Difference between revisions of "Soil NOx emissions"

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This page describes the soil NOx emissions schemes contained within GEOS-Chem.
 
This page describes the soil NOx emissions schemes contained within GEOS-Chem.
  
== Original soil NOx emissions algorithm ==
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== Hudman et al 2012 soil NOx emissions algorithm ==
  
'''''NOTE: In [[GEOS-Chem v9-02]] and higher versions, the original soil NOx emissions algorithm (based on Yienger & Levy [1995] has been replaced by the [[#Updated soil NOx emissions algorithm|updated soil NOx algorithm]] described below.'''''
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The default soil NOx emissions scheme in GEOS-Chem is based on the work on Rynda Hudman and Neil Moore.  Bram Maasakkers further updated this scheme and incorporated it into [[GEOS-Chem v9-02]].  Please see our [[Hudman et al 2012 soil NOx emissions algorithm]] wiki page for a complete description of this emissions scheme.
 
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=== Overview ===
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The original soil NOx emissions scheme in GEOS-Chem was based on the work of ''Yienger and Levy'' [1995] and ''Wang et al'' [1998].  A brief description is given in Section 4.4 from ''Wang et al'' [1998]:
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<blockquote>Nitrogen oxides are emitted by soil microbes during nitrification and denitrification processes.  Following ''Yienger and Levy'' [1995], we compute NO emission fluxes as a function of vegetation type (from the ''Olson'' [1992] map), temperature, precipitation history, fertilizer usage if any, and a canopy reduction factor, &eta;.  Parameter &eta; is the fraction of soil emitted NOx that is deposited within the canopy before it is exported to the atmosphere; it reflects the oxidation of NO to NO2 in the canopy air followed by uptake of NO2 by vegetation [''Jacob and Bakwin'', 1991].  This result was extened by ''Yienger and Levy'' [1995] to other ecosystems by assuming an arbitrary function of LAI and stomatal area index (the product of LAI and the ratio of stomatal area to leaf area).  We attempt here to formulate &eta; on a more physical basis. ...</blockquote>
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<blockquote>We estimate ... a canopy reduction factor &eta; = 70% for the Amazon forest in April, as obtained by ''Jacob and Bakwin'' [1991].  However, our computed global average &eta; is only 20%.  Compared with the Amazon Forest, most ecoystems have smaller values of LAI and gamma, stronger winds above the canopy , and higher canopy surface resistances for NO2 deposition.  Our global mean &eta; is considerably less than the estimate of 50% by ''Yienger & Levy'' [1995].  Our global above-canopy emission of NOx from soils is 6 Tg N/yr, only 10% higher than that of ''Yienger and Levy'' [1995], likely reflecting differences in the meterological fields used for surface temperature and precipitation.</blockquote>
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=== Validation ===
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See ''Wang et al'' [1998] and ''Bey et al'' [2001].
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=== Source code and data ===
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The source code files for the GEOS-Chem soil NOx emissions scheme are:
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#commsoil.h
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#fertadd.f
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#pulsing.f
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#precipfrac.f
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#sfcwindsqr.f
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#soilbase.f
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#soilcrf.f
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#soilnoxems.f
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#soiltemp.f
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#soiltype.f
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For more information about the data, please see the README files in the following GEOS-Chem data directories:
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# 0.5 x 0.666 China nested grid: [ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_0.5x0.666_CH/soil_NOx_200203/README GEOS_0.5x0.666_CH/soil_NOx_200203/README]
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# 0.5 x 0.666 North America nested grid: [ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_0.5x0.666_NA/soil_NOx_200203/README GEOS_0.5x0.666_NA/soil_NOx_200203/README]
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# 2 x 2.5 global data: [ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_2x2.5/soil_NOx_200203/README GEOS_2x2.5/soil_NOx_200203/README]
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# 4 x 5 global data: [ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_4x5/soil_NOx_200203/README GEOS_4x5/soil_NOx_200203/README]
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--[[User:Bmy|Bob Y.]] 09:43, 24 February 2010 (EST)
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== Updated soil NOx emissions algorithm==
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'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02b|v9-02b]] and approved on 29 Oct 2012.'''''
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=== Overview ===
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[mailto:hudman@berkeley.edu Rynda Hudman] has developed a [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/Description_of_New_Soil_Code.pdf new soil NOx emissions scheme], based on the work of Neil Moore (formerly of Dalhousie University)This new soil NOx emissions scheme shall replace the existing scheme.  It is slated to be incorporated into [[GEOS-Chem v9-01-02]] or later.
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--[[User:Bmy|Bob Y.]] 16:40, 9 March 2011 (EST)
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Bram Maasakkers (Eindhoven) further updated the soil NOx emissions scheme developed by Hudman et al. (2012). This update was implemented in [[GEOS-Chem v9-02]].
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'''''[mailto:j.d.maasakkers@student.tue.nl Bram Maasakkers] wrote:'''''
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:The most important changes in the submitted version are:
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:*Minor changes originating from the update from v8-02-02 to v9-01-03. Furthermore, to allow the parametrization to work with non-local planet-boundary layer (PBL) mixing, a soil NOx section has been added to the non-local PBL mixing module. This was required to report the deposition of N to the soil NOx module.
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:*The Jacob and Bakwin (1991) reduction factor has been implemented, representing the deposition of emitted NOx in the canopy. Implementation leads to a decrease of annual soil NOx emissions from 10.7 to 9.5 Tg N yr-1. The largest impact occurs over the tropical rain-forests in South America and central Africa.
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:*To allow the model to work at all resolutions (the provided code only worked at 2x2.5), online regridding has been implemented using new high resolution input files.
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--[[User:Melissa Payer|Melissa Payer]] 12:11, 30 October 2012 (EDT)
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=== Validation ===
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See [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/Description_of_New_Soil_Code.pdf this validation document by Rynda Hudman].
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--[[User:Bmy|Bob Y.]] 16:45, 9 March 2011 (EST)
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=== Source code and data ===
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'''''[mailto:j.d.maasakkers@student.tue.nl Bram Maasakkers] wrote:'''''
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:Four new input files are read in separate modules.
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:*Surface resistance values (for canopy_nox_mod): nc_soilnox_read.F90
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:**soilNOx.Inputs_MODIS_Biomes.nc
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:*Clim file (includes regridding): readclim.F
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:**soilNOx.climate.generic.05x05.nc
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:*Fertilizer reservoir (includes regridding): readfert.F
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:**soilNOx.fert_res.generic.05x05.nc
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:*MODIS/Koppen landcover map (includes regridding): readsoil.F
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:**soilNOx.landtype.generic.025x025.nc
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Data files for the updated soil NOx emissions scheme can be found at:
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  ftp://ftp.as.harvard.edu/pub/geos-chem/data/GEOS_NATIVE/soil_NOx_201208/
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You can download these directories with anonymous FTP or the Wget utility.  For instructions, please see [http://acmg.seas.harvard.edu/geos/doc/man/chapter_2.html#2.4 Chapter 2.4, Downloading the GEOS-Chem shared data directories] in the GEOS-Chem Online User's Guide.
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--[[User:Melissa Payer|Melissa Payer]] 12:22, 30 October 2012 (EDT)
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== References ==
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#Bey I., D. J. Jacob, R. M. Yantosca, J. A. Logan, B. Field, A. M. Fiore, Q. Li, H. Liu, L. J. Mickley, and M. Schultz, ''Global modeling of tropospheric chemistry with assimilated meteorology: Model description and evaluation'', <u>J. Geophys. Res.</u>, '''106''', 23,073-23,096, 2001. [http://acmg.seas.harvard.edu/publications/bey2001a.pdf PDF]
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#Hudman, R.C., N.E. Moore, R.V. Martin, A.R. Russell, A.K. Mebust, L.C. Valin, and R.C. Cohen, ''A mechanistic model of global soil nitric oxide emissions: implementation and space based-constraints'', <u>Atm. Chem. Phys.</u>, '''12''', 7779-7795, doi:10.5194/acp-12-7779-2012. [http://www.atmos-chem-phys.net/12/7779/2012/acp-12-7779-2012.html HTML]
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#Jacob, D.J., and P.S. Bakwin, ''Cycling of NOx in tropical forest canopies and its implications for the global source of biogenic NOx to the atmosphere'', in <u>Microbial Production and Consumption of Greenhouse Gases</u>, edited by W.B. Whitman, American Society of Microbiology, Washington DC, 1991.
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#Olson, J. ''World Ecosystems (WEI.4): Digital raster data on a 10 minute geographic 1080 x 2160 grid, in <u>Global ecosystems database, version 1.0: Disc A</u>, edited by NOAA Natl. Geophys. Data Center, Boulder, Colorado, 1992.
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#Yienger, J.J, and H. Levy, ''Empirical model of global soil-biogenic NOx emissions'', <u>J. Geophys. Res.</u>, '''100''', D6, 11,447-11464, June 20, 1995.
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#Wang, Y., D.J. Jacob, and J.A. Logan, ''Global Simulation of tropospheric O3-NOx-hydrocarbon chemistry: 1. Model formulation'', <u>J. Geophys. Res.</u>, '''103''', pp. 10713-10725, 1998. [http://acmg.seas.harvard.edu/publications/wang1998a.pdf PDF]
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--[[User:Bmy|Bob Y.]] 14:20, 19 February 2010 (EST)
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== Previous issues that have now been resolved ==
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=== Dependency between soil NOx emissions and dry deposition ===
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<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''NOTE: This issue is now resolved with the new soil NOx algorithm that was added to [[GEOS-Chem v9-02]].  The new module <tt>GeosCore/canopy_nox_mod.F</tt> computes the NOx from the canopy independently of the dry deposition module.  We shall leave this post here for reference. (Bob Yantosca, 06 Feb 2014)'''</div>
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In GEOS-Chem there is a code dependency between the [[Dry deposition|dry deposition routines]] and the soil NOx emissions routines.  This is purely historical baggage that goes back to the days of the old 9-layer Harvard-GISS CTM (from which these routines were taken).
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Please see the full discussion on the [[Dry deposition#Dependency between dry deposition and soil NOx emissions|dry deposition wiki page]].
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--[[User:Bmy|Bob Y.]] 10:41, 19 February 2010 (EST)
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=== Quantities zeroed at startup ===
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<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''NOTE: This issue is now resolved with the new soil NOx algorithm that was added to [[GEOS-Chem v9-02]].  A soil NOx restart file is saved at the end of each simulation to ensure that the quantities are preserved between stages of a long simulation.  We shall leave this post here for reference. (Bob Yantosca, 06 Feb 2013)'''</div>
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The existing GEOS-Chem soil NOx emissions code zeroes several quantities at startup, among which are the soil pulsing factors.  These are the multiplicative factors which compute the sudden increase (or "pulse") of NOx from soils after precipitation falls on dry soil.  There are factors for 3 pulsing types in the code: after 5 days, after 10 days, and after 15 days.  These are stored in the SOILPULS array, along with a flag to denote dry or wet soil.
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Here is an illustration of the problem.  The soil pulsing and resultant quantities for a run that started on Feb 1, 2000 are printed out below.
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---> DATE: 2000/02/01  GMT: 00:00  X-HRS:      0.000
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###----------------------------------------------------
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### I, J        :          69          51
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### SOILPULS 1  :    1.00000000000000      ! dry/wet soil
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### SOILPULS 2  :  0.000000000000000E+000  ! 5-day pulsing factor
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### SOILPULS 3  :  0.000000000000000E+000  ! 10-day pulsing factor
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### SOILPULS 4  :  0.000000000000000E+000  ! 15-day pulsing factor
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### PULSE        :    1.00000000000000      ! Resultant pulsing factor
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### SOIL TOT    :    11112048160.8142      ! Soil NOx emissions @ box (69,51)
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Note that all of the soil pulsing factors are zero because this is the very first timestep of the run.  However, if we compare this to a run which started on Jan 1, 2000:
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---> DATE: 2000/02/01  GMT: 00:00  X-HRS:    744.000
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###----------------------------------------------------
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### I, J        :          69          51     
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### SOILPULS 1  :    1.00000000000000      ! dry/wet soil flag
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### SOILPULS 2  :  2.843218125816628E-003  ! 5-day pulsing factor
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### SOILPULS 3  :  2.189570703768949E-002  ! 10-day pulsing factor
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### SOILPULS 4  :  4.879111537477707E-002  ! 15-day pulsing factor
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### PULSE        :    1.89150985108935      ! Resultant pulsing factor
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### SOIL TOT    :    21018548561.9593      ! Soil NOx emissions @ box (69,51)
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we see that the soil pulsing factors have already been initialized to non-zero values from the January spinup.  This leads to different soil NOx emissions than in the run which started on Feb 1, 2000.  This is an inherent flaw in the design of the original soil NOx code, which was taken from the old Harvard-GISS CTM.
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[mailto:hudman@berkeley.edu Rynda Hudman] is currently working on updating the soil NOx algorithm.  The pulsing information (as well as other quantities) will be stored in a soil NOx restart file.  This will eliminate the problem.
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--[[User:Bmy|Bob Y.]] 10:49, 18 February 2010 (EST)
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=== Routine SOIL_DRYDEP produces NaN values when ND44 diagnostic is turned off===
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'''''This issue was tested in the 1-year benchmark simulation [[GEOS-Chem v9-02 benchmark history#v9-02f-Run0|v9-02f]] and approved on 20 Mar 2013.'''''
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This error is suspected of producing anomalously high NOx emissions over Greenland in the 1-year benchmark to GEOS-Chem v9-02f.  We will re-run that benchmark with this fix.
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'''''[mailto:shiki.kim@gmail.com Patrick Kim] wrote:'''''
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:I have discovered [an] error when we run with non-local PBL mixing.... It actually has nothing to do with the non-local mixing itself, but rather is a result of the soil NOx emissions. NIT was being passed as an NaN into <tt>SOIL_DRYDEP</tt> from the <tt>CHEM_NIT</tt> subroutine (in <tt>GeosCore/sulfate_mod.F</tt>), and therefore you get a <tt>NaN</tt> for <tt>DRY_NIT</tt> (in module <tt>GeosCore/get_ndep_mod.F</tt>). This causes the <tt>A_FERT</tt> term to be an NaN in the call to routine <tt>SOILNOX</tt> and it propagates down in the calculation from there.
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:Looking at the <tt>CHEM_NIT</tt> subroutine, it looks like this is because I did not have ND44 turned on in my input.geos file.  In the code, [array] <tt>T44</tt> is only initialized and calculated if the diagnostic is turned on, but this is what is passed to <tt>SOIL_DRYDEP</tt>.  My suggestion would be to change the code to allow the calculation of the dry deposition quantities earlier without having to specifically turn on this diagnostic....  I've run tests with the diagnostic on and have not run into any problems since.
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We have fixed this as follows:
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#<p><tt>GeosCore/sulfate_mod.F</tt>: In routines <tt>CHEM_NH3</tt>, <tt>CHEM_NH4</tt>, <tt>CHEM_NH4aq</tt>, and <tt>CHEM_NIT</tt>, we save drydep fluxes into an array that is defined whether or not you have the ND44 diagnostic turned on.  Then we pass values from that array to <tt>SOIL_DRYDEP</tt>.  Also, we now prevent <tt>SOIL_DRYDEP</tt> and ND44 from being updated if <tt>LNLPBL = .TRUE.</tt>, since in that case those operations will be done in the non-local PBL mixing module (<tt>GeosCore/vdiff_mod.F90</tt>).</p>
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#<p><tt>GeosCore/drydep_mod.F</tt>: Moved the call to <tt>SOIL_DRYDEP</tt> out of the <tt>!$OMP CRITICAL block</tt>, this is not necessary.</p>
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#<p><tt>GeosCore/vdiff_mod.F90</tt>: Cosmetic changes and added comments.</p>
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--[[User:Bmy|Bob Y.]] 16:56, 13 March 2013 (EDT)
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=== Prevent LOG(0) error from occurring in soil NOx module ===
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'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02r|v9-02r]] and approved on 14 Nov 2013.'''''
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In function <tt>PULSING</tt> (in module <tt>GeosCore/soil_nox_mod.F</tt>), a numerical floating-point error may occur if the argument of a logarithm is zero.  To prevent this from occurring, we added this fix:
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!-----------------------------------------------------------------------------
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! Prior to 10/28/13:
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! Now add a numerical trap to prevent log(0) from occurring, which would
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! cause a floating-point error. (mpayer, bmy, 10/28/13)
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!            !Initialize new pulse factor (dry period hours)
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!            PFACTOR = 13.01 * LOG( DRYPERIOD ) - 53.6
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!-----------------------------------------------------------------------------
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            ! Initialize new pulse factor (dry period hours)
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            IF ( DRYPERIOD > 0 ) THEN
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                PFACTOR = 13.01 * LOG( DRYPERIOD ) - 53.6
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            ELSE
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                PFACTOR = -53.6
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            ENDIF
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This issue was discovered with the [[Debugging with the GEOS-Chem unit tester|GEOS-Chem Unit Tester]] while validating the GEOS-4 4x5 full-chemistry simulation.
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--[[User:Bmy|Bob Y.]] 15:28, 14 November 2013 (EST)
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== Outstanding issues that are not yet resolved ==
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None at this time.
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Latest revision as of 18:59, 2 January 2019

This page describes the soil NOx emissions schemes contained within GEOS-Chem.

Hudman et al 2012 soil NOx emissions algorithm

The default soil NOx emissions scheme in GEOS-Chem is based on the work on Rynda Hudman and Neil Moore. Bram Maasakkers further updated this scheme and incorporated it into GEOS-Chem v9-02. Please see our Hudman et al 2012 soil NOx emissions algorithm wiki page for a complete description of this emissions scheme.