Soil NOx emissions
This page describes the soil NOx emissions schemes contained within GEOS-Chem.
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.
Rynda Hudman is currently implementing a new soil NOx emissions scheme, based on the work of Neil Moore (formerly of Dalhousie University). This has not yet been implemented into the standard mainline GEOS-Chem.
New soil NOx emissions scheme
The new soil NOx scheme is being given to Bob for testing.
Old: The current implementation of the YL scheme in GEOS-Chem produces 6.2 Tg N yr-1 for the year 2006. Soil NOx is computed as a function of vegetation type (from Olson  map), temperature, precipitation history, fertilizer use, and a canopy reduction factor:
ENOx = f[ T, Aw/d(biome) ] x Pulse(precip) x canopy uptake + FERT
where f[T, biome, w/d] is a constant, linear, or exponential function of soil temperature (T) and Aw/d(biome) is a coefficient to distinguish between vegetation type. The subscript w/d refers to ‘dry’ or ‘wet’ soils. P(precipitation) is a scaling factor used to adjust the flux during pulsing events, and Fert is fertilizer emissions which are set to 2.5% of total fertilizer applied, evenly emitted over the growing season. CRF(LAI,SAI) is a scaling factor to account for loss of NOx to plant canopy based on Jacob and Bakwin .
The new implementation produces 7.5 Tg N yr-1 for the year 2006 with improved comparison with surface and satellite observations.
ENOx = f( T, biome, WFPS, Fert) x Pulse(dryspell) x canopy uptake
1 - Update moisture treatment: soil moisture as a continuous variable using WFPS rather than discrete wet/dry states and purely exponential T impact (impact = -1. Tg N/yr)
2 - Update to Fertilizer: new fertilizer maps including chemical and manure fertilizer from Potter et al.,  distributed using MODIS EVI seasonality, online-N deposition as a fertilizer source, and N-fertilizer source subject to T, WFPS, and pulsing like other N (impact = +1.3 Tg N/yr)
3- Update Pulsing Scheme: Yan et al.,  (shorter, stronger pulses) (impact = +1. Tg N/yr). Also added restart file containing dry spell information to properly account for dry spell length in continuing runs.
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)
- 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
- 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)
Dependency between soil NOx emissions and dry deposition
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
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)