#!/bin/csh -f

# Version @(#)$Id$
# Path    $Source$
# Date    $Date$

# This script sets up needed environment variables for running SMOKE point
# sources using daily and/or hourly emissions for 1 or more months.  The 
# "onetime" steps are intended to be run in another script.  This script runs
# only Smkinven (for daily/hourly), Temporal, Laypoint, Smkmerge, optionally 
# Smk2emis, and Smkreport for date-specific reports.
#
# This script is intended to be used with the EMF
# source emissions in SMOKE for the EPA 2002 modeling platform, and 
# calls the scripts that runs the SMOKE programs. 
#
# Script created by : M. Houyoux, Environmental Protection Agency
# October, 2007
#
#*********************************************************************

## log w/ EMF server that script is running
$EMF_CLIENT -k $EMF_JOBKEY -s "Running" 

# set source category
setenv SMK_SOURCE P           # source category to process
setenv MRG_SOURCE $SMK_SOURCE # source category to merge

## day-dependent programs
set run_smkinven = Y       #  run inventory import program
set run_temporal = Y       #  run temporal allocation program
set run_laypoint = Y       #  run layer fractions program
set run_smkmerge = Y       #  run merge program
set run_elevpoint = N      #  run elevated source selection program (once per day; default is N unless ELEVPOINT_DAILY = Y)
set run_smk2emis = N       #  run conversion of 2-d to UAM binary

if ( $?ELEVPOINT_DAILY ) then
   if ( $ELEVPOINT_DAILY == Y ) then
      set run_elevpoint = Y
   endif
endif

## quality assurance
set run_smkreport = Y        # Y runs reporting for state reports
set run_m3stat    = Y

# allow the user to turn these things off in his/her case
if (! $?REGISTER_REPOUT) then
   setenv REGISTER_REPOUT    Y       # Imports Smkreport and Smkmerge reports into EMF
endif
if (! $?REGISTER_AQMOUT) then
   setenv REGISTER_AQMOUT    Y       # Imports Smkmerge I/O API outputs in EMF
endif
setenv PROMPTFLAG         N       # Y (never set to Y for batch processing)
setenv AUTO_DELETE        Y       # Y deletes SMOKE I/O API output files (recommended)
setenv AUTO_DELETE_LOG    Y       # Y automatically deletes logs without asking
if ( ! $?DEBUGMODE ) then
   setenv DEBUGMODE          N       # Y changes script to use debugger
endif
#setenv DEBUG_EXE    totalview     # Sets the debugger to use when DEBUGMODE = Y
setenv DEBUG_EXE    idb    # Sets the debugger to use when DEBUGMODE = Y

## If MRG_LAYERS_YN is not set by EMF, default to Y
if (! $?MRG_LAYERS_YN ) then
  setenv MRG_LAYERS_YN      Y
endif

## If MRG_LAYERS_YN is N, don't run Laypoint
if ( $MRG_LAYERS_YN == N ) then
  set run_laypoint = N
endif

##############################################################################

switch ( $#argv )
   case 0:
   case 1:
   case 2:
   case 3:
      echo "SCRIPT ERROR: Script requires arguments for a grid name"
      echo "              and the -m or -q option with 3 settings."
      echo " "
      echo "  This script expects to be called using one of the following argument lists:"
      echo "     <grid abbrv> <I/O API gridname> -m <monthlist> <spinup> <label>"
      echo "     <grid abbrv> <I/O API gridname> -q <quarters> <spinup> <label>"
      echo " "
      echo "  You can either use one approach or the other (differing by the -m or -q options)."
      echo " "
      echo "  In the above list, the arguments are defined as follows:"
      echo "     <grid abbrv>       : Grid abbreviation (e.g., 36US1)"
      echo "     <I/O API gridname> : I/O API gridname that needs to match entry in the"
      echo "                          GRIDDESC input file"
      echo "     <monthlist>        : list of months to run when using the -m option"
      echo "     <quarters>         : list of quarters to run when using the -q option"
      echo "     <spinup>           : set to number of days between 1 and 20 to run a spinup" 
      echo "                          period (value sets number of days), and N otherwise"
      echo "     <label>            : label to put on TIMELOG file and helper-scripts list"
      echo " "
      echo "  Examples:"
      echo "     <script name> 36US1 36US1_148X112 -m '1 2 3' 0 jan-sep"
      echo "              This example runs the script for Jan, Feb, & Mar"
      echo "              for the 36US1 grid, with no spinup days and"
      echo "              gives a label to the TIMELOG file of jan-sep." 
      echo " "
      echo "     <script name> 12EUS1 12EUS1_279X240 -q '2 3' 10 apr-sep:"
      echo "               This example runs the script for the 2nd & 3rd quarters,"
      echo "               for the 12EUS1 grid, including 10 spin-up days, and gives"
      echo "               a label to the TIMELOG file of apr-sep."
      $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: smoke script did not receive more than 3 arguments" -t "e"
      exit( 1 )
endsw

## Set Smkmerge settings depending on script setting for output format
#     (Note: these must be set before calling Assigns file)
set aqmodel = `echo $OUTPUT_FORMAT | cut -d" " -f1`
switch ($aqmodel)
   case cmaq:
   case CMAQ:
      setenv MRG_TEMPORAL_YN      Y          # Y merges with hourly emissions
      setenv MRG_SPCMAT_YN        Y          # Y merges with speciation matrix
      setenv MRG_GRDOUT_YN        Y          # Y outputs gridded file
      setenv MRG_GRDOUT_UNIT      moles/s    # units for gridded output file
      setenv MRG_TOTOUT_UNIT      moles/day  # units for state and/or county
      breaksw
   case camx:
   case CAMX:
   case CAMx:
      setenv MRG_TEMPORAL_YN      Y          # Y merges with hourly emissions
      setenv MRG_SPCMAT_YN        Y          # Y merges with speciation matrix
      setenv MRG_GRDOUT_YN        Y          # Y outputs gridded file
      setenv MRG_GRDOUT_UNIT      moles/hr   # units for gridded output file
      setenv MRG_TOTOUT_UNIT      moles/day  # units for state and/or county
      setenv RUN_SMK2EMIS         Y        #  run conversion of 2-d to UAM binary
      breaksw
   default:
      echo  ERROR: OUTPUT_FORMAT of \"$OUTPUT_FORMAT\" is not known
      echo "      by main run script $EMF_JOBNAME."
      $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: OUTPUT_FORMAT = $OUTPUT_FORMAT is not recognized" -t "e"
      exit ( 1 )
endsw

## Set EVs accordingly depending on whether we want inline approach or not
## If INLINE_MODE isn't set, default to "off"
if (! $?INLINE_MODE ) then
  setenv INLINE_MODE      off
endif

if ( $INLINE_MODE == only ) then
   setenv MRG_GRDOUT_YN   N
endif

if ( $INLINE_MODE == only || $INLINE_MODE == both ) then
   setenv SMK_ELEV_METHOD 2
   setenv MRG_LAYERS_YN   N
   set run_laypoint     = N
else
   # Don't overwrite SMK_ELEV_METHOD if it's already defined, for backwards compatibility
   if (! $?SMK_ELEV_METHOD ) setenv SMK_ELEV_METHOD 1
endif

# Get the first two options for the grid abbreviation and I/O API grid
setenv GRID "$argv[1]"
setenv IOAPI_GRIDNAME_1 "$argv[2]"

setenv RUN_TEMPORAL  $run_temporal
setenv RUN_SMKMERGE  $run_smkmerge
if (! $?RUN_SMKREPORT) then
#  if not set already, set it from the variable.
   setenv RUN_SMKREPORT $run_smkreport
else
#  this allows for someone to override the run report setting in their case
   set run_smkreport = $RUN_SMKREPORT
   if ($RUN_SMKREPORT == 'N') then
       setenv REGISTER_REPOUT    N
#      don't register the reports if you are not creating them
   endif
endif
setenv RUN_SMK2EMIS  $run_smk2emis

## source the ASSIGN file
source $ASSIGNS_FILE

## List of all the helper scripts that are run in this script
set emf_cleanup  = $SCRIPTS/run/emf_cleanup.csh
set set_months   = $SCRIPTS/run/set_months_v4.csh
set timetracker  = $SCRIPTS/run/timetracker_v2.csh
set combine_data = $SCRIPTS/run/combine_data_v5.csh
set smk_run      = $SCRIPTS/run/smk_run_v8.csh
set qa_run       = $SCRIPTS/run/qa_run_v6.csh
set m3stat       = $SCRIPTS/run/m3stat_chk_v5.csh
set set_days     = $SCRIPTS/run/set_days_v4.csh
set log_analyzer = $SCRIPTS/log_analyzer/log_analyzer.py
set msg_list     = $SCRIPTS/log_analyzer/known_messages.txt
set duplic_chk   = $SCRIPTS/run/duplicate_check.csh
set python_annl  = $SCRIPTS/annual_report/annual_report.py
set path_parser  = $SCRIPTS/run/path_parser.py

## If running from EMF, move old EMF-created scripts to "old"
if ( $?EMF_JOBID ) then
   source $emf_cleanup
   if ( $status != 0 ) then
	echo "ERROR: running EMF script/log cleanup script"
	$EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: running EMF script/log cleanup script" -t "e" -x $emf_cleanup
	exit ( 1 )
   endif
endif

## Invoke script to interpret calling arguments
$EMF_CLIENT -k $EMF_JOBKEY -m "Running set_months" -x $set_months  ## log w/ EMF server
set exitstat = 0
switch ( $#argv )
   case 4:
      source $set_months $argv[3] "$argv[4]"
      if ( $status != 0 ) set exitstat = 1
   breaksw
   case 5: 
      source $set_months $argv[3] "$argv[4]" $argv[5]
      if ( $status != 0 ) set exitstat = 1
   breaksw
   case 6:
      source $set_months $argv[3] "$argv[4]" $argv[5]
      if ( $status != 0 ) set exitstat = 1
      setenv TLABEL $argv[6]
   breaksw
endsw
if ( $exitstat != 0 ) then
    echo "ERROR: setting months"
    $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: setting months" -t "e" -x $set_months  
    exit ( 1 )
endif

# Set spinup duration - the set_months will have QA'f the $argv[5] value
if ( $#argv > 4 ) setenv SPINUP_DURATION $argv[5]

# Save spinup array from set_months
set spinup_array = ( $SPINUP_LIST )

## Set naming label
set namelabel = ${SECTOR}_${CASE}_${GRID}
if ( $?TLABEL ) set namelabel = ${namelabel}_$TLABEL

## Record the helper scripts being used
set suffix = _$namelabel.txt
echo "# Helper scripts used for $SECTOR" > $LOGS/helper_scripts_list$suffix
echo $emf_cleanup >> $LOGS/helper_scripts_list$suffix
echo $set_months >> $LOGS/helper_scripts_list$suffix
echo $timetracker >> $LOGS/helper_scripts_list$suffix
echo $combine_data >> $LOGS/helper_scripts_list$suffix
echo $smk_run >> $LOGS/helper_scripts_list$suffix
echo $qa_run >> $LOGS/helper_scripts_list$suffix
echo $m3stat >> $LOGS/helper_scripts_list$suffix
echo $set_days >> $LOGS/helper_scripts_list$suffix
echo $log_analyzer >> $LOGS/helper_scripts_list$suffix
echo $msg_list >> $LOGS/helper_scripts_list$suffix
echo $duplic_chk >> $LOGS/helper_scripts_list$suffix
echo $python_annl >> $LOGS/helper_scripts_list$suffix
echo $path_parser >> $LOGS/helper_scripts_list$suffix

## Set Time Log filename and initialize file
setenv TIMELOG $LOGS/timelog_$namelabel.txt

# Only initialize TIMELOG if it doesn't already exist, since the timeracker 
#   can now delete/add entries to prevent duplicates
if ( ! -e $TIMELOG ) then 
   $EMF_CLIENT -k $EMF_JOBKEY -m "Initializing Time Log" -x $timetracker  ## log w/ EMF server
   $timetracker Y $TIMELOG
   if ( $status != 0 ) then
	echo "ERROR: running timetracker"
	$EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: running timetracker to initialize time log" -t "e" -x $timetracker
	exit ( 1 )
   endif
endif

echo "SCRIPT NOTE: Scanning PTREF for duplicate records"
$duplic_chk $PTREF T
if ( $status != 0 ) then
    echo "ERROR: Duplicate records detected in PTREF by duplic_chk.csh, or other script problem"
    $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: Duplicate records detected in PTREF by duplic_chk.csh, or other script problem" -t "e" -x $duplic_chk
    exit ( 1 )
endif

setenv RUN_PART1 N

## Set up scripting environment variables prior to calling the Assigns file
setenv SUBSECT $SECTOR                   # set variable for input/output names
setenv SRCABBR $SUBSECT                  # set abbreviation for naming log files
setenv EISECTOR $SECTOR

set monname = ( jan feb mar apr may jun jul aug sep oct nov dec )
set moncode = ( 01 02 03 04 05 06 07 08 09 10 11 12)

# Loop through months as determined from calling arguments
set mc = 0
set diff = 0
set g_stdate_all = $G_STDATE
set anymerge  = N
set anytmprep = N

foreach mon ( $MONTHS_LIST )   # MONTHS_LIST set by set_months.csh

   @ mc = $mc + 1   # month array counter

   setenv MONTH   ${monname[$mon]}         # set variable for month name
   setenv SUBSECT ${SECTOR}_$MONTH
   setenv SRCABBR $SUBSECT
   setenv EMF_PERIOD "${MONTH}_${YEAR}"

   ## Setup to run Smkinven to import day-specific inventories
   setenv RUN_PART1 Y

   ## No need to import annual inventory, since done in "onetime" script
   setenv IMPORT_AVEINV_YN  N            

   setenv RUN_SMKINVEN  $run_smkinven

   source $ASSIGNS_FILE                  # Invoke Assigns file to set for current month

   # Call EMF Client for current period 
   $EMF_CLIENT -k $EMF_JOBKEY -m "Running SMOKE steps for month $MONTH" -p $EMF_PERIOD   ## log w/ EMF server

   ## Setup environment variables for using in the PTDAY list files
   # If using daily data, set PTDAY file names
   ## Create the month-specific list file of daily data for import to Smkinven

   ## If using external MULTIFILE approach, then setup list file accordingly.
   #if ( $?NAMEBREAK_DAILY ) then
   #   setenv MULTIFILE_NAMEBREAK $NAMEBREAK_DAILY
   #   $combine_data EMISDAY $DAYLISTFILE list $moncode[$mon] Daily
   #   if ( $status != 0 ) then
   #       echo "ERROR: Could not run combine_data.csh for daily list file in $EMF_JOBNAME"
   #       $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: Could not run combine_data for daily list file in $EMF_JOBNAME for $MONTH" -t "e" -p $EMF_PERIOD
   #       exit ( 1 )
   #   endif

   ## Otherwise, daily files are internal
   #else
   #   if ( $?MULTIFILE_NAMEBREAK ) unsetenv MULTIFILE_NAMEBREAK
   #   $combine_data EMISDAY $DAYLISTFILE list $moncode[$mon]
   #   if ( $status != 0 ) then
   #       echo "ERROR: Could not run combine_data.csh for daily list file in $EMF_JOBNAME"
   #       $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: Could not run combine_data for daily list file in $EMF_JOBNAME for $MONTH" -t "e" -p $EMF_PERIOD
   #       exit ( 1 )
   #   endif

   #endif
   setenv PTDAY $DAYLISTFILE  #  Set the point daily-specific inventory list file to the generic list file

   ## Create the month-specific list file of hourly data for import to Smkinven
   if ( $?NAMEBREAK_HOURLY ) then
      setenv MULTIFILE_NAMEBREAK $NAMEBREAK_HOURLY
      $combine_data EMISHOUR $HOURLISTFILE list $moncode[$mon] Hourly
      if ( $status != 0 ) then
          echo "ERROR: Could not run combine_data.csh for hourly list file in $EMF_JOBNAME"
          $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: Could not run combine_data for hourly list file in $EMF_JOBNAME for $MONTH" -t "e" -p $EMF_PERIOD
          exit ( 1 )
      endif
      setenv PTHOUR $HOURLISTFILE  #  Set the point hour-specific inventory list file to the generic list file
   endif

   ## Run Smkinven to import day-specific and hour-specific inventories
   source $smk_run    # Run program
   if ( $status != 0 ) then
       echo "ERROR: Running Smkinven for daily data import in $EMF_PERIOD"
       $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: Running smk_run for part 1 in $EMF_PERIOD" -t "e" -p $EMF_PERIOD
       goto end_of_script
   endif

   setenv RUN_PART1 N

   ## Determine dates to run in this month
   setenv RUN_PART2 Y
   setenv MONTH_ARRAY  $mon              # MONTH_ARRAY can have as many months listed as needed
   setenv SPINUP_ARRAY $spinup_array[$mc]

   # Source assigns file BEFORE set_days_v3.csh to set PROCDATES and SMK_RUN_DATES settings
   source $ASSIGNS_FILE                  # Invoke Assigns file to set PROCDATES and SMK_RUN_DATES for this month
   setenv SMK_RUN_DATES $SMK_RUN_DATES_1

   setenv T_TYPE $L_TYPE                 # Set temporal type to type for temporal
   source $set_days   # Call script to set dates for run
   if ( $status != 0 ) then
	echo "ERROR: Running set_days"
	$EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: Running set_days" -t "e" -x $set_days -p $EMF_PERIOD
 	exit ( 1 )
   endif

   # Settings so that ESDATE will be first date in procdates file, after Assigns file
   #    is sourced
   set line = `head -1 $SMK_RUN_DATES`
   @ diff = $line[1] - $g_stdate_all
   setenv G_STDATE_ADVANCE $diff

   setenv RUN_TEMPORAL  $run_temporal

   # Source assigns file AFTER set_days_v3.csh so that it can use PROCDATES file to delete Temporal outputs
   source $ASSIGNS_FILE                  # Invoke Assigns file to delete Temporal outputs

   ## Run Temporal (using PROCDATES file - run for all days in month)
   source $smk_run       # Run programs
   if ( $status != 0 ) then
	echo "ERROR: Running smk_run for part 2 in $EMF_PERIOD" 
	$EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: Running smk_run for part 2 in $EMF_PERIOD" -t "e" -x $smk_run -p $EMF_PERIOD
        set exitstat = 1
	goto end_of_script
   endif

   setenv RUN_PART2 N

   ## Determine the number of days to run for Temporal QA
   set ndays = `cat $SMK_RUN_DATES | wc -l`
   echo "Number of dates to run for month ($mon)" : $ndays

   ## Loop through days of Temporal QA
   set n = 0
   set diff = 0
   set g_stdate_sav = $g_stdate_all

   # Loop through days to run temporal QA during the month.
   while ( $n < $ndays )

      @ n = $n + 1   

      setenv RUN_SMKREPORT $run_smkreport

      ## Setup for iterating the date in the Assigns file.
      set line = `head -$n $SMK_RUN_DATES | tail -1`
      @ diff = $line[1] - $g_stdate_sav

      setenv G_STDATE_ADVANCE $diff
      setenv RUN_TEMPORAL N
      setenv RUN_PART2 Y
      source $ASSIGNS_FILE               # Invoke Assigns file to set new dates

      ## Set EMF_PERIOD for this day
      setenv EMF_PERIOD $ESDATE

      ## Run QA for part 2
      setenv QA_TYPE  temporal           # Used to name the report inputs and outputs
      setenv QA_LABEL $SUBSECT           # Used to name the report inputs and outputs
      setenv REPLABEL $SUBSECT           # Used internally by Smkreport

      source $qa_run  
      if ( $status != 0 ) then
	 echo "ERROR: running Smkreport for $ESDATE"
	 $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: running Smkreport for $ESDATE" -t "e" -x $qa_run -p $EMF_PERIOD
         set exitstat = 1
	 goto end_of_script
      endif

      setenv RUN_PART2 N

      if ( $RUN_SMKREPORT == Y ) set anytmprep = Y

   end  # End loop through days run per month for QA

   ## Determine the number of days to run for Laypoint, Smkmerge, and Smk2emis
   setenv T_TYPE $M_TYPE                 # Set temporal type to type for temporal
   setenv SMK_RUN_DATES $SMK_RUN_DATES_2

   source $set_days   # Call script to set dates for run

   # Check status of run to see if it worked. Give error if failed
   if ( $status != 0 ) then
      echo "ERROR: Running set_days in $EMF_PERIOD"
      $EMF_CLIENT - k $EMF_JOBKEY -m "ERROR: Running set_days" -t "e" -x $set_days -p $EMF_PERIOD
      exit ( 1 )
   endif

   ## Determine the number of days to run
   set ndays = `cat $SMK_RUN_DATES | wc -l`
   echo "Number of dates to run for $MONTH" : $ndays

   ## Loop through days of Laypoint, Smkmerge, and optionally Smk2emis
   set n = 0
   set diff = 0
   set g_stdate_sav = $g_stdate_all

   while ( $n < $ndays )   # Expecting M_TYPE == all (for all days of year)

      @ n = $n + 1   

      ## Setup for iterating the date in the Assigns file.
      set line = `head -$n $SMK_RUN_DATES | tail -1`
      set mon = `echo $line[2] | cut -c 5-6`
      @ diff = $line[1] - $g_stdate_sav

      setenv G_STDATE_ADVANCE $diff
      
      ## (C. Allen) Run Elevpoint for each day; RUN_ELEVPOINT is always N unless ELEVPOINT_DAILY == Y (set earlier in the script)
      setenv RUN_ELEVPOINT $run_elevpoint
      
      setenv RUN_PART3 Y
      source $ASSIGNS_FILE                 # Invoke Assigns file to set new dates

      ## Set EMF_PERIOD for this day
      setenv EMF_PERIOD $ESDATE
      
      source $smk_run 
      if ( $status != 0 ) then
          echo "ERROR: Running smk_run for Elevpoint for $ESDATE"
          $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: Running smk_run for Elevpoint for $ESDATE" -t "e" -x $smk_run -p $EMF_PERIOD 
          set exitstat = 1
          goto end_of_script
      endif

      setenv RUN_PART3 N

      ## Run Laypoint, Smkmerge, M3stat, and optionally, Smk2emis
      setenv RUN_LAYPOINT  $run_laypoint
      setenv RUN_SMKMERGE  $run_smkmerge
      setenv RUN_SMK2EMIS  $run_smk2emis
      setenv RUN_M3STAT    $run_m3stat  

      setenv RUN_PART4 Y
      source $ASSIGNS_FILE                  # Invoke Assigns file to set new dates

      ## Set EMF_PERIOD for this day
      setenv EMF_PERIOD $ESDATE

      ## Unzip PTMP file if it's zipped, and there is no already unzipped file, and we're running Laypoint or Smkmerge
      if ( -e $PTMP.gz && ! -e $PTMP && ( $RUN_LAYPOINT == Y || $RUN_SMKMERGE == Y ) ) gunzip -v $PTMP.gz
      ## Unzip PLAY file if it's zipped, and there is no already unzipped file, and we're running Smkmerge but not Laypoint
      if ( -e $PLAY.gz && ! -e $PLAY && $RUN_LAYPOINT == N && $RUN_SMKMERGE == Y ) gunzip -v $PLAY.gz

      # Run programs for part 4
      source $smk_run        
      if ( $status != 0 ) then	    
	 echo "ERROR: Running smk_run for part 4 for $ESDATE"
	 $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: Running smk_run for part 4 for $ESDATE" -t "e" -x $smk_run -p $EMF_PERIOD 
         set exitstat = 1
	 goto end_of_script
      endif

      # Run m3stat script on POUT, unless we're only creating INLN file
      if ( $INLINE_MODE != only ) then
         # Run m3stat script on Smkmerge output file
         ## C. Allen configured for multiple files per day (All of my comments contain [c])
         if ( $?POUT && $RUN_M3STAT == Y ) then
      
            # [c] If $POUT exists, this implies there is only one Smkmerge file per day. In this case, run m3stat once and get out
	    if ( -e $POUT ) then
               $m3stat $POUT
               if ( $status != 0 ) then
   	          echo "ERROR: running m3stat_chk for $ESDATE"
	          $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: running m3stat_chk for $ESDATE" -t "e" -x $m3stat -p $EMF_PERIOD
                  set exitstat = 1
	          goto end_of_script
               endif
	    # [c] Otherwise, check to see how many files there are, and run m3stat on each one
	    else
	       # [c] "pout_prefix" is prefix of $POUT, everything before the file number
	       set pout_prefix = $INTERMED/emis_${MM}_${SECTOR}_${ESDATE}_${GRID}_${SPC}_${CASE}
	       set num_smkmerge_files = `/bin/ls -1 $pout_prefix.*.ncf | wc -l`
	       echo "SCRIPT NOTE: Running m3stat on $num_smkmerge_files model-ready files"
	       set fc = 0
	       # [c] This allows for case where number of files is 0; in that case the while loop is skipped altogether
	       # [c] The run_m3stat script has an optional 3rd command-line parameter that I originally added to handle inline approach;
   	       # [c]   this is a "file stamp" appended to the file names so that the files don't get overwritten each time
               while ( $fc < $num_smkmerge_files )
 	          @ fc = $fc + 1
   	          $m3stat $pout_prefix.$fc.ncf $fc
                  if ( $status != 0 ) then
                     echo "ERROR: running m3stat_chk for $ESDATE"
	             $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: running m3stat_chk for $ESDATE" -t "e" -x $m3stat -p $EMF_PERIOD
                     set exitstat = 1
                     goto end_of_script
                  endif
   	       end # while
	    endif # -e $POUT
         endif # $?POUT
      endif

      # Run m3stat script on INLN, unless we're not running inline approach
      # C. Allen update 3/31/09: Added support for multiple INLN files per day, required for tagging runs
      #   (We had never done a tagging, inline run prior to now)
      if ( $INLINE_MODE != off ) then
         if ( $?INLN && $RUN_M3STAT == Y ) then
	 
           # [c] If $POUT exists, this implies there is only one Smkmerge file per day. In this case, run m3stat once and get out
	    if ( -e $INLN ) then
               $m3stat $INLN inln
               if ( $status != 0 ) then
   	          echo "ERROR: running m3stat_chk for $ESDATE"
	          $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: running m3stat_chk for $ESDATE" -t "e" -x $m3stat -p $EMF_PERIOD
                  set exitstat = 1
	          goto end_of_script
               endif
	    # [c] Otherwise, check to see how many files there are, and run m3stat on each one
	    else
	       # [c] "inln_prefix" is prefix of $INLN, everything before the file number
	       set inln_prefix = $INTERMED/inln_${MM}_${SECTOR}_${ESDATE}_${GRID}_${SPC}_${CASE}
	       set num_smkmerge_files = `/bin/ls -1 $inln_prefix.*.ncf | wc -l`
	       echo "SCRIPT NOTE: Running m3stat on $num_smkmerge_files model-ready inline files"
	       set fc = 0
	       # [c] This allows for case where number of files is 0; in that case the while loop is skipped altogether
	       # [c] The run_m3stat script has an optional 3rd command-line parameter that I originally added to handle inline approach;
   	       # [c]   this is a "file stamp" appended to the file names so that the files don't get overwritten each time
               while ( $fc < $num_smkmerge_files )
 	          @ fc = $fc + 1
   	          $m3stat $inln_prefix.$fc.ncf inln_$fc
                  if ( $status != 0 ) then
                     echo "ERROR: running m3stat_chk for $ESDATE"
	             $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: running m3stat_chk for $ESDATE" -t "e" -x $m3stat -p $EMF_PERIOD
                     set exitstat = 1
                     goto end_of_script
                  endif
   	       end # while
	    endif # -e $INLN

         endif # $?INLN && $RUN_M3STAT == Y
      endif # $INLINE_MODE != off

      setenv RUN_PART4 N

      # Zip the laypoint output if it exists
      if ( -e $PLAY ) then
         gzip -vf $PLAY
      endif
      # Zip the smkmerge output (POUT and INLN) if if ZIPOUT = Y
      # The "-e" statements take care of the different inline modes
      if ( $?ZIPOUT ) then
         if ( $ZIPOUT == Y ) then
            setenv POUT  $INTERMED/emis_mole_${SECTOR}_${ESDATE}_${GRID}_${SPC}_${CASE}.ncf # in case smkmerge isn't run, so this doesn't crash it
            setenv INLN  $INTERMED/inln_mole_${SECTOR}_${ESDATE}_${GRID}_${SPC}_${CASE}.ncf # in case smkmerge isn't run, so this doesn't crash it
	    # C. Allen configured for multiple output files, all of which probably should be zipped
	    #  Process similar to m3stat
	    if ( -e $INLN ) then
	       gzip -vf $INLN
	    else # possibility of multiple INLNs
	       # [c] "inln_prefix" is prefix of $INLN, everything before the file number
	       set inln_prefix = $INTERMED/inln_${MM}_${SECTOR}_${ESDATE}_${GRID}_${SPC}_${CASE}
	       set num_smkmerge_files = `/bin/ls -1 $inln_prefix.*.ncf | wc -l`
	       set fc = 0
	       # [c] This allows for case where number of files is 0; in that case the while loop is skipped altogether
               while ( $fc < $num_smkmerge_files )
 	          @ fc = $fc + 1
   	          if ( -e $inln_prefix.$fc.ncf ) gzip -vf $inln_prefix.$fc.ncf
   	       end # while
	    endif # -e $INLN
            if ( -e $POUT ) then
	       gzip -vf $POUT
	    else # possibility of multiple POUTs
	       # [c] "pout_prefix" is prefix of $POUT, everything before the file number
	       set pout_prefix = $INTERMED/emis_${MM}_${SECTOR}_${ESDATE}_${GRID}_${SPC}_${CASE}
	       set num_smkmerge_files = `/bin/ls -1 $pout_prefix.*.ncf | wc -l`
	       set fc = 0
	       # [c] This allows for case where number of files is 0; in that case the while loop is skipped altogether
               while ( $fc < $num_smkmerge_files )
 	          @ fc = $fc + 1
   	          if ( -e $pout_prefix.$fc.ncf ) gzip -vf $pout_prefix.$fc.ncf
   	       end # while
	    endif # -e $POUT
	 endif # zipout = y
      endif # $?zipout

   end  # End loop over days

   unsetenv G_STDATE_ADVANCE

end  # End loop over parts

## Set day count depending on leap year and spinup period
if ( $BASE_YEAR == 2000 || $BASE_YEAR == 2004 ||  $BASE_YEAR == 2008 || $BASE_YEAR == 2012 ) then
   set alldays = 366
else
   set alldays = 365
endif

@ alldays = $alldays + $SPINUP_DURATION

## Set the expected file counts needed for Smkreport output registration
switch ( $L_TYPE ) 
  case all:
     set tmprep_expected = $alldays
  breaksw

  case week:
     set tmprep_expected = 84
     if ( $RUN_HOLIDAYS == Y ) set tmprep_expected = 100
  breaksw

  case mwdss:
     set tmprep_expected = 48
     if ( $RUN_HOLIDAYS == Y ) set tmprep_expected = 64
  breaksw

  case aveday:
     set tmprep_expected = 12
     if ( $RUN_HOLIDAYS == Y ) set tmprep_expected = 28
  breaksw
endsw

## Set the expected file counts needed for Smkmerge output registration
switch ( $M_TYPE ) 
  case all:
     set mrg_expected = $alldays
  breaksw

  case week:
     set mrg_expected = 84
     if ( $RUN_HOLIDAYS == Y ) set mrg_expected = 100
  breaksw

  case mwdss:
     set mrg_expected = 48
     if ( $RUN_HOLIDAYS == Y ) set mrg_expected = 64
  breaksw

  case aveday:
     set mrg_expected = 12
     if ( $RUN_HOLIDAYS == Y ) set mrg_expected = 28
  breaksw
endsw

## Determine if all temporal report files are available to import
##   Use state temporal report as sample.
set tmprepcnt = `/bin/ls -1 $REPOUT/temporal/rep_${SECTOR}_*_${CASE}_*_temporal_state.txt | wc -l`

## Determine if all smkmerge report files are available to import
set mrgrepcnt = `/bin/ls -1 $REPOUT/smkmerge/$SECTOR/rep_mole_${SECTOR}_*_${GRID}_*.txt | wc -l`

## Determine if all smkmerge model-ready files are available to import
set mrgcnt = `/bin/ls -1 $INTERMED/emis_mole_${SECTOR}_*_${GRID}_*.ncf* | wc -l`

# Register Smkreport temporal outputs with EMF for current month
# Make sure Smkreport was run for any days thus far (don't want to re-register data if it wasn't run)
if ( $REGISTER_REPOUT == Y ) then
   if ( $tmprepcnt == $tmprep_expected ) then
      echo "SCRIPT NOTE: Registering external Smkreport temporal reports"
      $EMF_CLIENT -k $EMF_JOBKEY \
           -D $REPOUT/temporal \
           -P "rep_${SECTOR}_*_${CASE}_*_temporal_county.txt" \
           -T "Smkreport county daily (External Multifile)" \
           -N "rep_${SECTOR}_temporal_county_$CASE" \
           -O "county daily Smkreport $SECTOR (External)"

      $EMF_CLIENT -k $EMF_JOBKEY \
           -D $REPOUT/temporal \
           -P "rep_${SECTOR}_*_${CASE}_*_temporal_county_moncode.txt" \
           -T "Smkreport county-moncode daily (External Multifile)" \
           -N "rep_${SECTOR}_temporal_county_moncode_$CASE" \
           -O "county/moncode daily Smkreport $SECTOR (External)"

      $EMF_CLIENT -k $EMF_JOBKEY \
           -D $REPOUT/temporal \
           -P "rep_${SECTOR}_*_${CASE}_*_temporal_state.txt" \
           -T "Smkreport state daily (External Multifile)" \
           -N "rep_${SECTOR}_temporal_state_$CASE" \
           -O "state daily Smkreport $SECTOR (External)"

      $EMF_CLIENT -k $EMF_JOBKEY \
           -D $REPOUT/temporal \
           -P "rep_${SECTOR}_*_${CASE}_*_temporal_state_scc.txt" \
           -T "Smkreport state-SCC daily (External Multifile)" \
           -N "rep_${SECTOR}_temporal_state_scc_$CASE" \
           -O "state/SCC daily Smkreport $SECTOR (External)"
   else
      echo "SCRIPT NOTE: Not registering Smkreport temporal reports because only found"
      echo "             $tmprepcnt state temporal reports out of expected $tmprep_expected" 

   endif

   ## Register Smkmerge reports
   if ( $mrgrepcnt == $mrg_expected ) then
      echo "SCRIPT NOTE: Registering Smkmerge reports"
      $EMF_CLIENT -k $EMF_JOBKEY \
           -D $REPOUT/smkmerge/$SECTOR \
           -P "rep_mole_${SECTOR}_*_${GRID}_*.txt" \
           -T "Smkmerge Report state (External Multifile)" \
           -N "Smkmerge $SECTOR $CASE state reports" \
           -O "state Smkmerge $SECTOR (External)"

      ## Run python annual report script, if all Smkmerge reports are there,
      #  and if RUN_PYTHON_ANNUAL parameter is Y (default is N)
      if ( ! $?RUN_PYTHON_ANNUAL ) then
         setenv RUN_PYTHON_ANNUAL N
      endif	 
      if ( $RUN_PYTHON_ANNUAL != N  && $?SECTORLIST ) then

         echo "SCRIPT NOTE: Running python annual report script"

         ## Get root of the merge dates directory from smk merge date file
         if ( $?MRGDATE_FILES) then
	    ## get path from first merge date file
	    echo "Getting merge dates path from MRGDATE_FILES"
	    set mrgdate_root = `$path_parser $MRGDATE_FILES`
         else 
	    ## no merge dates file, so get from parent case's inputs/mrggrid
	    echo "MRGDATE_FILES not defined, so merge dates path defaults to $INVDIR/mrggrid"
     	    set mrgdate_root = $INVDIR/mrggrid
         endif

         if (! -e $REPOUT/annual_report) mkdir -p $REPOUT/annual_report
         $python_annl -R $REPOUT/smkmerge -D $mrgdate_root \
                      -O $REPOUT/annual_report \
		      -o annual_${CASE}_${SECTOR}_${GRID}_${SPC} \
	              $SCRIPTS/annual_report/parameter_file_$SPC.txt

         if ($status == 0) then
            ## Register the output w/ the EMF
            echo "SCRIPT NOTE: Registering smkmerge state totals"
            $EMF_CLIENT -k $EMF_JOBKEY \
   	        -F  $REPOUT/annual_report/annual_${CASE}_${SECTOR}_${GRID}_${SPC}_emf.csv \
                -T "Smkmerge report state annual summary (CSV)" -O "state totals ${namelabel}"    
         endif

      endif
   else
      echo "SCRIPT NOTE: Not registering Smkmerge reports because only found"
      echo "             $mrgrepcnt Smkmerge reports out of expected $mrg_expected" 

   endif

endif

# Register Smkmerge AQM-ready outputs with EMF for current month
if ( $REGISTER_AQMOUT == Y ) then
   if ( $mrgcnt == $mrg_expected ) then
      echo "SCRIPT NOTE: Registering Smkmerge outputs"
      $EMF_CLIENT -k $EMF_JOBKEY \
           -D $INTERMED \
           -P "emis_mole_${SECTOR}_*_${GRID}_*.ncf*" \
           -T "CMAQ Model Ready Emissions: Sector-specific (External)" \
           -N "Model-ready CMAQ $SECTOR $CASE" \
           -O "AQM-ready data $SECTOR"
   else
      echo "SCRIPT NOTE: Not registering Smkmerge model-ready files because only found"
      echo "             $mrgcnt Smkmerge outputs out of expected $mrg_expected" 

   endif
endif

# Label for the end of the script, used during script abort
end_of_script:

## Register time log
echo "SCRIPT NOTE: Registering time log"
$EMF_CLIENT -k $EMF_JOBKEY -F $TIMELOG -T "SMOKE time log (External)" -N "SMOKE timelog $namelabel" -O "Timelog $namelabel (External)"

## Run log file analyzer
$log_analyzer -k $msg_list --list_unknowns -l 3 -f $REPOUT/log_analyzer/rep_logs_${namelabel}_level3.csv -d $LOGS
if ( $status != 0 ) then
   echo "ERROR: running log_analyzer, level 3"
   $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: running log_analyzer, level3" -t "e" -x $log_analyzer
   set exitstat = 1

## Register log analyzer output
#else
#   echo "SCRIPT NOTE: Registering log summary, level3"
#   $EMF_CLIENT -k $EMF_JOBKEY -F $REPOUT/log_analyzer/rep_logs_${namelabel}_level3.csv \
#        -T "Log summary level 3" -O "Level 3 log summary ${namelabel}"
endif

## If log analyzer returns exit status 10, then the log analyzer ran to completion, but found some errors or unrecognized
#  warnings. In this case, we want this script to exit with "Failed" status, but we still want to register the level 1 report in the EMF.
#  If log analyzer returns exit status 1, it didn't work at all, so bomb out immediately.

$log_analyzer -k $msg_list --list_unknowns -e 1 -f $REPOUT/log_analyzer/rep_logs_${namelabel}_level1.csv -d $LOGS
if ( $status == 10 ) then
   echo "SCRIPT NOTE: Registering log summary, level1"
   $EMF_CLIENT -k $EMF_JOBKEY -F $REPOUT/log_analyzer/rep_logs_${namelabel}_level1.csv \
        -T "Log summary level 1" -O "Level 1 log summary ${namelabel}"
	
   echo "ERROR: Level 1 errors or Level 0 warnings found. Check log files, fix inputs, and rerun."
   $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: Level 1 errors or Level 0 warnings found. Check log files, fix inputs, and rerun." -t "e" -x $log_analyzer
   set exitstat = 1

## Register log analyzer output
else if ( $status != 0 ) then
   echo "ERROR: running log_analyzer, level 1"
   $EMF_CLIENT -k $EMF_JOBKEY -m "ERROR: running log_analyzer, level 1" -t "e" -x $log_analyzer
   set exitstat = 1
else
   echo "SCRIPT NOTE: Registering log summary, level1"
   $EMF_CLIENT -k $EMF_JOBKEY -F $REPOUT/log_analyzer/rep_logs_${namelabel}_level1.csv \
        -T "Log summary level 1" -O "Level 1 log summary ${namelabel}"
endif

## Ending of script
#
exit( $exitstat )
