceans, but the absolute differences are very small due to low surface PAN mixing ratios in these regions (< 30 pptv). Weak decreases for R4N2 in a couple spots. <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ACET, R4N2 <br />
|-<br />
|Comments on 500 hPa differences:<br />
|ACET decreases of 10-25% over many regions at 500hPa. Weak decreases for R4N2 in a couple spots. <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|ACET, PAN<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Changes exceeding 10% for ACET and PAN, consistent with the above. <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|ACET <br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|Changes as expected based on emission updates. <br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes (--[[User:Dbm|Dbm]] 11:17, 14 December 2011 (EST))<br>Yes (--[[User:Emily Fischer] 3:32, 14 December 2011 (EST))<br />
|-<br />
|Date of approval:<br />
|12-14-2011<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 13:42, 13 December 2011 (EST)<br>--[[User:Bmy|Bob Y.]] 17:06, 14 December 2011 (EST)<br />
<br />
=== v9-01-03a ===<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-03a'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Chemistry_Issues#GLCO3.2C_GLPAN_bug_in_standard_mechanism|Fix for GLCO3/GLPAN bug in standard chemistry mechanism]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Fabien Paulot (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-03, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Wed Dec 7 16:06:38 EST 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-04-c.as.harvard.edu (2.925 GHz x 8 CPU) <br />
*Wall time: 0:57<br />
*Scalability: 7.4849<br />
|-<br />
|Compared to previous benchmark:<br />
|[[GEOS-Chem v9-01-02 benchmark history#v9-01-02s|v9-01-02s]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, '''Chemistry''', Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/gcgrid/geos-chem/1mo_benchmarks/v9-01-03a/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.2473124589166 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7300 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|PAN (downwind of South America), ALK4 over oceanic basins, ISOP downwind of South America, MEK tropics, MVK, MACR (downwind of South America), PMN, PPN, PRPE, N2O5, DMS<br />
|-<br />
|Comments on SURFACE differences:<br />
|Sort of makes sense. Changes are in regions that are NOx starved (South America) or cold (the loss from GLPAN will be greatest). Changes are small overall and almost always negative. The changes for DMS are relatively large (10-20% decrease)<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ALK4, ISOP, MEK, MVK, MACR, PRPE (large changes in polar regions > 20%), DMS<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Changes are generally bigger than at the surface (temperature dependence of GLPAN)<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|ISOP (but at high altitude and in polar regions), ALK4 in polar regions, MEK, MVK, MACR, PMN, PRPE<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Small changes overall (in an absolute sense). DMS has the largest change.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|none <br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| <br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|Approved 08 Dec 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 11:21, 8 December 2011 (EST)<br>--[[User:Melissa Payer|Melissa Payer]] 13:48, 13 December 2011 (EST)</div>Psk9https://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_v9-01-02_benchmark_history&diff=7978GEOS-Chem v9-01-02 benchmark history2011-09-22T20:50:28Z<p>Psk9: /* v9-01-02n */</p>
<hr />
<div>On this page we have posted complete information about all benchmark simulations (both 1-month and 1-year) for [[GEOS-Chem v9-01-02]].<br />
<br />
== v9-01-02n ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02n'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Biomass burning emissions#GFED3|GFED3 biomass burning emissions]]<br />
*[[GEOS-Chem v9-01-02#Minor fixes in APM microphysics|Minor fixes in APM microphysics]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''GFED3'': Prasad Kasibhatla (Duke U.)<br />
*''APM fixes'': Gan Luo (SUNY Albany)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Thu Sep 8 16:57:34 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-03-c.as.harvard.edu (2.659 GHz x 8 CPU)<br />
*Wall time: 1:39<br />
*Scalability: 7.5995<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02m|v9-01-02m]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, '''Biomass Emiss''', Photolysis, Chemistry, Diagnostics, Other (please specify): '''APM Microphysics (will not affect the standard simulation)'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-02n/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1946336476655 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7422 years <br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|Most species changed in specific regions by more than 10% <br />
|-<br />
|Comments on SURFACE differences:<br />
|Changes reflect changes from GFED2 to GFED3 inventory, as well as due to the resulting change in OH <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|A few species changed is specific reginon <br />
|-<br />
|Comments on 500 hPa differences:<br />
|Smaller effect of change from GFED2 to GFED3 at 500 hPa relative to surface <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|Most species changed, especially at high northern latitudes <br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Changes reflect changes from GFED2 to GFED3 inventory, as well as due to the resulting change in OH in lower troposphere <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|Most species changed in specific regional locations <br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|Reflects chamges from GFED2 to GFED3<br />
|-<br />
|Additional or summary comments:<br />
|Zonal-mean OH diff plots seems to show large change in stratosphere - I assume this is some sort of artifact of how plot was done? <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
| <br />
|- <br />
|Approved:<br />
|Yes (Prasad Kasibhatla) <br />
|-<br />
|Date of approval:<br />
|9/22/11 <br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 13:42, 9 September 2011 (EDT)<br />
<br />
== v9-01-02m ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02m'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Grid-independent GEOS-Chem#Elimination of COMMON blocks|Elimination of COMMON blocks + Other source code updates for ESMF compatibility]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*[[GEOS-Chem Support Team]]<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Wed Aug 31 11:22:03 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU)<br />
*Wall time: 01:39<br />
*Scalability: 7.6143<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02l|v9-01-02l]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify): <br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02m/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1547959532210 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7594 years <br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on SURFACE differences:<br />
| <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Small numerical noise where concentrations are low cause large % differences. This is still due to ISORROPIA.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Small numerical noise where concentrations are low cause large % differences. This is still due to ISORROPIA<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|<br />
|-<br />
|Additional or summary comments:<br />
|Further testing by Bob Yantosca has shown that the current implementation of ISORROPIA still introduces numerical noise in GEOS-Chem simulations after a few days of run time. The <tt>-fp-model source</tt> is not sufficient to eliminate this numerical noise.<br />
<br />
To eliminate the effect from ISORROPIA, we re-ran the benchmarks for v9-01-02l and v9-01-02m with ISORROPIA turned off. We have created [ftp://ftp.as.harvard.edu/pub/exchange/bmy/1mo_quick_look/v9-01-02m/v9-01-02m-X.freq_distribution.pdf this frequency distribution histogram plot]. As you can see, both benchmarks have identical results (i.e. 100% of all grid boxes in the central bar of the histogram).<br />
<br />
We have received a fix from Shannon Capps that should eliminate the ISORROPIA numerical noise issue. We will evaluate this fix in the next benchmark.<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|07 Sep 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 15:42, 7 September 2011 (EDT)<br />
<br />
== v9-01-02l ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02l'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[APM aerosol microphysics]]<br />
*[[ISORROPIA II#Solution|Eliminate numerical noise in ISORROPIA II (ifort compiler only)]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''APM'': Fangqun Yu and Gan Luo (SUNY Albany)<br />
*''ISORROPIA fix'': Shannon Capps (Georgia Tech)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Mon Aug 22 17:05:14 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-04-c.as.harvard.edu (2.926 GHz x 8 CPU)<br />
*Wall time: 00:58<br />
*Scalability: 7.2856<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02k|v9-01-02k]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify): '''APM code should not affect 1-month standard simulation'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02l/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1547627780606 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7594 years <br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on SURFACE differences:<br />
| <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
|The concentrations of NH3, NIT in the areas where differences occur are very small. This is the numerical noise caused by ISORROPIA in version v9-01-02k.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Small numerical differences cause large percent differences. Also attributable to the ISORROPIA numerical noise issue in v9-01-02k.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| <br />
|-<br />
|Additional or summary comments:<br />
|In v9-01-02l, we have added the fix to prevent numerical noise in ISORROPIA from entering into the output. This fix was not present in the previous benchmark v9-01-02k. Therefore, in the benchmark output plots we see some minor numerical differences in NH3 and NIT, which are species directly affected by ISORROPIA II.<br />
<br />
To remove the effect of the numerical noise in ISORROPIA II, we ran two 1-week simulations of v9-01-02k and v9-01-02l with the numerical fix applied. The binary punch files from both simulations were 100% binary identical. Also, both simulations had an identical Mean OH concentration (12.9882039409349 x 1e5 molec/cm3). We created [ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02l/v9-01-02l-2.freq_distribution.pdf this frequency distribution plot] from both 1-week simulations. As you can see, the output of both simulations are identical.<br />
<br />
Therefore, we can say that the source code updates made to implement APM microphysics do not affect the 1-month benchmark simulation. (We recommend that the developers of APM do further testing to make sure that the microphysics package is working properly.)<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|23 Aug 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 14:37, 26 August 2011 (EDT)<br />
<br />
== v9-01-02k ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02k'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Implementation of RETRO Anthropogenic Emissions]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Wes Reinhart (U. Minnesota)<br />
*Dylan Millet (U. Minnesota)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Wed Aug 17 12:52:36 EDT 2011 <br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-04-c.as.harvard.edu (2.926 GHz x 8 CPU) <br />
*Wall time: 00:57<br />
*Scalability: 7.3259<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02j|v9-01-02j]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, '''Anthro Emiss''', Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify): <br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02k/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1547845430825 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7594 years <br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|Large relative changes for ALK4, PRPE, C3H8. Smaller relative changes for PAN, ACET, MEK, ALD2, RCHO, PPN, R4N2, C2H6, N2O5 and HNO4, DMS (the last three barely 10% in 1 spot)<br />
|-<br />
|Comments on SURFACE differences:<br />
|Emission changes relative to GEIA and to the regional inventories are described [http://wiki.seas.harvard.edu/geos-chem/images/GC_RETRO_update_v831_final.pdf here]. Absolute differences are as expected based on the emission changes. ALK4 emissions do not change very much globally but there are large regional changes. RETRO includes non-zero hydrocarbon emissions over the oceans due to ship traffic; this leads to quite large relative but small absolute changes for some hydrocarbons over the oceans (e.g., PRPE, ALK4, C3H8). Acetone changes are due to changes in precursor emissions as anthropogenic acetone emissions are not in RETRO.<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ALK4, MEK, ALD2, RCHO, R4N2, PRPE, C3H8. NH3 and NIT exhibit random changes as noted previously. <br />
|-<br />
|Comments on 500 hPa differences:<br />
|The larger surface changes propagate to 500 hPa to a certain extent.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|ALK4 and C3H8 change by >10% over much of NH. Absolute differences generally < 0.5ppbC. Zonal means for MEK, RCHO, PPN, R4N2 also change by >10% in certain latitudes in line with precursor emission changes. Large relative changes for PRPE, but absolute changes only exceed 0.01 ppbC in the tropics due to emission changes over Africa and S. America. <br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|See above. <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|ALK4, C2H6, C3H8, MEK, PRPE.<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|Emission changes as expected. They are described in more detail [http://wiki.seas.harvard.edu/geos-chem/images/GC_RETRO_update_v831_final.pdf here], including the chemical impacts. One point to note is that global emissions of C3H8 and C2H6 decrease by >2x with RETRO. Applications looking specifically at these tracers will need to keep this in mind. Other compounds such as ALK4 and PRPE have large regional emission changes but don't change as much globally. <br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes (dbm), Yes (wfr). <br />
|-<br />
|Date of approval:<br />
|08/17/2011 <br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 12:59, 17 August 2011 (EDT)<br />
<br />
== v9-01-02j ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02j'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Anthropogenic emissions#Streets 2000|Imposed seasonality on NH3 emissions from David Streets 2000 inventory]]<br />
*[[GEOS-Chem v9-01-02#Minor issues in MERRA cloud convection|Fixed minor issues in MERRA cloud convection routine <tt>DO_MERRA_CONVECTION</tt>]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Jenny Fisher (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Tue Aug 16 12:44:35 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-10-c.as.harvard.edu (2.659 GHz x 8 CPU)<br />
*Wall time: 01:31<br />
*Scalability: 7.6058<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02i|v9-01-02i]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, '''Convection (MERRA only)''', Met Fields, Dry Dep, Wet Dep, Stratosphere, '''Anthro Emiss''', Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, '''Diagnostics (MERRA only)''', Other (please specify): <br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02j/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1516003618353 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7610 years <br />
|-<br />
|Did either of these change by more than 5%?<br />
|No <br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
| HNO3, NH3, NH4, NIT<br />
|-<br />
|Comments on SURFACE differences:<br />
| New simulation introduces seasonal variation in NH3 emissions in Asia (previously used annual mean values). This 1-month benchmark is for July, when agricultural emissions in India and China are high, so as expected surface NH3 is higher in this simulation. NH3 is lower over Indonesia, which is consistent with the monthly scalars for July for that region. Other species (NH4, HNO3, NIT) are affected via thermodynamic partitioning with NH3.<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
| HNO3, NH3, NH4, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
| As expected from changes at surface<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
| HNO3, NH3, NH4, NIT<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
| As expected from NH3 emission changes, differences are greatest at ~30N at surface, but extend latitudinally and vertically.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
| NH3 anthro<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| This update directly changes NH3 anthro emissions<br />
|-<br />
|Additional or summary comments:<br />
|NOTE: The minor fixes in routine <tt>DO_MERRA_CONVECTION</tt> do not impact the results of this benchmark simulation. <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|16 Aug 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 16:32, 16 August 2011 (EDT)<br />
<br />
== v9-01-02i ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02i'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Dry deposition#Aerosol dry deposition velocities over snow and ice surfaces|Updated dry deposition velocities for aerosols over ice and snow]]<br />
*[[GEOS-Chem v9-01-02#Archive the MERRA SWGDN field in the ND67 diagnostic|Archive the MERRA SWGDN (incident radiation @ sfc) field in the ND67 diagnostic]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Jenny Fisher (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Mon Aug 15 13:00:01 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-11-c.as.harvard.edu (2.660 GHz x 8 CPU)<br />
*Wall time: 01:32<br />
*Scalability: 7.5741<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02h|v9-01-02h]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, '''Dry Dep''', Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, '''Diagnostics''', Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/data/1mo_benchmarks/v9-01-02i/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1718619904482 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7556 years <br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
| HNO3, SO4, MSA, NH3, NH4, NIT, BCPI, OCPI, BCPO, OCPO<br />
|-<br />
|Comments on SURFACE differences:<br />
| Dry deposition velocity generally decreased, so aerosol concentrations at the polar surface increased (60-90S, 70-90N). Related impacts on a few gas-phase species (NH3, HNO3) with concentrations governed by thermodynamic equilibrium of aerosol species.<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
| NH3, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
| Quasi-random differences due to change in aerosol species that drive thermodynamic partitioning.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
| HNO3, SO4, MSA, NH3, NH4, NIT, BCPI, OCPI, BCPO, OCPO<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
| Dry deposition velocity generally decreased, so aerosol concentrations at the polar surface increased (60-90S, 70-90N). Related impacts on a few gas-phase species (NH3, HNO3) with concentrations governed by thermodynamic equilibrium of aerosol species.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
| None<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| N/A<br />
|-<br />
|Additional or summary comments:<br />
|NOTE: The ND67 diagnostic modification for MERRA does not impact the results of this benchmark simulation.<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|15 Aug 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 09:56, 16 August 2011 (EDT)<br />
<br />
== v9-01-02h ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02h'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[GEOS-Chem v9-01-02#Fix for GEIA emissions scaling factor over Botswana|Fix for GEIA emissions scaling factor over Botswana]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Dylan Millet (U. Minnesota)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Thu Aug 11 11:30:21 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-05-c.as.harvard.edu (2.793 GHz x 16 CPU)<br />
*Wall time: 00:58<br />
*Scalability: 7.6116<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02g|v9-01-02g]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, '''Anthro Emiss''', Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02h/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1718562359138 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7556 years <br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|Large changes (> 50%) for: ALK4, PAN, ACET, MEK, ALD2, RCHO, PPN, R4N2, PRPE, C3H8, C2H6, N2O5, MP. Smaller changes (~10-25%) for NOx, ISOP, HNO3, H2O2, MVK, MACR, PMN, CH2O, HNO4, DMS, SO4, NH3, NH4, NIT<br />
|-<br />
|Comments on SURFACE differences:<br />
|Changes are all over and immediately downwind of southern Africa, as expected. Large changes to the anthropogenic hydrocarbons because their emissions were strongly decreased over Botswana to correct scaling bug. Large changes to some of their immediate oxidation products (ACET, RCHO, PPN, ALD2, PAN, etc.). Some smaller changes to other species due to secondary chemical effects (OH has increased somewhat in the outflow from southern Africa because we no longer have the artificially elevated VOC concentrations).<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ALK4, ISOP, MEK, ALD2, RCHO, PPN, R4N2, PRPE, C3H8, C2H6. NH3 and NIT exhibit random noisy changes at 500 hPa.<br />
|-<br />
|Comments on 500 hPa differences:<br />
|The changes over and downwind of southern Africa propagate to the free troposphere for some of the species. Changes are weaker than at the surface and exhibit the expected patterns. For NH3 and NIT the 500 hPa absolute changes are near zero; this issue has been reported [[#v9-01-02a|previously]].<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|PAN, ALK4, ACET, MEK, ALD2, RCHO, PPN, R4N2, PRPE, C3H8, C2H6, N2O5, NH3, NIT. OH changes by ~5% in the zonal mean around 25 degrees South.<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Zonal mean differences of >10% are restricted to the emitted anthropogenic hydrocarbons and some of their immediate oxidation products, as expected. Same issue as above for NH3 and NIT; the absolute changes are negligible. Changes in N2O5 just exceed 10% due to corresponding changes in NOx of <10%. <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|ACET, ALK4, C2H6, C3H8, MEK, PRPE <br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|Emission changes for the anthropogenic hydrocarbons over southern Africa as expected. <br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No <br />
|- <br />
|Approved:<br />
|Yes <br />
|-<br />
|Date of approval:<br />
|12 Aug 2011 <br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 11:31, 15 August 2011 (EDT)<br />
<br />
== v9-01-02g ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02g'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[GEOS-Chem v9-01-02#Overhaul of aerosol optical depth diagnostics|Overhaul of AOD diagnostics]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Sungshik Patrick Kim (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Wed Aug 3 15:00:30 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU)<br />
*Wall time: 01:32<br />
*Scalability: 7.6115<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02f|v9-01-02f]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, '''Diagnostics''', Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02g/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1512226781986 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7648 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on SURFACE differences:<br />
| <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
|These are are likely due to small number differences, probably caused by ISORROPIA.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NIT<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Caused by small number differences near the limit of single precision.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| <br />
|-<br />
|Additional or summary comments:<br />
|Aerosol optical depths (AOD) are recomputed after chemistry but before diagnostics are archived. This will make sure that any removal of aerosol by chemistry or deposition will be reflected in the archived AOD diagnostics.<br />
<br />
There is a [[ISORROPIA_II#Optimization_and.2For_parallelization_issues_in_ISORROPIA_II|known issue in ISORROPIA]] that can cause random differences, especially in species like HNO3, NH3, and NIT. This issue has not been resolved in v9-01-02g.<br />
<br />
In order to remove the effects of the ISORROPIA II issue, we have created [ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02g/v9-01-02g-2.freq_distribution.pdf this frequency distribution histogram]. The histogram reflects results from GEOS-Chem 1-week simulations of v9-01-02g vs v9-01-02f with ISORROPIA turned off. As you can see, 100% of all of the transported tracers fall into the central bin in the histogram. This lets us say with certainty that the small differences that we see in the output plots for v9-01-02g are not caused by the AOD diagnostic updates, but are caused by the bug in ISORROPIA II.<br />
<br />
*'''''Update 8/17/11''''': We now understand the source of this ISORROPIA error. Please see [[ISORROPIA II#Solution|this wiki post]] for more information.<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|10 Aug 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 13:38, 18 August 2011 (EDT)<br />
<br />
== v9-01-02f ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02f'''. This is a re-submission of v9-01-02b.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Wet deposition#Washout fix for non-aerosol species|Washout fix for non-aerosol species]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Helen Amos (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Mon Aug 1 13:36:33 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-03-c.as.harvard.edu (2.659 GHz x 8 CPU)<br />
*Wall time: 01:28<br />
*Scalability: 7.6258 <br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02e|v9-01-02e]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, '''Wet Dep''', Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02f/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1512320861717 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7648 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No. <br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|ISOP, HNO3, H2O2, MVK, MACR, PMN, PRPE, CH2O, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT<br />
|-<br />
|Comments on SURFACE differences:<br />
|Largest changes: H2O2, NIT, NH3<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ISOP, HNO3, H2O2, MVK, MACR, PMN, PRPE, CH2O, MP, DMS, SO2, SO4, NH3, NH4, NIT <br />
|-<br />
|Comments on 500 hPa differences:<br />
|Largest changes: H2O2, ISOP, NIT, NH3 <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|ISOP, HNO3, H2O2, MVK, MACR, PMN, PRPE, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, <br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Species change by 10% north of 30N and south of 30S. <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None. <br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|None. <br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|YES<br />
|-<br />
|Date of approval:<br />
|01 Aug 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 12:32, 1 August 2011 (EDT)<br />
<br />
== v9-01-02e ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02e'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|Various source-code updates and fixes that will have no impact on the standard 1-month full-chemistry benchmark simulation:<br />
#[[GEOS-Chem v9-01-02#Various bug fixes for the offline Hg simulation|Various bug fixes for the offline Hg simulation]]<br />
#[[GEOS-Chem v9-01-02#Bug fix for leap years with GCAP|Bug fixes for leap years when using GCAP met fields]]<br />
#[[GEOS-Chem v9-01-02#Minor bug fixes for emissions routines affecting offline simulations|Minor bug fixes for emissions routines affecting offline simulations]]<br />
#[[GEOS-Chem v9-01-02#Fixes for minor issues affecting nested-grid simulations|Fixes for minor issues affecting nested-grid simulations]]<br />
#[[GEOS-Chem v9-01-02#Bug fixes for compatibility with the PGI compiler|Fixes for better compatibility with the PGI compiler]]<br />
#[[GEOS-Chem v9-01-02#Planeflight diagnostic update|Add MERRA SEAICExx fields to the planeflight diagnostic]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
#Jenny Fisher (Harvard); Helen Amos (Harvard); Chris Holmes (UC Irvine)<br />
#GEOS-Chem Support Team<br />
#GEOS-Chem Support Team<br />
#Luke Schiferl (Colo. State); Lin Zhang (Harvard)<br />
#Gan Luo (SUNY Albany)<br />
#Jenny Fisher (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Fri Jul 29 16:00:03 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU) <br />
*Wall time: 01:30<br />
*Scalability: 7.6186<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02d|v9-01-02d]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify): '''We expect to see no changes from v9-01-02d'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02e/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1838752732688 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7493 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No. Both are identical to the previous run v9-01-02d.<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on SURFACE differences:<br />
|<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on 500 hPa differences:<br />
|<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
| <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| <br />
|-<br />
|Additional or summary comments:<br />
|All of the changes were to fix mostly minor issues in (1) the Hg simulation, (2) the GCAP simulation, (3) nested-grid simulations, (4) offline simulations, and (5) the planeflight diagnostics. We did not add any scientific updates to the code; therefore, the standard chemistry simulation was not affected. The output file from this benchmark (<tt>ctm.bpch.v9-01-02e</tt>) is 100% binary identical to the output file from the previous benchmark (<tt>ctm.bpch.v9-01-02d</tt>). <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|YES<br />
|-<br />
|Date of approval:<br />
|01 Aug 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 10:37, 1 August 2011 (EDT)<br />
<br />
== v9-01-02d ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02d'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Grid-independent_GEOS-Chem#Source_code_cleanup_and_initial_ESMF_prep|Initial source code modifications for compatibility with Earth System Model Framework]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*[[GEOS-Chem Support Team]]<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Tue Jul 26 12:35:13 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-01-c.as.harvard.edu (2.926 GHz x 16 CPU)<br />
*Wall time: 01:07<br />
*Scalability: 7.4958<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02c|v9-01-02c]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify): '''We expect to see no changes from v9-01-02c'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02d/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1838752732688 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7493 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No.<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|none<br />
|-<br />
|Comments on SURFACE differences:<br />
|<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|none<br />
|-<br />
|Comments on 500 hPa differences:<br />
|<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|none<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|none<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|<br />
|-<br />
|Additional or summary comments:<br />
|This benchmark was to test the initial importation of source code for ESMF. We did this in such a way so that the standard chemistry simulation is not affected. The output file from this benchmark (<tt>ctm.bpch.v9-01-02d</tt>) is 100% binary identical to the output file from the previous benchmark (<tt>ctm.bpch.v9-01-02c</tt>). <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|YES<br />
|-<br />
|Date of approval:<br />
|26 Jul 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 14:52, 26 July 2011 (EDT)<br />
<br />
== v9-01-02c ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02c'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
* [[Restart_files#Potential_issue_with_reading_restart.cspec_file|Fix for mis-indexing error in the CSPEC restart file]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Jingqiu Mao (NOAA/Princeton)<br />
*[[GEOS-Chem Support Team]]<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Wed Jul 20 16:47:00 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-06-c.as.harvard.edu (2.792 GHz x 16 CPU)<br />
*Wall time: 00:57<br />
*Scalability: 7.5008<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02a|v9-01-02a]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify): '''Chemical species restart file'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02c/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1838752732688 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7493 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No. The Mean OH is identical to v9-01-02a and the MCL lifetime has a small difference in the very last digit (see Summary Comments).<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|none<br />
|-<br />
|Comments on SURFACE differences:<br />
|<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|<br />
|-<br />
|Comments on 500 hPa differences:<br />
|<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|none<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|none<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|<br />
|-<br />
|Additional or summary comments:<br />
|NOTE: This update corrects an erroneous situation in the [[Restart_files#Chemical_species|chemical species restart file (aka "CSPEC restart file"]]. This fix ONLY gets invoked for long GEOS-Chem simulations that have to be broken into several stages for the purpose of submitting to computational queues with fixed time limits. When each run stage ends, GEOS-Chem will write the chemical species concentrations into a restart file. When the next run stage begins, GEOS-Chem will read the chemical species information back into the CSPEC array (which gets passed to the SMVGEAR and KPP solvers).<br />
<br />
For short simulations that can finish within the time limits of the computatational queues (such as this 1-month benchmark simulation), we do not use the CSPEC restart file. Therefore, when comparing v9-01-01c to v9-01-01a, we should expect to see identical results to v9-01-02a (which we do see as evidenced by the plots and Mean OH concentration).<br />
<br />
In v9-01-02c, we use the grid box surface areas saved out directly from GEOS-Chem (via the ND69 diagnostic) to compute the MCL lifetime. In v9-01-02a, we computed the grid box surface areas using IDL code. The surface areas from both methods should be similar, but perhaps not strictly numerically equal to all double-precision digits. This causes the very slight difference in the last digit of the MCL lifetime for v9-01-02c.<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|YES<br />
|-<br />
|Date of approval:<br />
|21 Jul 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 10:51, 21 July 2011 (EDT)<br />
<br />
== v9-01-02b ==<br />
<br />
GEOS-Chem 1-month benchmark simulation v9-01-02b was withdrawn and re-submitted as [[#v9-01-02f|v9-01-02f]].<br />
<br />
--[[User:Bmy|Bob Y.]] 12:30, 1 August 2011 (EDT)<br />
<br />
== v9-01-02a ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02a'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Dynamic tropopause#Problems with dynamic tropopause and adjoint model|Corrected mis-indexing of grid boxes in <tt>partition.f</tt>]] caused by the [[Dynamic tropopause]]<br />
*[[GEOS-Chem v9-01-02#Out-of-bounds_error in readchem.f|Corrected out-of-bounds error in <tt>readchem.f</tt>]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Dynamic tropopause fix: Daven Henze (Colorado University) and Jamin Koo (MIT)<br />
*Out-of-bounds error: [[GEOS-Chem Support Team]]<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Mon Jun 13 18:02:07 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU) <br />
*Wall time: 01:29<br />
*Scalability: 7.6141<br />
|-<br />
|Compared to previous benchmark:<br />
|v9-01-01<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, '''Chemistry''', Other (please specify): '''Tropopause'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02a/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1838752732688 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7490 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on SURFACE differences:<br />
|None <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NIT, NH3<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Follow up calculations indicate that these changes are owing to an unresolved OpenMP issue, not the v9-01-02a code updates. NIT seems particularly sensitive to this issue, and this probably drives changes in NH3. <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NOx, N2O5, NIT, NH3<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|<br />
*Small changes in tropospheric OH on order of +/-0.05%. <br />
*NOx changes follow from the variable tropopause fix and are small in absolute value.<br />
*There are also small percent changes for most gas-phase species near the tropopause.<br />
*The changes to NIT and NH3 have a random structure with large (>1000%) differences in spots throughout the troposphere, likely owing to the issue mentioned above. However, absolute changes are still small.<br />
*There are small (a few percent or less) changes visible for all chemically active gas and aerosol species. These changes are likely owing to both the code updates and the random OpenMP error, with the former having structure around the tropopause and the latter contributing to random scatter throughout the troposphere.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None <br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|No changes in emissions.<br />
|-<br />
|Additional or summary comments:<br />
| <br />
*There is an unidentified OpenMP error which contributes to differences shown here, as confirmed by independent tests of consecutive evaluations of a single executable compiled with and without parallelization. The impacts of this OpenMP error are typically less than a fraction of a percent, and negligible in terms of absolute value, with the exception of NIT and NH3. This is an issue to investigate further.<br />
**'''''Update 8/17/11''''': We now have attributed this error to ISORROPIA. Please see [[ISORROPIA II#Solution|this wiki post]] for more information.<br />
*I think this code update obfuscates the need to copy CSPEC to CSPEC_FULL and back when variable tropopause is turned on, as this fix now recalls the proper mapping from the previous time step when performing partitioning. Perhaps a future update could clean this up. <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
| See above<br />
|- <br />
|Approved:<br />
| Daven Henze<br />
|-<br />
|Date of approval:<br />
| 06/28/2011<br />
<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 13:37, 18 August 2011 (EDT)</div>Psk9https://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_v9-01-02_benchmark_history&diff=7975GEOS-Chem v9-01-02 benchmark history2011-09-22T20:39:15Z<p>Psk9: /* v9-01-02n */</p>
<hr />
<div>On this page we have posted complete information about all benchmark simulations (both 1-month and 1-year) for [[GEOS-Chem v9-01-02]].<br />
<br />
== v9-01-02n ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02n'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Biomass burning emissions#GFED3|GFED3 biomass burning emissions]]<br />
*[[GEOS-Chem v9-01-02#Minor fixes in APM microphysics|Minor fixes in APM microphysics]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''GFED3'': Prasad Kasibhatla (Duke U.)<br />
*''APM fixes'': Gan Luo (SUNY Albany)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Thu Sep 8 16:57:34 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-03-c.as.harvard.edu (2.659 GHz x 8 CPU)<br />
*Wall time: 1:39<br />
*Scalability: 7.5995<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02m|v9-01-02m]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, '''Biomass Emiss''', Photolysis, Chemistry, Diagnostics, Other (please specify): '''APM Microphysics (will not affect the standard simulation)'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/exchange/mpayer/1mo_quick_look/v9-01-02n/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1946336476655 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7422 years <br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|Most species changed in specific regions by more than 10% reflecting changes from GFED3 to GFED2 emissions, as well as due to the resulting change in OH <br />
|-<br />
|Comments on SURFACE differences:<br />
| <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
| <br />
|-<br />
|Comments on 500 hPa differences:<br />
| <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
| <br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
| <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
| <br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|<br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
| <br />
|- <br />
|Approved:<br />
| <br />
|-<br />
|Date of approval:<br />
| <br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 13:42, 9 September 2011 (EDT)<br />
<br />
== v9-01-02m ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02m'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Grid-independent GEOS-Chem#Elimination of COMMON blocks|Elimination of COMMON blocks + Other source code updates for ESMF compatibility]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*[[GEOS-Chem Support Team]]<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Wed Aug 31 11:22:03 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU)<br />
*Wall time: 01:39<br />
*Scalability: 7.6143<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02l|v9-01-02l]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify): <br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02m/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1547959532210 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7594 years <br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on SURFACE differences:<br />
| <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Small numerical noise where concentrations are low cause large % differences. This is still due to ISORROPIA.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Small numerical noise where concentrations are low cause large % differences. This is still due to ISORROPIA<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|<br />
|-<br />
|Additional or summary comments:<br />
|Further testing by Bob Yantosca has shown that the current implementation of ISORROPIA still introduces numerical noise in GEOS-Chem simulations after a few days of run time. The <tt>-fp-model source</tt> is not sufficient to eliminate this numerical noise.<br />
<br />
To eliminate the effect from ISORROPIA, we re-ran the benchmarks for v9-01-02l and v9-01-02m with ISORROPIA turned off. We have created [ftp://ftp.as.harvard.edu/pub/exchange/bmy/1mo_quick_look/v9-01-02m/v9-01-02m-X.freq_distribution.pdf this frequency distribution histogram plot]. As you can see, both benchmarks have identical results (i.e. 100% of all grid boxes in the central bar of the histogram).<br />
<br />
We have received a fix from Shannon Capps that should eliminate the ISORROPIA numerical noise issue. We will evaluate this fix in the next benchmark.<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|07 Sep 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 15:42, 7 September 2011 (EDT)<br />
<br />
== v9-01-02l ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02l'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[APM aerosol microphysics]]<br />
*[[ISORROPIA II#Solution|Eliminate numerical noise in ISORROPIA II (ifort compiler only)]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*''APM'': Fangqun Yu and Gan Luo (SUNY Albany)<br />
*''ISORROPIA fix'': Shannon Capps (Georgia Tech)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Mon Aug 22 17:05:14 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-04-c.as.harvard.edu (2.926 GHz x 8 CPU)<br />
*Wall time: 00:58<br />
*Scalability: 7.2856<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02k|v9-01-02k]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify): '''APM code should not affect 1-month standard simulation'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02l/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1547627780606 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7594 years <br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on SURFACE differences:<br />
| <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
|The concentrations of NH3, NIT in the areas where differences occur are very small. This is the numerical noise caused by ISORROPIA in version v9-01-02k.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Small numerical differences cause large percent differences. Also attributable to the ISORROPIA numerical noise issue in v9-01-02k.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| <br />
|-<br />
|Additional or summary comments:<br />
|In v9-01-02l, we have added the fix to prevent numerical noise in ISORROPIA from entering into the output. This fix was not present in the previous benchmark v9-01-02k. Therefore, in the benchmark output plots we see some minor numerical differences in NH3 and NIT, which are species directly affected by ISORROPIA II.<br />
<br />
To remove the effect of the numerical noise in ISORROPIA II, we ran two 1-week simulations of v9-01-02k and v9-01-02l with the numerical fix applied. The binary punch files from both simulations were 100% binary identical. Also, both simulations had an identical Mean OH concentration (12.9882039409349 x 1e5 molec/cm3). We created [ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02l/v9-01-02l-2.freq_distribution.pdf this frequency distribution plot] from both 1-week simulations. As you can see, the output of both simulations are identical.<br />
<br />
Therefore, we can say that the source code updates made to implement APM microphysics do not affect the 1-month benchmark simulation. (We recommend that the developers of APM do further testing to make sure that the microphysics package is working properly.)<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|23 Aug 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 14:37, 26 August 2011 (EDT)<br />
<br />
== v9-01-02k ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02k'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Implementation of RETRO Anthropogenic Emissions]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Wes Reinhart (U. Minnesota)<br />
*Dylan Millet (U. Minnesota)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Wed Aug 17 12:52:36 EDT 2011 <br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-04-c.as.harvard.edu (2.926 GHz x 8 CPU) <br />
*Wall time: 00:57<br />
*Scalability: 7.3259<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02j|v9-01-02j]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, '''Anthro Emiss''', Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify): <br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02k/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1547845430825 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7594 years <br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|Large relative changes for ALK4, PRPE, C3H8. Smaller relative changes for PAN, ACET, MEK, ALD2, RCHO, PPN, R4N2, C2H6, N2O5 and HNO4, DMS (the last three barely 10% in 1 spot)<br />
|-<br />
|Comments on SURFACE differences:<br />
|Emission changes relative to GEIA and to the regional inventories are described [http://wiki.seas.harvard.edu/geos-chem/images/GC_RETRO_update_v831_final.pdf here]. Absolute differences are as expected based on the emission changes. ALK4 emissions do not change very much globally but there are large regional changes. RETRO includes non-zero hydrocarbon emissions over the oceans due to ship traffic; this leads to quite large relative but small absolute changes for some hydrocarbons over the oceans (e.g., PRPE, ALK4, C3H8). Acetone changes are due to changes in precursor emissions as anthropogenic acetone emissions are not in RETRO.<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ALK4, MEK, ALD2, RCHO, R4N2, PRPE, C3H8. NH3 and NIT exhibit random changes as noted previously. <br />
|-<br />
|Comments on 500 hPa differences:<br />
|The larger surface changes propagate to 500 hPa to a certain extent.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|ALK4 and C3H8 change by >10% over much of NH. Absolute differences generally < 0.5ppbC. Zonal means for MEK, RCHO, PPN, R4N2 also change by >10% in certain latitudes in line with precursor emission changes. Large relative changes for PRPE, but absolute changes only exceed 0.01 ppbC in the tropics due to emission changes over Africa and S. America. <br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|See above. <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|ALK4, C2H6, C3H8, MEK, PRPE.<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|Emission changes as expected. They are described in more detail [http://wiki.seas.harvard.edu/geos-chem/images/GC_RETRO_update_v831_final.pdf here], including the chemical impacts. One point to note is that global emissions of C3H8 and C2H6 decrease by >2x with RETRO. Applications looking specifically at these tracers will need to keep this in mind. Other compounds such as ALK4 and PRPE have large regional emission changes but don't change as much globally. <br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes (dbm), Yes (wfr). <br />
|-<br />
|Date of approval:<br />
|08/17/2011 <br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 12:59, 17 August 2011 (EDT)<br />
<br />
== v9-01-02j ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02j'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Anthropogenic emissions#Streets 2000|Imposed seasonality on NH3 emissions from David Streets 2000 inventory]]<br />
*[[GEOS-Chem v9-01-02#Minor issues in MERRA cloud convection|Fixed minor issues in MERRA cloud convection routine <tt>DO_MERRA_CONVECTION</tt>]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Jenny Fisher (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Tue Aug 16 12:44:35 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-10-c.as.harvard.edu (2.659 GHz x 8 CPU)<br />
*Wall time: 01:31<br />
*Scalability: 7.6058<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02i|v9-01-02i]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, '''Convection (MERRA only)''', Met Fields, Dry Dep, Wet Dep, Stratosphere, '''Anthro Emiss''', Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, '''Diagnostics (MERRA only)''', Other (please specify): <br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02j/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1516003618353 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7610 years <br />
|-<br />
|Did either of these change by more than 5%?<br />
|No <br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
| HNO3, NH3, NH4, NIT<br />
|-<br />
|Comments on SURFACE differences:<br />
| New simulation introduces seasonal variation in NH3 emissions in Asia (previously used annual mean values). This 1-month benchmark is for July, when agricultural emissions in India and China are high, so as expected surface NH3 is higher in this simulation. NH3 is lower over Indonesia, which is consistent with the monthly scalars for July for that region. Other species (NH4, HNO3, NIT) are affected via thermodynamic partitioning with NH3.<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
| HNO3, NH3, NH4, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
| As expected from changes at surface<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
| HNO3, NH3, NH4, NIT<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
| As expected from NH3 emission changes, differences are greatest at ~30N at surface, but extend latitudinally and vertically.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
| NH3 anthro<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| This update directly changes NH3 anthro emissions<br />
|-<br />
|Additional or summary comments:<br />
|NOTE: The minor fixes in routine <tt>DO_MERRA_CONVECTION</tt> do not impact the results of this benchmark simulation. <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|16 Aug 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 16:32, 16 August 2011 (EDT)<br />
<br />
== v9-01-02i ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02i'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Dry deposition#Aerosol dry deposition velocities over snow and ice surfaces|Updated dry deposition velocities for aerosols over ice and snow]]<br />
*[[GEOS-Chem v9-01-02#Archive the MERRA SWGDN field in the ND67 diagnostic|Archive the MERRA SWGDN (incident radiation @ sfc) field in the ND67 diagnostic]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Jenny Fisher (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Mon Aug 15 13:00:01 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-11-c.as.harvard.edu (2.660 GHz x 8 CPU)<br />
*Wall time: 01:32<br />
*Scalability: 7.5741<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02h|v9-01-02h]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, '''Dry Dep''', Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, '''Diagnostics''', Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/data/1mo_benchmarks/v9-01-02i/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1718619904482 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7556 years <br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
| HNO3, SO4, MSA, NH3, NH4, NIT, BCPI, OCPI, BCPO, OCPO<br />
|-<br />
|Comments on SURFACE differences:<br />
| Dry deposition velocity generally decreased, so aerosol concentrations at the polar surface increased (60-90S, 70-90N). Related impacts on a few gas-phase species (NH3, HNO3) with concentrations governed by thermodynamic equilibrium of aerosol species.<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
| NH3, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
| Quasi-random differences due to change in aerosol species that drive thermodynamic partitioning.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
| HNO3, SO4, MSA, NH3, NH4, NIT, BCPI, OCPI, BCPO, OCPO<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
| Dry deposition velocity generally decreased, so aerosol concentrations at the polar surface increased (60-90S, 70-90N). Related impacts on a few gas-phase species (NH3, HNO3) with concentrations governed by thermodynamic equilibrium of aerosol species.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
| None<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| N/A<br />
|-<br />
|Additional or summary comments:<br />
|NOTE: The ND67 diagnostic modification for MERRA does not impact the results of this benchmark simulation.<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|15 Aug 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 09:56, 16 August 2011 (EDT)<br />
<br />
== v9-01-02h ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02h'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[GEOS-Chem v9-01-02#Fix for GEIA emissions scaling factor over Botswana|Fix for GEIA emissions scaling factor over Botswana]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Dylan Millet (U. Minnesota)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Thu Aug 11 11:30:21 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-05-c.as.harvard.edu (2.793 GHz x 16 CPU)<br />
*Wall time: 00:58<br />
*Scalability: 7.6116<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02g|v9-01-02g]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, '''Anthro Emiss''', Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02h/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1718562359138 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7556 years <br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|Large changes (> 50%) for: ALK4, PAN, ACET, MEK, ALD2, RCHO, PPN, R4N2, PRPE, C3H8, C2H6, N2O5, MP. Smaller changes (~10-25%) for NOx, ISOP, HNO3, H2O2, MVK, MACR, PMN, CH2O, HNO4, DMS, SO4, NH3, NH4, NIT<br />
|-<br />
|Comments on SURFACE differences:<br />
|Changes are all over and immediately downwind of southern Africa, as expected. Large changes to the anthropogenic hydrocarbons because their emissions were strongly decreased over Botswana to correct scaling bug. Large changes to some of their immediate oxidation products (ACET, RCHO, PPN, ALD2, PAN, etc.). Some smaller changes to other species due to secondary chemical effects (OH has increased somewhat in the outflow from southern Africa because we no longer have the artificially elevated VOC concentrations).<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ALK4, ISOP, MEK, ALD2, RCHO, PPN, R4N2, PRPE, C3H8, C2H6. NH3 and NIT exhibit random noisy changes at 500 hPa.<br />
|-<br />
|Comments on 500 hPa differences:<br />
|The changes over and downwind of southern Africa propagate to the free troposphere for some of the species. Changes are weaker than at the surface and exhibit the expected patterns. For NH3 and NIT the 500 hPa absolute changes are near zero; this issue has been reported [[#v9-01-02a|previously]].<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|PAN, ALK4, ACET, MEK, ALD2, RCHO, PPN, R4N2, PRPE, C3H8, C2H6, N2O5, NH3, NIT. OH changes by ~5% in the zonal mean around 25 degrees South.<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Zonal mean differences of >10% are restricted to the emitted anthropogenic hydrocarbons and some of their immediate oxidation products, as expected. Same issue as above for NH3 and NIT; the absolute changes are negligible. Changes in N2O5 just exceed 10% due to corresponding changes in NOx of <10%. <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|ACET, ALK4, C2H6, C3H8, MEK, PRPE <br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|Emission changes for the anthropogenic hydrocarbons over southern Africa as expected. <br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No <br />
|- <br />
|Approved:<br />
|Yes <br />
|-<br />
|Date of approval:<br />
|12 Aug 2011 <br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 11:31, 15 August 2011 (EDT)<br />
<br />
== v9-01-02g ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02g'''. <br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[GEOS-Chem v9-01-02#Overhaul of aerosol optical depth diagnostics|Overhaul of AOD diagnostics]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Sungshik Patrick Kim (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Wed Aug 3 15:00:30 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU)<br />
*Wall time: 01:32<br />
*Scalability: 7.6115<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02f|v9-01-02f]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, '''Diagnostics''', Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02g/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1512226781986 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7648 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on SURFACE differences:<br />
| <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NH3, NIT<br />
|-<br />
|Comments on 500 hPa differences:<br />
|These are are likely due to small number differences, probably caused by ISORROPIA.<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NIT<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Caused by small number differences near the limit of single precision.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| <br />
|-<br />
|Additional or summary comments:<br />
|Aerosol optical depths (AOD) are recomputed after chemistry but before diagnostics are archived. This will make sure that any removal of aerosol by chemistry or deposition will be reflected in the archived AOD diagnostics.<br />
<br />
There is a [[ISORROPIA_II#Optimization_and.2For_parallelization_issues_in_ISORROPIA_II|known issue in ISORROPIA]] that can cause random differences, especially in species like HNO3, NH3, and NIT. This issue has not been resolved in v9-01-02g.<br />
<br />
In order to remove the effects of the ISORROPIA II issue, we have created [ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02g/v9-01-02g-2.freq_distribution.pdf this frequency distribution histogram]. The histogram reflects results from GEOS-Chem 1-week simulations of v9-01-02g vs v9-01-02f with ISORROPIA turned off. As you can see, 100% of all of the transported tracers fall into the central bin in the histogram. This lets us say with certainty that the small differences that we see in the output plots for v9-01-02g are not caused by the AOD diagnostic updates, but are caused by the bug in ISORROPIA II.<br />
<br />
*'''''Update 8/17/11''''': We now understand the source of this ISORROPIA error. Please see [[ISORROPIA II#Solution|this wiki post]] for more information.<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|Yes<br />
|-<br />
|Date of approval:<br />
|10 Aug 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 13:38, 18 August 2011 (EDT)<br />
<br />
== v9-01-02f ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02f'''. This is a re-submission of v9-01-02b.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Wet deposition#Washout fix for non-aerosol species|Washout fix for non-aerosol species]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Helen Amos (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Mon Aug 1 13:36:33 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-03-c.as.harvard.edu (2.659 GHz x 8 CPU)<br />
*Wall time: 01:28<br />
*Scalability: 7.6258 <br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02e|v9-01-02e]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, '''Wet Dep''', Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify):<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02f/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1512320861717 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7648 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No. <br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|ISOP, HNO3, H2O2, MVK, MACR, PMN, PRPE, CH2O, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT<br />
|-<br />
|Comments on SURFACE differences:<br />
|Largest changes: H2O2, NIT, NH3<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|ISOP, HNO3, H2O2, MVK, MACR, PMN, PRPE, CH2O, MP, DMS, SO2, SO4, NH3, NH4, NIT <br />
|-<br />
|Comments on 500 hPa differences:<br />
|Largest changes: H2O2, ISOP, NIT, NH3 <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|ISOP, HNO3, H2O2, MVK, MACR, PMN, PRPE, CH2O, N2O5, HNO4, MP, DMS, SO2, SO4, SO4s, NH3, NH4, NIT, <br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|Species change by 10% north of 30N and south of 30S. <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None. <br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|None. <br />
|-<br />
|Additional or summary comments:<br />
| <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|YES<br />
|-<br />
|Date of approval:<br />
|01 Aug 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 12:32, 1 August 2011 (EDT)<br />
<br />
== v9-01-02e ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02e'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|Various source-code updates and fixes that will have no impact on the standard 1-month full-chemistry benchmark simulation:<br />
#[[GEOS-Chem v9-01-02#Various bug fixes for the offline Hg simulation|Various bug fixes for the offline Hg simulation]]<br />
#[[GEOS-Chem v9-01-02#Bug fix for leap years with GCAP|Bug fixes for leap years when using GCAP met fields]]<br />
#[[GEOS-Chem v9-01-02#Minor bug fixes for emissions routines affecting offline simulations|Minor bug fixes for emissions routines affecting offline simulations]]<br />
#[[GEOS-Chem v9-01-02#Fixes for minor issues affecting nested-grid simulations|Fixes for minor issues affecting nested-grid simulations]]<br />
#[[GEOS-Chem v9-01-02#Bug fixes for compatibility with the PGI compiler|Fixes for better compatibility with the PGI compiler]]<br />
#[[GEOS-Chem v9-01-02#Planeflight diagnostic update|Add MERRA SEAICExx fields to the planeflight diagnostic]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
#Jenny Fisher (Harvard); Helen Amos (Harvard); Chris Holmes (UC Irvine)<br />
#GEOS-Chem Support Team<br />
#GEOS-Chem Support Team<br />
#Luke Schiferl (Colo. State); Lin Zhang (Harvard)<br />
#Gan Luo (SUNY Albany)<br />
#Jenny Fisher (Harvard)<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Fri Jul 29 16:00:03 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU) <br />
*Wall time: 01:30<br />
*Scalability: 7.6186<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02d|v9-01-02d]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify): '''We expect to see no changes from v9-01-02d'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02e/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1838752732688 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7493 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No. Both are identical to the previous run v9-01-02d.<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on SURFACE differences:<br />
|<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on 500 hPa differences:<br />
|<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
| <br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
| <br />
|-<br />
|Additional or summary comments:<br />
|All of the changes were to fix mostly minor issues in (1) the Hg simulation, (2) the GCAP simulation, (3) nested-grid simulations, (4) offline simulations, and (5) the planeflight diagnostics. We did not add any scientific updates to the code; therefore, the standard chemistry simulation was not affected. The output file from this benchmark (<tt>ctm.bpch.v9-01-02e</tt>) is 100% binary identical to the output file from the previous benchmark (<tt>ctm.bpch.v9-01-02d</tt>). <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|YES<br />
|-<br />
|Date of approval:<br />
|01 Aug 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 10:37, 1 August 2011 (EDT)<br />
<br />
== v9-01-02d ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02d'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Grid-independent_GEOS-Chem#Source_code_cleanup_and_initial_ESMF_prep|Initial source code modifications for compatibility with Earth System Model Framework]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*[[GEOS-Chem Support Team]]<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Tue Jul 26 12:35:13 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-01-c.as.harvard.edu (2.926 GHz x 16 CPU)<br />
*Wall time: 01:07<br />
*Scalability: 7.4958<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02c|v9-01-02c]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify): '''We expect to see no changes from v9-01-02c'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02d/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1838752732688 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7493 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No.<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|none<br />
|-<br />
|Comments on SURFACE differences:<br />
|<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|none<br />
|-<br />
|Comments on 500 hPa differences:<br />
|<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|none<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|none<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|<br />
|-<br />
|Additional or summary comments:<br />
|This benchmark was to test the initial importation of source code for ESMF. We did this in such a way so that the standard chemistry simulation is not affected. The output file from this benchmark (<tt>ctm.bpch.v9-01-02d</tt>) is 100% binary identical to the output file from the previous benchmark (<tt>ctm.bpch.v9-01-02c</tt>). <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|YES<br />
|-<br />
|Date of approval:<br />
|26 Jul 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 14:52, 26 July 2011 (EDT)<br />
<br />
== v9-01-02c ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02c'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
* [[Restart_files#Potential_issue_with_reading_restart.cspec_file|Fix for mis-indexing error in the CSPEC restart file]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Jingqiu Mao (NOAA/Princeton)<br />
*[[GEOS-Chem Support Team]]<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Wed Jul 20 16:47:00 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-06-c.as.harvard.edu (2.792 GHz x 16 CPU)<br />
*Wall time: 00:57<br />
*Scalability: 7.5008<br />
|-<br />
|Compared to previous benchmark:<br />
|[[#v9-01-02a|v9-01-02a]]<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, Chemistry, Diagnostics, Other (please specify): '''Chemical species restart file'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02c/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1838752732688 x 10<sup>5</sup> molec cm<sup>-3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7493 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No. The Mean OH is identical to v9-01-02a and the MCL lifetime has a small difference in the very last digit (see Summary Comments).<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|none<br />
|-<br />
|Comments on SURFACE differences:<br />
|<br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|<br />
|-<br />
|Comments on 500 hPa differences:<br />
|<br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|none<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|none<br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|<br />
|-<br />
|Additional or summary comments:<br />
|NOTE: This update corrects an erroneous situation in the [[Restart_files#Chemical_species|chemical species restart file (aka "CSPEC restart file"]]. This fix ONLY gets invoked for long GEOS-Chem simulations that have to be broken into several stages for the purpose of submitting to computational queues with fixed time limits. When each run stage ends, GEOS-Chem will write the chemical species concentrations into a restart file. When the next run stage begins, GEOS-Chem will read the chemical species information back into the CSPEC array (which gets passed to the SMVGEAR and KPP solvers).<br />
<br />
For short simulations that can finish within the time limits of the computatational queues (such as this 1-month benchmark simulation), we do not use the CSPEC restart file. Therefore, when comparing v9-01-01c to v9-01-01a, we should expect to see identical results to v9-01-02a (which we do see as evidenced by the plots and Mean OH concentration).<br />
<br />
In v9-01-02c, we use the grid box surface areas saved out directly from GEOS-Chem (via the ND69 diagnostic) to compute the MCL lifetime. In v9-01-02a, we computed the grid box surface areas using IDL code. The surface areas from both methods should be similar, but perhaps not strictly numerically equal to all double-precision digits. This causes the very slight difference in the last digit of the MCL lifetime for v9-01-02c.<br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
|No<br />
|- <br />
|Approved:<br />
|YES<br />
|-<br />
|Date of approval:<br />
|21 Jul 2011<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 10:51, 21 July 2011 (EDT)<br />
<br />
== v9-01-02b ==<br />
<br />
GEOS-Chem 1-month benchmark simulation v9-01-02b was withdrawn and re-submitted as [[#v9-01-02f|v9-01-02f]].<br />
<br />
--[[User:Bmy|Bob Y.]] 12:30, 1 August 2011 (EDT)<br />
<br />
== v9-01-02a ==<br />
<br />
Here is the assessment form for 1-month benchmark simulation '''v9-01-02a'''.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-bgcolor="#cccccc"<br />
!width="325px"|Description<br />
! <br />
|- <br />
|New features added into GEOS-Chem:<br />
|<br />
*[[Dynamic tropopause#Problems with dynamic tropopause and adjoint model|Corrected mis-indexing of grid boxes in <tt>partition.f</tt>]] caused by the [[Dynamic tropopause]]<br />
*[[GEOS-Chem v9-01-02#Out-of-bounds_error in readchem.f|Corrected out-of-bounds error in <tt>readchem.f</tt>]]<br />
|- <br />
|Developer name(s) and institution(s):<br />
|<br />
*Dynamic tropopause fix: Daven Henze (Colorado University) and Jamin Koo (MIT)<br />
*Out-of-bounds error: [[GEOS-Chem Support Team]]<br />
|-<br />
|Version, resolution, met fields used:<br />
|v9-01-02, GEOS-5 (47L), 4x5<br />
|-<br />
|1-month benchmark finished on:<br />
|Mon Jun 13 18:02:07 EDT 2011<br />
|-<br />
|Performance statistics:<br />
|<br />
*Ran on 8 CPUs of terra-02-c.as.harvard.edu (2.659 GHz x 8 CPU) <br />
*Wall time: 01:29<br />
*Scalability: 7.6141<br />
|-<br />
|Compared to previous benchmark:<br />
|v9-01-01<br />
|-<br />
|This update will impact:<br>(select all that apply with '''boldface''')<br />
|Advection, BL Mixing, Convection, Met Fields, Dry Dep, Wet Dep, Stratosphere, Anthro Emiss, Biogenic Emiss, Biomass Emiss, Photolysis, '''Chemistry''', Other (please specify): '''Tropopause'''<br />
|-<br />
|Plots may be viewed at:<br />
|<tt>ftp://ftp.as.harvard.edu/pub/geos-chem/1mo_benchmarks/v9-01-02a/</tt><br />
|-bgcolor="#cccccc"<br />
!Metrics<br />
! <br />
|-<br />
|Global mean OH (from log file):<br />
|13.1838752732688 x 10<sup>5</sup> molec/cm<sup>3</sup><br />
|-<br />
|Methyl chloroform lifetime:<br />
|4.7490 years<br />
|-<br />
|Did either of these change by more than 5%?<br />
|No<br />
|-<br />
|At the SURFACE, list all species that changed by 10% or more:<br />
|None<br />
|-<br />
|Comments on SURFACE differences:<br />
|None <br />
|-<br />
|At 500 hPa, list all species that changed by 10% or more:<br />
|NIT, NH3<br />
|-<br />
|Comments on 500 hPa differences:<br />
|Follow up calculations indicate that these changes are owing to an unresolved OpenMP issue, not the v9-01-02a code updates. NIT seems particularly sensitive to this issue, and this probably drives changes in NH3. <br />
|-<br />
|In the ZONAL MEAN differences, list all species that changed by 10% or more:<br />
|NOx, N2O5, NIT, NH3<br />
|-<br />
|Comments on ZONAL MEAN differences:<br />
|<br />
*Small changes in tropospheric OH on order of +/-0.05%. <br />
*NOx changes follow from the variable tropopause fix and are small in absolute value.<br />
*There are also small percent changes for most gas-phase species near the tropopause.<br />
*The changes to NIT and NH3 have a random structure with large (>1000%) differences in spots throughout the troposphere, likely owing to the issue mentioned above. However, absolute changes are still small.<br />
*There are small (a few percent or less) changes visible for all chemically active gas and aerosol species. These changes are likely owing to both the code updates and the random OpenMP error, with the former having structure around the tropopause and the latter contributing to random scatter throughout the troposphere.<br />
|-<br />
|In the EMISSION RATIO maps, list all species that changed by 10% or more:<br />
|None <br />
|-<br />
|Comments on EMISSION RATIO differences:<br />
|No changes in emissions.<br />
|-<br />
|Additional or summary comments:<br />
| <br />
*There is an unidentified OpenMP error which contributes to differences shown here, as confirmed by independent tests of consecutive evaluations of a single executable compiled with and without parallelization. The impacts of this OpenMP error are typically less than a fraction of a percent, and negligible in terms of absolute value, with the exception of NIT and NH3. This is an issue to investigate further.<br />
**'''''Update 8/17/11''''': We now have attributed this error to ISORROPIA. Please see [[ISORROPIA II#Solution|this wiki post]] for more information.<br />
*I think this code update obfuscates the need to copy CSPEC to CSPEC_FULL and back when variable tropopause is turned on, as this fix now recalls the proper mapping from the previous time step when performing partitioning. Perhaps a future update could clean this up. <br />
|-bgcolor="#cccccc"<br />
!Approval<br />
! <br />
|-<br />
|Requires further investigation:<br />
| See above<br />
|- <br />
|Approved:<br />
| Daven Henze<br />
|-<br />
|Date of approval:<br />
| 06/28/2011<br />
<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 13:37, 18 August 2011 (EDT)</div>Psk9