README -- Describes contents of 27 Aug 2015 GEOS-Chem Support Team geos-chem-support@g.harvard.edu Overview: =============================================================================== This directory contains input files (in COARDS-compliant netCDF format) for the GEOS-Chem ocean mercury module. These used to be read from binary punch files in the GEOS_2x2.5/mercury_200511 and GEOS_2x2.5/mercury_201007 folders in the prior GEOS-Chem data structure. Files: =============================================================================== ekman_upvel.geos.2x25.nc -- Ekman updraft velocity Resolution : GEOS-Chem 2 x 2.5 grid (144 x 91 boxes) Units : m s-1 Timestamps : Monthly, 1985/01 thru 1985/12 Compression : Level 1 (e.g. nccopy -d1) mld.geos.2x25.nc -- Ocean mixed layer depth Resolution : GEOS-Chem 2 x 2.5 grid (144 x 91 boxes) Units : m Timestamps : Monthly, 1985/01 thru 1985/12 Compression : Level 1 (e.g. nccopy -d1) NPP_2003.geos.2x25.nc -- Mean monthly Net Primary Production from MODIS satellite data in mgC m-2 d-1 for 2003 taken from Behrenfeld et al (1997). Resolution : GEOS-Chem 2 x 2.5 grid (144 x 91 boxes) Units : kg m-2 Timestamps : Monthly, 1985/01 thru 1985/12 Compression : Level 1 (e.g. nccopy -d1) MLD_DReqDT.geos.2x25 -- Mean monthly mixed layer depths of the surface ocean in meters. Data is from de Boyer Montegut et al (2004). Resolution : GEOS-Chem 2 x 2.5 grid (144 x 91 boxes) Units : m Timestamps : Monthly, 1985/01 thru 1985/12 Compression : Level 1 (e.g. nccopy -d1) dMLD1_DReqDT.geos.2x25 -- Mixed layer depths tendency [cm/s] for the first half of the month Resolution : GEOS-Chem 2 x 2.5 grid (144 x 91 boxes) Units : m Timestamps : Monthly, 1985/01 thru 1985/12 Compression : Level 1 (e.g. nccopy -d1) dMLD2_DReqDT.geos.2x25 -- Mixed layer depths tendency [cm/s] for the second half of the month Resolution : GEOS-Chem 2 x 2.5 grid (144 x 91 boxes) Units : m Timestamps : Monthly, 1985/01 thru 1985/12 Compression : Level 1 (e.g. nccopy -d1) NPP_ocn_2009.geos.2x25.nc -- Arctic ocean net primary productivity (provided by Jenny Fisher, 8/21/15) Resolution : GEOS-Chem 2 x 2.5 grid (144 x 91 boxes) Units : mg/m2/day Timestamps : Monthly, 2009/01 thru 2009/12 Compression : Level 1 (e.g. nccopy -d1) CHL_ocn_2009.geos.2x25.nc -- Arctic ocean chlorophyll-a (provided by Jenny Fisher, 8/21/15) Resolution : GEOS-Chem 2 x 2.5 grid (144 x 91 boxes) Units : mg/m3 Timestamps : Monthly, 2009/01 thru 2009/12 Compression : Level 1 (e.g. nccopy -d1) References: =============================================================================== Behrenfeld, M.J., P.G. Falkowski, Photosynthetic rates derived from satellite- based chlorophyll concentration. Limnol. Oceanogr., 42(1), 1-20, 1997. de Boyer Montegut, C., G. Madec, A.S. Fischer, A. Lazar, D. Iudicone, Mixed layer depth over the global ocean: An examination of profile data and a profile-based climatology. J. Geophys. Res. [Oceans], 109, C12003, doi:10.1029/2004JC002378, 2004. Jin, M., C. Deal, S. H. Lee, S. Elliot, E. Hunke, M. Maltrud, and N. Jeffery (2011), Investigation of Arctic seas ice and ocean primary production for the period 1992-2007 using a 3-D global ice-ocean ecosystem model, Deep-Sea Res. Pt. II, 81-84, 28-35, doi: 10.1016/j.dsr2.2011.06.003. Mao, J., D.J. Jacob, M.J. Evans, J.R. Olson, X. Ren, W.H. Brune, J.M.S. Clair, J.D. Crounse, K.M. Spencer, M.R. Beaver, P.O. Wennberg, M.J. Cubison, J.L. Jimenez, A. Fried, P. Weibring, J.G. Walega, S.R. Hall, A.J. Weinheimer, R.C. Cohen, G. Chen, J.H. Crawford, L. Jaegle, J.A. Fisher, R.M. Yantosca, P. Le Sager, and C. Carouge, Chemistry of hydrogen oxide radicals (HOx) in the Arctic troposphere in spring, Atmos. Chem. Phys., 10, 5823-5838, doi:10.5194/acp-10-5823-2010, 2010. Mintz, Y., and G. K. Walker, Global fields of soil moisture and land surface evapotranspiration derived from observed precipitation and surface air temperature, J. Appl. Meteorol., 32(8), 1305-1334, 1993. Parrella, J. P., M. J. Evans, D. J. Jacob, Q. Liang, L. J. Mickley, B. Miller, J. A. Pyle, and X. Yang, Effect of bromine chemistry on natural tropospheric ozone: improved simulation of observations from the turn of the 20th century, (in preparation). Selin, N.E., D.J. Jacob, R.M. Yantosca, S. Strode, L. Jaegl, and E.M. Sunderland, Global 3-D land-ocean-atmosphere model for mercury: present-day vs. pre-industrial cycles and anthropogenic enrichment factors for deposition, Global Biogeochemical Cycles, 22, GB2011, doi:10.1029/2007GB003040, 2008. Selin, N.E., D.J. Jacob, R.J. Park, R.M. Yantosca, S. Strode, L. Jaegle and D. Jaffe, Chemical cycling and deposition of atmospheric mercury: Global constraints from observations, Journal of Geophysical Research-Atmopsheres, 112, D02308, doi:10.1029/2006JD007450, 2007. Strahan, S. E., Duncan, B. N., and Hoor, P.: Observationally derived transport diagnostics for the lowermost stratosphere and their application to the GMI chemistry and transport model, Atmos. Chem. Phys., 7, 24352445, doi:10.5194/acp-7-2435-2007, 2007. Yang, X., Cox, R., Warwick, N., Pyle, J., Carver, G., O'Connor, F., and Savage, N.: Tropospheric bromine chemistry and its impacts on ozone: A model study, J. Geophys. Res., 110, D23311, doi:10.1029/2005JD006244, 2005. Note from Jenny Fisher for arctic ocean NPP and CHL as part of v11-01c updates to Arctic Hg processes (8/21/15): "We now use new present-day (2009) fields for NPP and Chl based on Jin et al. (2012) as compiled by Anne Soerensen. These are scaled interannually using the relationship between Arctic NPP and summer minimum sea ice extent derived by Arrigo & van Djiken (2011). Values from their paper were converted to an interannual scaling factor relative to 2009." How the netCDF files were created: =============================================================================== Bob Yantosca converted the bpch files in the prior GEOS_2x25/mercury_201007/ data directory to netCDF using the GAMAP routine BPCH2COARDS, following the procedure outlined here: http://wiki.geos-chem.org/Preparing_data_files_for_use_with_HEMCO#Converting_files_from_b inary_punch_format_to_netCDF The following NCO operations were then done to edit attributes for better COARDS compliance: ncrename -v EKMAN_V__EKMAN_V,EKMAN_V ekman_upvel.geos.2x25.nc ncatted -a gamap_category,EKMAN_V,o,c,"EKMAN_V" ekman_upvel.geos.2x25.nc ncatted -a References,global,o,c,"www.geos-chem.org; wiki.geos-chem.org" ekman_upvel.geos.2x25.nc ncatted -a Contact,global,o,c,"GEOS-Chem Support Team (geos-chem-support@g.harvard.edu)" ekman_upvel.geos.2x25.nc ncap2 -v -s EKMAN_V=EKMAN_V/100.0f ekman_upvel.geos.2x25.nc out.nc ncatted -a units,EKMAN_V,o,c,m/s out.nc mv out.nc ekman_upvel.geos.2x25.nc ncrename -v BXHGHT_S__MLD,MLD mld.geos.2x25.nc ncatted -a gamap_category,MLD,o,c,"BXHEIGHT-$" mld.geos.2x25.nc ncatted -a References,global,o,c,"www.geos-chem.org; wiki.geos-chem.org" mld.g eos.2x25.nc ncatted -a Contact,global,o,c,"GEOS-Chem Support Team (geos-chem-support@g.harvard.edu)" mld.geos.2x25.nc ncrename -v GLOB_NPP__NPP,NPP modis_npp.geos.2x25.nc ncatted -a gamap_category,NPP,o,c,"GLOB-NPP" modis_npp.geos.2x25.nc ncatted -a References,global,o,c,"www.geos-chem.org; wiki.geos-chem.org" modis_npp.geos.2x25.nc ncatted -a Contact,global,o,c,"GEOS-Chem Support Team (geos-chem-support@g.harvard.edu)" modis_npp.geos.2x25.nc ncrename -v GLOB_NPP__NPP,NPP NPP_2003.geos.2x25.nc ncatted -a gamap_category,NPP,o,c,"GLOB-NPP" NPP_2003.geos.2x25.nc ncncatted -a References,global,o,c,"www.geos-chem.org; wiki.geos-chem.org" NPP_2003.geos.2x25.nc ncatted -a Contact,global,o,c,"GEOS-Chem Support Team (geos-chem-support@g.harvard.edu)" NPP_2003.geos.2x25.nc ncap2 -v -s NPP=NPP/1000000.0f NPP_2003.geos.2x25.nc out.nc ncatted -a units,NPP,o,c,kg/m3 out.nc mv out.nc NPP_2003.geos.2x25.nc ncrename -v BXHGHT_S__MLD,MLD MLD_DReqDT.geos.2x25.nc ncatted -a gamap_category,MLD,o,c,"BXHEIGHT-$" MLD_DReqDT.geos.2x25.nc ncatted -a References,global,o,c,"www.geos-chem.org; wiki.geos-chem.org" MLD_DReqDT.geos.2x25.nc ncatted -a Contact,global,o,c,"GEOS-Chem Support Team (geos-chem-support@g.harvard.edu)" MLD_DReqDT.geos.2x25.nc ncatted -a units,MLD,o,c,"m" MLD_DReqDT.geos.2x25.nc ncatted -a End_Date,global,o,i,19860101 MLD_DReqDT.geos.2x25.nc Arctic ocean NPP and CHL netcdf files were created from bpch files by Lundgren Lundgren using the following bash shell script: FILE1="CHL_ocn_2009.geos.2x25" FILE2="NPP_ocn_2009.geos.2x25" OFILE1="tmp1.%DATE%.nc" OFILE2="tmp2.%DATE%.nc" OUTFILE1="CHL_ocn_2009.geos.2x25.nc" OUTFILE2="NPP_ocn_2009.geos.2x25.nc" # read files and convert to netcdf idl << idlenv bpch2coards, '$FILE1','$OFILE1' bpch2coards, '$FILE2','$OFILE2' idlenv # merge into output files cdo mergetime tmp1.*.nc $OUTFILE1 cdo mergetime tmp2.*.nc $OUTFILE2 # Change variable names cdo chname,CHLO_A_S__,CHLO_A $OUTFILE1 tmp1.nc cdo chname,GLOB_NPP__DTOMS2,NPP_A $OUTFILE2 tmp2.nc # Change long names ncatted -a long_name,CHLO_A,o,c,'Arctic Ocean Chlorophyl-a' tmp1.nc $OUTFILE1 ncatted -a long_name,NPP_A,o,c,'Arctic Ocean Net Primary Productivity' tmp2.nc $OUTFILE2 #Cleanup rm -f tmp1.*.nc rm -f tmp2.*.nc rm -f tmp*.nc exit 0