INLINE_EMISSIONS_DEPV_NOTES - 31 October 2008

 With the release of CMAQ 4.7, the user can incorporate the processing of 
 either biogenic emissions (BEIS) processing or point source plume rise 
 emissions processing (or both) directly into the computational processing 
 in CMAQ. The advantages are that: (1) the emissions are meteorologically 
 modulated at the synchronization (chemistry) time step rather than being 
 linearly time-interpolated within each simulation hour, (2) the possible 
 saving of disk space, since a 3D emissions file is no longer needed, and 
 (3) the ability to more easily allow CMAQ to be in-lined in a meteorology 
 model, such as WRF, enabling direct emissions modulation by the underlying,
 freshly computed meteorological variables.

 CMAQ 4.7 now also calculates deposition velocities in-line by default,
 which provides advantages similar to the first one mentioned above for the
 in-line emissions processing, as well as providing a possible bi-directional
 deposition capability.

 These new features also permit the writing of deposition velocity, biogenic
 and plume rise emissions diagnostic files, options which, if the user choses,
 will not save disk space vs. the standard use of SMOKE 3D emissions files.

 To use the emissions options, new files from the standard SMOKE or other
 emissions pre-processing sequence will be required to be made available to
 CMAQ.  Please see the SMOKE documentation for more information.

 In particular, for BEIS, the following files are required:
 1) A speciation profile file, "GSPRO"
 2) A normalized biogenics file, "B3GRD"
 3) A frost date file, "BIOSEASON" - not required for a fixed season run, i.e.
    summer or winter
 4) A soil moisture file for the soil NO emissions processing, "SOILINP"
    This file is not available at the very start of a scenario, see below.

 The following environment variables must be set for inline BEIS:
    setenv CTM_BIOGEMIS Y
    setenv GSPRO     < path to gspro file >
    setenv BIOG_SPRO < speciation profile to use > e.g. B10C5
    setenv B3GRD     < path to b3grd file >
    setenv INITIAL_RUN Y  - if there is no previously-created biogenic
                            NO soil input file, - otherwise,
    setenv INITIAL_RUN N
    setenv SOILINP < path to previously-created biogenic NO soil input file >

 The following environment variables may be set for inline BEIS:
    setenv BIOSEASON < path to bioseason file >
    setenv BIOSW_YN  < use frost date switch? > defaults to Y
    setenv SUMMER_YN < Use summer normalized emissions? > defaults to Y
    The preceding two env vars would be set to N, e.g. for a strictly
    winter scenario. The SUMMER_YN env var is ignored if BIOSW_YN is set to Y.

    If you want to capture the biogenic emissions (mass units) in a diagnostic
    file, you must also set:
       setenv B3GTS_DIAG Y

 For the in-line plume rise emissions, the following must be supplied:
 1) The 2D area source (combined mobile, all other non-point, and point source)
    emissions files.
 2) The number of point source sectors that are not already relegated to
    surface layer area sources and their corresponding "stack parameters"
    (stack groups) files and emissions files. Some sectors will have one
    set of stack groups but day-specific emissions files, whereas other
    sectors, e.g. wild-fires, will have day-specific stack groups as well as
    day-specific emissions files. Additionally, the sector emissions files
    may have "representative" day mappings, e.g. Saturday, Sunday, Monday,
    Weekday, Holiday, for a whole month or year. If so, these mappings to
    the current computational run day must be correctly set in the run
    script. See the sample run scripting below.

 The following environment variables must be set:
    setenv CTM_PT3DEMIS Y

    set MERGE_DATES = /4w/yoj/work/amber/emis/plrise/smk_merge_dates_

    setenv NPTGRPS < number of input emission sector file groups> e.g. 5
    (Allows for a maximum of 9 sectors. If not set, defaults to 1.)

    A series of "stack group" and "stack emissions" environment variables.
    STK_GRPS_nn, STK_EMIS_nn, where nn = 01, 02, ..., NPTGRPS. Each nn
    refers to one of the plume rise point source sectors. For example, with
    NPTGRPS set to 5;
       sector:    day mapping key:
       ptnonipm   mwdss_Y
       ptipm      all
       othpt      mwdss_N
       ptfire     all
       seca_c3    aveday_N

       where mwdss_Y = monday weekday saturday sunday and Yes, use holidays,
             mwdss_N =   "       "       "       "         No holidays,
             all = map on a one-to-one basis for each scenario day,
             aveday_N = one day represents the entire month - No holidays.
       These mappings typically apply on a monthly basis.
       This example would have the following environment variables:

         #> scenario "constant" files
          setenv STK_GRPS_01 < path to sector 1 stack_groups file >
          setenv STK_GRPS_02 < path to sector 2 stack_groups file >
          setenv STK_GRPS_03 < path to sector 3 stack_groups file >
          setenv STK_GRPS_05 < path to sector 5 stack_groups file >

         #> scenario daily files
          setenv STK_GRPS_04 < path to sector 4 stack_groups file >
          setenv STK_EMIS_01 < path to sector 1 emissions file >
          setenv STK_EMIS_02 < path to sector 2 emissions file >
          setenv STK_EMIS_03 < path to sector 3 emissions file >
          setenv STK_EMIS_04 < path to sector 4 emissions file >
          setenv STK_EMIS_05 < path to sector 5 emissions file >

    setenv LAYP_STTIME $STTIME
    setenv LAYP_NSTEPS $NSTEPS

    setenv CTM_EMLAYS 24  # Number of emission layers
    NOTE: This optional environment variable only applies to in-line plume
          rise emissions.  The default for the number of emission layers
          is the number of layers in the model (NLAYS).

    If you want to capture the average 3D plume rise emissions in a diagnostic
    file, you must also set:
       setenv PT3DDIAG Y

    Doing this on a regular basis would defeat the benefit described in item
    (2) in the first paragraph above.

 Finally, the in-line deposition velocity calculations are enabled in CMAQ
 as default.  Thus, there is no need to set an environment variable to turn
 the capability on.  In order to turn this feature off and rely on the
 MCIP-generated deposition velocities (in MET_CRO_2D), it is necessary to
 set the environment variable:
    setenv CTM_ILDEPV N

    Note that the surface HONO interaction would be automatically turned off
    as well.

    If you want to capture the computed deposition velocities in a diagnostic
    file, you must also set:
       setenv CTM_DEPV_FILE Y

 For a sample complete run script, see INLINE_RUN_SCRIPT.txt