CMAQv5.0 Bidirectional Exchange of NH3

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Bidirectional NH3 exchange release notes September 26th 2011

Jesse Bash and Ellen Cooter

Ammonia (NH3) is an important precursor for particulate matter, yet NH3 emissions are challenging to estimate and concentrations are difficult to measure. NH3 flux measurements taken over the past two decades have shown ammonia fluxes to be bidirectional over managed agricultural and natural ecosystems. A NH3 bidirectional exchange model was developed for the Community Multiscale Air Quality (CMAQ) model using field scale (~100 ha) observations from Lillington, NC (Bash et al. 2010) and published NH3 air-surface exchange parameterizations (Massad et al. 2010 and references therein). Soil ammonium (NH4+), pH, and soil emission potential (&Gammasoil = [NH4+]/[H+]) were modeled as a function of fertilizer application, crop type, soil type, and meteorology based upon the U. S. Department of Agriculture’s processes based Environmental Policy and Integrated Climate (EPIC) model (Cooter et al. 2010). Emission potentials from vegetation were modeled as a function of land cover type.


CMAQ v5.0 with bidirectional NH3 exchange estimates emissions from fertilizer application in-line, thus NH3 emissions from fertilizer applications to agricultural crops should be removed from the emissions inventory to avoid double counting of this source.

Run time configuration

NH3 bidirectional flux is turned on in CMAQ v5.0 by setting the environment variable CTM_ABFLUX = Y. Set ASXfile to the output path for the additional CMAQ output file with the soil emission potential and pH for both soil layers.

The following four input files are required to run the ammonia bidirectional flux model.

  1. B4LU_file - set this to point to the BELD 4 land use file that contains the gridded fractional crop distributions for the domain
  2. E2C_Soilfile - set this to point to the EPIC soil properties file for each crop type gridded to the modeling domain. This time independent file contains the soil pH for each agricultural crop being modeled for a surface layer, assumed 1 cm depth, and for the tilled depth of the soil, assumed to be 10 cm.
  3. E2C_Fertfile - set this to point to the daily EPIC output for each crop type gridded to the modeling domain. This file contains the initial soil ammonium concentrations for the first day of the simulation estimated by EPIC and the fertilizer application depth and rate.
  4. INIT_MEDC_1 - Set this to point to the previous days ASXfile to initialize the agricultural soil NH4+ concentration and pH.

The additional variables are written to the DRYDEP file

  1. NH3_Emis - An estimate of NH3 emissions for each grid cell due to fertilizer application and bidirectional exchange
  2. NH3_Dep - An estimate of the dry deposition only component of the gaseous NH3 flux.
  3. NH3_Ag - The NH3 flux for agricultural ecosystems
  4. NH3_Nat - The NH3 flux for unmanaged/natural ecosystems
  5. NH3_wat - The direct NH3 deposition to water surfaces
  6. NH3_Stom - The NH3 flux at the leaf stomata
  7. NH3_Cut - The NH3 flux at the leaf cuticle
  8. NH3_Soil - The NH3 flux at the soil surface

Effects of Changes:

The NH3 dry deposition flux is reduced when using the NH3 bidirectional flux option from spring to fall, by approximately 2/3 on the CONUS US domain. This results in increases in ambient NH4+ and NO3- aerosol concentrations in from late spring to early fall, increases in NHx wet deposition and an increase in the transport and ambient concentrations in background areas of NH3 and aerosol NH4+.