Soil NOx emissions
This page describes the soil NOx emissions schemes contained within GEOS-Chem.
Original soil NOx emissions algorithm
The original soil NOx emissions scheme in GEOS-Chem was based on the work of Yienger and Levy  and Wang et al . A brief description is given in Section 4.4 from Wang et al :
Nitrogen oxides are emitted by soil microbes during nitrification and denitrification processes. Following Yienger and Levy , we compute NO emission fluxes as a function of vegetation type (from the Olson  map), temperature, precipitation history, fertilizer usage if any, and a canopy reduction factor, η. Parameter η 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  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 η on a more physical basis. ...
We estimate ... a canopy reduction factor η = 70% for the Amazon forest in April, as obtained by Jacob and Bakwin . However, our computed global average η 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 η is considerably less than the estimate of 50% by Yienger & Levy . Our global above-canopy emission of NOx from soils is 6 Tg N/yr, only 10% higher than that of Yienger and Levy , likely reflecting differences in the meterological fields used for surface temperature and precipitation.
See Wang et al  and Bey et al .
Source code and data
The source code files for the GEOS-Chem soil NOx emissions scheme are:
For more information about the data, please see the README files in the following GEOS-Chem data directories:
- 0.5 x 0.666 China nested grid: GEOS_0.5x0.666_CH/soil_NOx_200203/README
- 0.5 x 0.666 North America nested grid: GEOS_0.5x0.666_NA/soil_NOx_200203/README
- 2 x 2.5 global data: GEOS_2x2.5/soil_NOx_200203/README
- 4 x 5 global data: GEOS_4x5/soil_NOx_200203/README
--Bob Y. 09:43, 24 February 2010 (EST)
Updated soil NOx emissions algorithm
This update was tested in the 1-month benchmark simulation v9-02b and approved on 29 Oct 2012.
Rynda Hudman has developed a 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.
--Bob Y. 16:40, 9 March 2011 (EST)
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.
Bram Maasakkers wrote:
- The most important changes in the submitted version are:
- 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.
- 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.
- 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.
--Melissa Payer 12:11, 30 October 2012 (EDT)
--Bob Y. 16:45, 9 March 2011 (EST)
Source code and data
Bram Maasakkers wrote:
- Four new input files are read in separate modules.
- Surface resistance values (for canopy_nox_mod): nc_soilnox_read.F90
- Clim file (includes regridding): readclim.F
- Fertilizer reservoir (includes regridding): readfert.F
- MODIS/Koppen landcover map (includes regridding): readsoil.F
- Surface resistance values (for canopy_nox_mod): nc_soilnox_read.F90
Data files for the updated soil NOx emissions scheme can be found at:
You can download these directories with anonymous FTP or the Wget utility. For instructions, please see Chapter 2.4, Downloading the GEOS-Chem shared data directories in the GEOS-Chem Online User's Guide.
--Melissa Payer 12:22, 30 October 2012 (EDT)
- 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, J. Geophys. Res., 106, 23,073-23,096, 2001. PDF
- 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, Atm. Chem. Phys., 12, 7779-7795, doi:10.5194/acp-12-7779-2012. HTML
- 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 Microbial Production and Consumption of Greenhouse Gases, edited by W.B. Whitman, American Society of Microbiology, Washington DC, 1991.
- Olson, J. World Ecosystems (WEI.4): Digital raster data on a 10 minute geographic 1080 x 2160 grid, in Global ecosystems database, version 1.0: Disc A, edited by NOAA Natl. Geophys. Data Center, Boulder, Colorado, 1992.
- Yienger, J.J, and H. Levy, Empirical model of global soil-biogenic NOx emissions, J. Geophys. Res., 100, D6, 11,447-11464, June 20, 1995.
- Wang, Y., D.J. Jacob, and J.A. Logan, Global Simulation of tropospheric O3-NOx-hydrocarbon chemistry: 1. Model formulation, J. Geophys. Res., 103, pp. 10713-10725, 1998. PDF
--Bob Y. 14:20, 19 February 2010 (EST)
Previous issues that have now been resolved
Dependency between soil NOx emissions and dry deposition
NOTE: This issue is now resolved with the new soil NOx algorithm that was added to GEOS-Chem v9-02. The new module GeosCore/canopy_nox_mod.F computes the NOx from the canopy independently of the dry deposition module.
In GEOS-Chem there is a code dependency between the 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).
Please see the full discussion on the dry deposition wiki page.
--Bob Y. 10:41, 19 February 2010 (EST)
Quantities zeroed at startup
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.
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.
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.
---> DATE: 2000/02/01 GMT: 00:00 X-HRS: 0.000 ###---------------------------------------------------- ### I, J : 69 51 ### SOILPULS 1 : 1.00000000000000 ! dry/wet soil ### SOILPULS 2 : 0.000000000000000E+000 ! 5-day pulsing factor ### SOILPULS 3 : 0.000000000000000E+000 ! 10-day pulsing factor ### SOILPULS 4 : 0.000000000000000E+000 ! 15-day pulsing factor ### PULSE : 1.00000000000000 ! Resultant pulsing factor ### SOIL TOT : 11112048160.8142 ! Soil NOx emissions @ box (69,51)
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:
---> DATE: 2000/02/01 GMT: 00:00 X-HRS: 744.000 ###---------------------------------------------------- ### I, J : 69 51 ### SOILPULS 1 : 1.00000000000000 ! dry/wet soil flag ### SOILPULS 2 : 2.843218125816628E-003 ! 5-day pulsing factor ### SOILPULS 3 : 2.189570703768949E-002 ! 10-day pulsing factor ### SOILPULS 4 : 4.879111537477707E-002 ! 15-day pulsing factor ### PULSE : 1.89150985108935 ! Resultant pulsing factor ### SOIL TOT : 21018548561.9593 ! Soil NOx emissions @ box (69,51)
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.
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.
--Bob Y. 10:49, 18 February 2010 (EST)
Routine SOIL_DRYDEP produces NaN values when ND44 diagnostic is turned off
This issue was tested in the 1-year benchmark simulation v9-02f and approved on 20 Mar 2013.
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.
Patrick Kim wrote:
- 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 SOIL_DRYDEP from the CHEM_NIT subroutine (in GeosCore/sulfate_mod.F), and therefore you get a NaN for DRY_NIT (in module GeosCore/get_ndep_mod.F). This causes the A_FERT term to be an NaN in the call to routine SOILNOX and it propagates down in the calculation from there.
- Looking at the CHEM_NIT subroutine, it looks like this is because I did not have ND44 turned on in my input.geos file. In the code, [array] T44 is only initialized and calculated if the diagnostic is turned on, but this is what is passed to SOIL_DRYDEP. 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.
We have fixed this as follows:
GeosCore/sulfate_mod.F: In routines CHEM_NH3, CHEM_NH4, CHEM_NH4aq, and CHEM_NIT, 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 SOIL_DRYDEP. Also, we now prevent SOIL_DRYDEP and ND44 from being updated if LNLPBL = .TRUE., since in that case those operations will be done in the non-local PBL mixing module (GeosCore/vdiff_mod.F90).
GeosCore/drydep_mod.F: Moved the call to SOIL_DRYDEP out of the !$OMP CRITICAL block, this is not necessary.
GeosCore/vdiff_mod.F90: Cosmetic changes and added comments.
--Bob Y. 16:56, 13 March 2013 (EDT)