#!/bin/csh

  # Set TABLE TYPE
  setenv TABLE_TYPE IMPROVE

  # Specify the variable names used in your observation inputs
  # and model output files for each of the species you are analyzing below.
  #
  # variable format:
  #    Obs_expression, Obs_units, [Mod_expression], [Mod_unit], [Variable_name]
  #
  # The expression is in the form:
  #       [factor1]*Obs_name1 [+][-] [factor2]*Obs_name2 ...
  setenv AERO_1 "SO4f_val,ug/m3,SO4,,SO4"                         # sulfate #renamed as my spec_def file #original line is: "SO4f_val,ug/m3,ASO4IJ,,SO4"# Renamed this particualr column for all other species and the post_only run to generate this file was done by only WRITE-SITEX  T option.
  setenv AERO_2 "NO3f_val,ug/m3,NO3,,NO3"                         # nitrate
  setenv AERO_3 "0.2903*NO3f_val+0.375*SO4f_val,ug/m3,NH4,,NH4"   # ammonium (estimated assuming fully neutralized SO4 and NO3)
  setenv AERO_4 "MF_val,ug/m3,PM25_TOT,ug/m3,PM25_TOT"          # Total PM2.5 mass # is it renmaed on AMETv1.4, the last column is PM_TOT?. In ametv1.2 last column is PM25_TOT 
  setenv AERO_5 "OCf_val,ug/m3,OC,,OC"                            # Organic Carbon
  setenv AERO_6 "ECf_val,ug/m3,EC,,EC"                            # Elemental Carbon
  #setenv AERO_7 "OCf_val+ECf_val,ug/m3,AOCIJ+AECIJ,,TC"              # Total Carbon
  setenv AERO_8 "CHLf_val,ug/m3,CL,ug/m3,Cl"                      # CL Ion # In AMET_v1.2 Rambolls file, it is CLf_Val but here it is CHLF_val
  setenv AERO_9 "MT_val,ug/m3,PM10_TOT,ug/m3,PM10"              # PM10
  setenv AERO_10 "CM_calculated_val,ug/m3,PMC_TOT,ug/m3,PMC_TOT"     # PM Course

# new AE6 species
## note: we use XRF sodium because there is not IC sodium mesaurement
## we use IC measurement for chlorid (CHLf_val) instead of XRF chlroine (CLf_Val)
  setenv AERO_11 "NAf_val,ug/m3, NA,,Na"                          # sodium
  #setenv AERO_12 "NAf_val + CHLf_val,ug/m3,ACLIJ + ANAIJ,,NaCl"      # sodium chloride
  #setenv AERO_13 "FEf_val,ug/m3, AFEJ,,Fe"                           # iron
  #setenv AERO_14 "ALf_val,ug/m3,AALJ,,Al"                            # aluminum 
  #setenv AERO_15 "SIf_val,ug/m3, ASIJ,,Si"                           # silicon
  #setenv AERO_16 "TIf_val,ug/m3, ATIJ,,Ti"                           # titanium
  #setenv AERO_17 "CAf_val,ug/m3,ACAJ,,Ca"                            # calcium
  #setenv AERO_18 "MGf_val,ug/m3,AMGJ,,Mg"                            # magnesium
  #setenv AERO_19 "Kf_val,ug/m3,AKJ,,K"                               # potassium
  #setenv AERO_20 "MNf_val,ug/m3,AMNJ,,Mn"                            # manganese
  setenv AERO_21 "2.20*ALf_val+2.49*SIf_val+1.63*CAf_val+2.42*FEf_val+1.94*TIf_val,ug/m3,SOIL,,PM25_SOIL"       # IMPROVE soil eqn.# The last part in AMETv1.2 RAMBOLLS file is 1.94*TIf_val,ug/m3,SOIL,,PM25_SOIL" # I renamed it as Rambolls # original last part name here was:1.94*TIf_val,ug/m3,ASOILJ,,soil"
  #setenv AERO_22 "MF_val-SO4f_val-NO3f_val-0.2903*NO3f_val-0.375*SO4f_val-OCf_val-ECf_val-NAf_val-CHLf_val-2.2*ALf_val-2.49*SIf_val-1.63*CAf_val-2.42*FEf_val-1.94*TIf_val,ug/m3,AUNSPEC1IJ,,OTHER"        # PM Other
 # setenv AERO_23 "0.8*OCf_val,ug/m3, ANCOMIJ,,NCOM"    # NCOM
  #setenv AERO_24 "MF_val-SO4f_val-NO3f_val-0.2903*NO3f_val-0.375*SO4f_val-OCf_val-ECf_val-NAf_val-CHLf_val-2.2*ALf_val-2.49*SIf_val-1.63*CAf_val-2.42*FEf_val-1.94*TIf_val,ug/m3, AUNSPEC2IJ,,OTHER_REM"    # PM Other remaining
  ### End Species List ###

  ## define time window
  setenv START_DATE 2016167
  setenv END_DATE 2016213
  setenv START_TIME 0
  setenv END_TIME 230000

  ## define the PRECIP variable
  setenv PRECIP RT

  ## adjust for daylight savings
  setenv APPLY_DLS N

  ## set missing value string
  setenv MISSING '-999'

  ## Projection sphere type (use type #19 to match CMAQ)
  setenv IOAPI_ISPH 20

  ## Time Shift for dealing with aconc files ##
  setenv TIME_SHIFT 0

  #############################################################
  #  Input files
  #############################################################
  # ioapi input files containing VNAMES (max of 10)
  setenv M3_FILE_1 /run/media/root/55A07B0360BDF544/postproc/AMET_v14/tools_src/combine/ARDEQ_outputs/ARDEQ_camxv7_cb6r4DMS.ADEQ_AR_2020.2016v1.JUL.grd02.nc


  #  SITE FILE containing site-id, longitude, latitude (tab delimited)
  setenv SITE_FILE /run/media/root/55A07B0360BDF544/postproc/AMET_v14/obs/AQ/site_metadata_files/IMPROVE_full_site_list.csv

  # : input table (exported file from Excel)
  #   containing site-id, time-period, and data fields
  setenv IN_TABLE /run/media/root/55A07B0360BDF544/postproc/AMET_v14/obs/AQ/2016/IMPROVE_data_2016.csv

  #############################################################
  #  Output files
  #############################################################

  #  output table (tab delimited text file importable to Excel)
  setenv OUT_TABLE /run/media/root/55A07B0360BDF544/postproc/AMET_v14/output/ARDEQ_JUL_TRIAL/sitex_output/IMPROVE_ARDEQ_JUL_TRIAL.csv

  /run/media/root/55A07B0360BDF544/postproc/AMET_v14/bin/sitecmp.exe