BIDIRECTIONAL_HG_EXCHANGE in CMAQ 4.7.1 -- 7 January 2010 In CMAQ the bidirectional surface exchange of mercury assumes that the evasion of semi-volatile pollutants deposited or produced in land surface media follow Fick's law. Multimedia concentration gradients are used to parameterize the bidirectional surface exchange of semi-volatile pollutants (Wesely and Hicks 2000). The exchange velocity of the pollutants between the surface media and the atmosphere are parameterized using a resistance analogy and partitioning coefficients. In CMAQ the surface concentrations and the exchange across different media is modeled using a multi-box model representing the surface storage /exposure/capacitance and exchange between media. The change in surface media concentrations, and thus changes in the atmosphere - surface concentration gradient, is parameterized by a system of ordinary differential equations (ODEs). The flux at the atmospheric surface interface over terrestrial systems is parameterized generally following Sutton et al. (1998) and Scholtz et al. (2003), where local deposition losses and evasive loadings are used to parameterize a concentration near the surface of the exchange and the net surface flux is driven by a concentration gradient of this near surface concentration and the modeled atmospheric concentration. The near surface concentration is modeled as a function of air-cuticle, - stomatal and - soil exchange. The air - cuticular exchange is parameterized following a cuticular capacitance model similar to Sutton et al. (1998) with partitioning coefficients parameterized following Trapp and Matthies (1995) and Scholtz et al. (2003). The air - stomatal exchange is parameterized using a big leaf model and the partitioning model of Trapp and Matthies (1995). The air-soil exchange is modeled following Schultz et al. (2003) where the bulk soil Hg(II) concentration is assumed to be constant with respect to the simulation period. The reduction of soil Hg(II) is assumed to follow pseudo first order kinetics at a constant rate of k = 8x10e-11 1/s following Schultz et al. (2003). The near surface concentration is parameterized as a weighted average of the exchange coefficients and fluxes at the atmospheric, cuticular, stomatal, and soil interfaces following Sutton et al. (1998) Partitioning of Hg(0) on stomatal surfaces, in the leaf apoplast, and in the soil solution are parameterized and tracked. The concentrations in these three compartments are modeled as a function of an initial concentration, evasive losses and deposition loadings in a 2-D surface media array (Table 1). Building CCTM with bidirectional Hg exchange requires different build settings than the original model (Table 2), and requires different input and output (Table 3). NOTE: CMAQ with bidirectional Hg exchange replaces the previous estimates of natural and recycled Hg emissions and will require a modified emissions inventory with anthropogenic Hg emissions only, other emission species should remain the same. Hg concentration and deposition fields will increase if CMAQ with bidirectional Hg exchange is run with an emissions inventory with off line estimates of natural and recycled Hg emissions. References Bash, J.O., Bresnahan, P., Miller, D.R., 2007: Dynamic surface interface exchanges of mercury: a review and compartmentalized modeling framework. Journal of Applied Meteorology and Climatology 56 1606-1618 Scholtz, M.T., Van Heyst, B.J., Schroeder, W.H., 2003: Modelling of mercury emissions from background soils, the Science of the Total Environment 304, 185-207 Scholtz, M.T., Voldner, E., McMillan, A.C., Van Heyst, B.J., 2002: A pesticide emission model (PEM) part I: model development, Atmospheric Environment 36 5005-5013 Sutton, M.A., Burkhardt, J.K., Guerin, D., Nemitz, E., Fowler, D., 1998: Development of resistance models to describe measurements of bi- directional ammonia surface-atmosphere exchange. Atmospheric Environment 32, 473-480 Trapp, S., Matthies, M., 1995: Generic one-compartment model for uptake of organic chemicals by foliar vegetation. Environmental Science and Technology 29, 2333-2338 Wesely, M.L., and Hicks, B.B., 2000: A review of the current status of knowledge in dry deposition, Atmospheric Environment 34, 2261-2282 Table 1. Species in the MEDIA_CONC file ============================================================================= Species Name Compound Units ============================================================================= DGM Dissolved Hg(0) ppmV DRM Dissolved reactive Hg(II) ppmV HGSOIL Dissolved Hg(0) in soil solution ppmV HGMES Hg(0) taken into the mesophyll umol/g HGCUT Hg(0) deposited to leaf surfaces umol/g ============================================================================= Table 2. changes to the bldit.cctm script to extract and compile CMAQ with bidirectional mercury exchange using the Portland Group compiler ============================================================================= 43c43 < set APPL = e3a --- > set APPL = r47a 96c96 < set ModVdiff = ( module acm2_inline $Revision; ) --- > set ModVdiff = ( module acm2_inline_txhgsim $Revision; ) 106c106 < set ModChem = ( module ebi_cb05cl_ae5 $Revision; ) --- > set ModChem = ( module ebi_cb05txhg_ae5 $Revision; ) 112c112 < set ModAero = ( module aero5 $Revision; ) --- > set ModAero = ( module aero5_txhg $Revision; ) 119c119 < set ModCloud = ( module cloud_acm_ae5 $Revision; ) --- > set ModCloud = ( module cloud_acm_ae5_txhgsim $Revision; ) 130c130 < set Mechanism = cb05cl_ae5_aq --- > set Mechanism = cb05txhg_ae5_aq 192c192 < set LIB3 = --- > set LIB3 = "-llapack -lblas" 201c201 < set LIB3 = --- > set LIB3 = "-llapack -lblas" ============================================================================= NOTE: This script uses the LAPACK and BLAS libraries distributed with the pgi FORTRAN compiler. Most FOTRAN compilers include these libraries, but there source code is available from netlib. LAPACK is an open source freely distributed FORTRAN 77 linear algebra library optimized for parallel and shared memory vector processor architecture. LAPACK provided routines for solving system of simultaneous linear equations, least squares solutions of linear systems, Eigenvalue problems, and singular value problems, http://www.netlib.org/lapack/index.html. Table 3. changes to the in_out.q and run.cctm scripts to run CMAQ with bidirectional mercury exchange ============================================================================= The surface media concentration file and the initial surface media concentration files must be declared in in_out.q to run CMAQ with bidirectional exchange. 59a60 > setenv INIT_MEDC_1 $MD_ICpath/$MD_ICfile 126a128 > setenv MEDIA_CONC "$OUTDIR1/$ASXfile -v" 143a146 > $MEDIA_CONC\ ============================================================================= NOTE: You can change the default scripts by using the Unix "patch" utility. Cut the indented section listed above into a file, say "mod." Then type, for example, "patch run.cctm mod." The location of these files then must be set in run.cctm, please see the examples below. MD_ICfile - is set up to be analogous to the GC_ICfile in that after the first day of simulation the initial surface media concentrations are read in from the previous day's output. Initial surface media Hg concentrations are estimated during the fist day of the simulation or if MD_ICfile can not be found. ASXfile - is the output file of the current simulation model surface media Hg concentrations. EXAMPLE: set ASXfile = $EXEC"_"$EPI".MEDIA".${APPL} set MD_ICfile = $EXEC"_"$EPI".MEDIA".$yesterday Where ${APPL} is the date of the current simulation and $yesterday is the date of the previous days simulation