CB05 Mechanism Notes March 15, 2006 An updated Carbon Bond (CB05) mechanism has been developed for use with the CMAQv4.5.1. The CB05 mechanism has been described in details by Yarwood et al. (2005). The CB05 mechanism contains 156 reactions involving 52 species. The CB05 mechanism has been implemented into the CMAQ model and an Euler Backward Solver (EBI) solver has been developed for the CB05 mechanism. In-house tests were conducted using the CB05 and CB4 mechanisms for summer and winter of 2001 using the 36-km continental US domain. Initial test results indicate that predicted ozone concentrations increases with the CB05 mechanism by about 8% compared to the CB4 mechanism in summer. Predicted ozone concentrations increases only by about 1% in winter compared to the CB4 mechanism. Detail comparisons of the CMAQ results with the CB05 and CB4 mechanisms have been described by Sarwar et al. (2006). A tar-file (containing the beta- version of the CB05 mechanism, the EBI solver, the ICON and BCON updates, and required input data files) is available at: ftp://ftp.epa.gov/amd/asmd/CMAQv4.5.1/CB05_BETA.tar.gz Please follow the steps outlined in the CMAQv4.5.1 "README" file before proceeding. To install the "beta" CBO5 files into your existing CMAQv4.5.1 archive, cd to $M3HOME and gunzip and untar the "beta" CB05 tar file, CB05_BETA.tar.gz. This will populate your existing CMAQv4.5.1 archive with the CB05 code and include files. In addition, the raw datafiles for the photolysis proprocessor JPROC will be installed into the "$M3HOME/data/raw/phot" directory. SMOKE The Sparse Matrix Operator Kernel Emissions (SMOKE) System is needed to generate model-ready CB05 emissions. The SMOKE system can generate model- ready CB05 emissions using the gspro file that has been developed for the CB05 mechanism. The gspro file was included in the CB05_BETA.tar.gz file, and is installed in the $M3HOME/data/raw/emis directory. JPROC: The absorption cross-section and quantum yield data have been updated for the CB05 mechanism. Photolysis tables (JTABLE) needed for the CB05 mechanism can be generated using the updated absorption cross-section and quantum yield data. You will need to compile JPROC to use the CB05 mechanism. The following is a "patch" style difference in the bldit.jproc.pgf script: 41c41 < set APPL = d1a --- > set APPL = f1a 58c58,59 < set Mechanism = cb4_ae4_aq --- > #set Mechanism = cb4_ae4_aq > set Mechanism = cb05_ae4_aq You will need to modify run.jproc. The following is a "patch" style difference in run.jproc: 8c8 < # Usage: run.jproc >&! jproc_d1a.log & # --- > # Usage: run.jproc >&! jproc_f1a.log & # 23c23 < set APPL = d1a --- > set APPL = f1a ICON: The ICON and BCON processors have been revised to include conversion of RADM2 species into CB05 species. Now, these processors can generate the clean air vertical profiles for initial and boundary concentrations that can be used to run the CMAQ model with the CB05 mechanism. You will need to compile ICON to use the CB05 mechanism. The following is a "patch" style difference in the bldit.icon.pgf script: 42c42 < set APPL = e1a --- > set APPL = f1a 64c64,65 < set ModMech = ( module radm2_to_cb4 $Revision; ) --- > #set ModMech = ( module radm2_to_cb4 $Revision; ) > set ModMech = ( module radm2_to_cb05 $Revision; ) 71c72,73 < set Mechanism = cb4_ae4_aq --- > #set Mechanism = cb4_ae4_aq > set Mechanism = cb05_ae4_aq Likewise you will need to modify run.icon. The following is a "patch" style difference in run.icon: 7c7 < # Usage: run.icon >&! icon_e2a.log & # --- > # Usage: run.icon >&! icon_f1a.log & # 22,23c22,23 < set APPL = cb4 < set CFG = e1a --- > set APPL = cb05 > set CFG = f1a BCON: You will also need to compile BCON to use the CB05 mechanism. The following is a "patch" style difference in the bldit.bcon.pgf script: 42c42 < set APPL = e1a --- > set APPL = f1a 62c62,63 < set ModMech = ( module radm2_to_cb4 $Revision; ) --- > #set ModMech = ( module radm2_to_cb4 $Revision; ) > set ModMech = ( module radm2_to_cb05 $Revision; ) 69c70,71 < set Mechanism = cb4_ae4_aq --- > #set Mechanism = cb4_ae4_aq > set Mechanism = cb05_ae4_aq You will need to modify run.bcon. The following is a "patch" style difference in run.bcon: 7c7 < # Usage: run.bcon >&! bcon_e2a.log & # --- > # Usage: run.bcon >&! bcon_f1a.log & # 22,23c22,23 < set APPL = cb4 < set CFG = e1a --- > set APPL = cb05 > set CFG = f1a CCTM: The build script distributed with the standard CMAQ model can be used to extract source codes for the CB05 mechanism and the relevant EBI solver. However, the script needs the following changes in order to extract the correct files: 43c43 < set APPL = e2a --- > set APPL = f2a 106c106,107 < set ModChem = ( module ebi_cb4 $Revision; ) --- > #set ModChem = ( module ebi_cb4 $Revision; ) > set ModChem = ( module ebi_cb05 $Revision; ) 129c130,131 < set Mechanism = cb4_ae4_aq --- > #set Mechanism = cb4_ae4_aq > set Mechanism = cb05_ae4_aq The run script distributed with the standard CMAQ model can be used to run the CMAQ model with the CB05 mechanism. However, you will need to provide your own CB05 emissions files. 7c7 < # Usage: run.cctm >&! cctm_e2a.log & # --- > # Usage: run.cctm >&! cctm_f2a.log & # 22,23c22,23 < set APPL = e2a < set CFG = e2a --- > set APPL = f2a > set CFG = f2a 106,109c106,109 < set EMISfile = e_32km_cb4.19990702.ncf < #set EMISfile = e_32km_cb4.19990703.ncf < #set EMISfile = e_08km_cb4.19990702.ncf < #set EMISfile = e_08km_cb4.19990703.ncf --- > set EMISfile = e_32km_cb05.19990702.ncf > #set EMISfile = e_32km_cb05.19990703.ncf > #set EMISfile = e_08km_cb05.19990702.ncf > #set EMISfile = e_08km_cb05.19990703.ncf 117c117 < set GC_ICfile = ICON_cb4_M_32_99TUT02_profile --- > set GC_ICfile = ICON_cb05_M_32_99TUT02_profile 120c120 < set GC_BCfile = BCON_cb4_M_32_99TUT02_profile --- > set GC_BCfile = BCON_cb05_M_32_99TUT02_profile References: Sarwar, G., D. Luecken, G.Yarwood, G. Whitten, and W. P.L. Carter, 2006. Impact of an Updated Carbon Bond Mechanism on Predictions from the Community Multiscale Air Quality Model, submitted to the Journal of Applied Meteorology and Climatology. Yarwood, G., S. Rao, M. Yocke, and G. Whitten, 2005, Updates to the Carbon Bond Chemical Mechanism: CB05. Final Report to the US EPA, RT-0400675. Available at http://www.camx.com/publ/pdfs/CB05_Final_Report_120805.pdf.