CHEMISTRY_NOTES - 8 January 2010 The CMAQ model uses constant values for AIR, O2, N2, CH4, and H2 for solving gas-phase chemistry. In CMAQv4.6, these values were hard-coded in the gas-phase chemistry solvers (EBI solver - hrcalcks.F, ROSENBROCK solver - rbcalcks.F, SMVGEAR solver - grcalcks.F). To increase transparency in CMAQv4.7, the specification of these values has been moved to mech.def. The chemical mechanism reader has been revised to incorporate these values in RXCM.EXT. Solvers have been revised to remove the hard-coded values; they now read these values from RXCM.EXT. Model runs were completed and results were unaffected by these changes. The following values have been added to the mech.def file: ATM_AIR = 1.0E+06 ATM_H2 = 0.56 ATM_N2 = 0.7808E+06 ATM_O2 = 0.2095E+06 ATM_CH4 = 1.85 In the CB05 mechanism in CMAQv4.6, the peroxyacetic acid (PACD) photolysis rate was not accounted for (zeroed out) because the quantum yield and absorption cross section information could not be found. The CB05 mechanism developers recently found literature on quantum yield and absorption cross sections for PACD (Giguère et al., 1956), so the CB05 mechanism in CMAQv4.7 has been updated to use this data. To run CMAQv4.7 with the CB05 mechanism, users must generate new photolysis tables that include the PACD photolysis reaction. This can be done using the JPROC program. Model runs were completed for a 3-day period in June of 2001 over the continental United States. The largest difference in ozone mixing ratios between the current model and the revised model was 0.03 ppbv. Differences in other pollutant mixing ratios between the current model and the revised model were also low. A new SOA module has been incorporated into CMAQv4.7 (please see AEROSOL_NOTES for details). When linked with the CB05 mechanism, the new aerosol module treats SOA production from TOL, XYL, BENZENE, ISOP, TERP, and sesquiterpenes (SESQ). When linked with the SAPRC99 mechanism, the new aerosol module treats SOA production from ALK5, ARO1, ARO2, BENZENE, ISOPRENE, TRP1, and SESQ. In both mechanisms in CMAQv4.7, SOA production from CRES has been removed. In the SAPRC99 mechanism in CMAQv4.7, SOA production from OLE2 has been removed. The new SOA treatment required several changes to the gas-phase chemical mechanisms. In total, ten new reactions were added to each chemical mechanism (see reactions through in the CB05 mech.def file; see , , , , , , , , , and in the SAPRC99 mech.def file). Three of these reactions track the oxidation of SESQ, one tracks the oxidation of BENZENE, and six tract the NOx-dependency in aromatic SOA formation. The addition of these reactions did not alter predictions of ozone. With both chemical mechanisms in CMAQv4.7, the dependence of aromatic SOA formation on NOx levels can be treated. In the CB05 mechanism, the TOLRO2, XYLRO2, and BENZRO2 species have been added as first generation products from TOL, XYL, and BENZENE. These species react with NO or HO2 to produce TOLNRXN, XYLNRXN, and BNZHRXN, or TOLHRXN, XYLHRXN, and BNZNRXN, respectively. TOLNRXN and TOLHRXN are new counter species for computing SOA from TOL under high and low-NOx conditions, respectively. Similarly, XYLNRXN and XYLHRXN are counter species for computing SOA from XYL. BNZNRXN and BNZHRXN are counter species for computing SOA from BENZENE. In the SAPRC99 mechanism in CMAQv4.7, the analogous reactions are treated but the species are named differently than in CB05 (e.g., ARO1* instead of TOL* and ARO2* instead of XYL*). To reduce misnomers, the variables formerly named as *AER have been renamed as *RXN (e.g., SULAER is now changed to SULRXN). Note that these variables merely count the number of times a given reaction occurs and do not necessarily correspond to the amount of aerosol material formed from the reaction. In addition to the new aromatic counter species described above, the chemical mechanisms in CMAQv4.7 include new counter species for isoprene oxidation (ISOPRXN) and sesquiterpene oxidation (SESQRXN). The new SOA module relies on emissions of BENZENE and SESQ to compute the SOA from these precursor gases. If these species are not found in the emission input files, the CMAQ run will proceed with a warning message but the modeled SOA concentrations from these precursors will be zero. To properly treat these SOA precursors in the CB05 mechanism, users should add BENZENE and SESQ to any emission files used with previous model versions. When running the SAPRC99 mechanism in CMAQv4.7, users should add SESQ emissions and should split the ARO1 emissions into BENZENE and ARO1NBZ (i.e., ARO1 minus benzene) to avoid double counting the SOA that originates from benzene. Please see www.smoke- model.org for details on the calculation of SESQ emissions. In the U.S., BENZENE emissions may be obtained from recent inventories of Hazardous Air Pollutants (HAP). CMAQv4.6 model significantly underpredicts HONO concentrations when compared to observed data. The predicted diurnal HONO profile in CMAQv4.6 is opposite to the observed diurnal profile. In observed data, peak HONO occurs at night while predicted HONO in CMAQv4.6 peaks during the day. Recent studies suggest that HONO emissions, heterogeneous reactions, and light-dependent reactions can produce HONO in the atmosphere. CMAQv4.7 model has been modified to incorporate HONO emisisons and a heterogeneous reaction involving NO2 and H2O. The CMAQv4.6 model did not use HONO emissions. HONO emissions are estimated from on-road and non-road sectors. In CMAQv4.6, NOx emissions from these sources were speciated into NO (90%) and NO2 (10%). In CMAQv4.7, NOx emissions from these sources should be speciated into NO (90%), NO2 (9.2%), and HONO (0.8%). The heterogeneous reaction producing HONO can occur on aerosol as well as ground surfaces. The details of the light-dependent HONO sources are not yet clearly understood by the atmospheric chemistry community; thus it is not incorporated into the model. A model run was completed for August of 2006 over the eastern United States. Before incorporating the heterogeneous reaction and HONO emissions, the largest HONO predictions occurred during the day and were lower than 1.0 ppb. The addition of the heterogeneous reaction and emissions increased the predicted HONO to several ppbv and captured the diurnal variability seen in the observed data. Predicted HONO concentrations were higher at night than during the day. The impacts on ozone and other chemical species were relatively minor. The changes increased ozone by 0.6% at AQS sites and increased aerosol sulfate by 0.4%, aerosol nitrate by 5.9%, and ammonium by 1% at STN sites. In addition, HNO3 increased by 2% at CASTNet sites. Details of the HONO treatment can be found at Sarwar et al., 2008. Chlorine chemistry has been shown to affect ozone predictions in some areas in the US. Thus, chlorine chemistry has been combined with the CB05 mechanism and incorporated into the CMAQv4.7 model. Chlorine chemistry contains 21 reactions (CL1-CL21 in mech.def) and the CB05 mechanism contains 156 chemical reactions (1-156 in mech.def file); thus the combined mechanism contains 177 chemical reactions. The CB05 mechanism contains 20 photolytic reactions and the chlorine chemistry contains 3 photolytic reactions (CL2, HOCL, FMCL). Thus, the combined mechanism contains 23 photolytic reactions. Chlorine chemistry in CMAQv4.7 requires emisisons of CL2 and HCL. In addition to the emissions needed for CMAQv4.6, emissions for CMAQv4.7 includes HONO, CL2, HCL, BENZENE, SESQ. In CMAQv4.6, BENZENE and CL2 were used only in the toxic version of the model. Now these species are used by the base model. 1) Build script for the CMAQv4.7 Model: Need to use "cb05cl_ae5_aq" to extract source code for the combined chemistry: set Mechanism = cb05cl_ae5_aq Need to use "ebi_cb05cl_ae5" to extract ebi solver source code for the combined chemistry: set ModChem = ( module ebi_cb05cl_ae5 $Revision; ) 2) Running the CMAQ Model: The run script can be used to run the CMAQ model. An environment variable (CTM_SFC_HONO) is used to turn on or off the heterogeneous reaction on ground surfaces producing HONO. The default value of the CTM_SFC_HONO is true; thus it is turned on by default. The user can choose to turn off the heterogeneous reaction on ground surfaces by selecting following option: setenv CTM_SFC_HONO N Please note that the environment variable for inline deposition velocities (CTM_ILDEPV) needs to be set as True otherwise the heterogeneous reaction on ground surfaces producing HONO will not be turned on. SMOKE The Sparse Matrix Operator Kernel Emissions (SMOKE) System is needed to generate model-ready CB05 emissions for CMAQv4.7. The SMOKE system can generate model-ready CB05 emissions using the gspro file that has been developed for the CB05 mechanism. The gspro file is included in the ?? directory. Photolysis rates 1) JPROC The photolysis rate preprocessor (JPROC) was updated in several ways. The dimensions of the JTABLE have been expanded to accommodate Southern Hemisphere and Global applications. The number of hour angles was increased (up to 12 hrs from local noon); the vertical extent was increased to 20km; an intermediate level was added to increase the resolution in the upper troposphere; the code that applies temperature/pressure adjustments to CS/QY data was updated. The algorithm that processes TOMS datasets was updated to read data with different lat/lon grid sizes (e.g. OMI), and the latitudinal band averaging was expanded to full width of TOMS dataset. This preprocessor is required for generating photolysis rates for CMAQv4.7.1 when you are using the "table" options. It is not required for the "phot_inline" option. 2) CCTM photolysis modules "phot_table" and "phot_sat" These CCTM modules were updated to use dynamic allocation on the input JTABLE, to allow for expanded version of the JTABLE produced by the updated JPROC, and to be backwardly compatible with previous versions of JTABLES. "phot_inline" The calculation of the asymmetry factor was updated using values of the asymmetry factor from Mie theory integrated over a log normal particle distribution. Added special treatment for large particles in the algorithm for calculating asymmetry factor to avoid numerical instabilities. References: Giguère, P. A. and A. W. Olmos, 1956. Sur le spectre ultraviolet de l'acide peracétique et l'hydrolyse des peracétates. Can. J. Chem., 34, 689-691, 1956. Sarwar, G., S. Roselle, R. Mathur, W. Appel, R. L. Dennis, B. Vogel, 2008. A Comparison of CMAQ HONO Predictions with Observations from the Northeast Oxidant and Particle Study, Atmospheric Environment, 42, 5760-5770.