#!/bin/bash
set -x
######################################################################################
#Define variables used for the call of the MARS retrieval scripts
######################################################################################

START_YEAR=2015              # Start year of your simulation
START_MONTH=01               # Start month of your simulation
START_DAY=01                 # Start day of your simulation
START_HOUR=00                # Start hour of your simulation

FORECAST_LENGTH="30"         # Length of the forcast cycle in hours, e.g. 30 hours
LAST_YEAR=2015               # Final end year of your simulation
LAST_MONTH=01                # Final end month of your simulation
LAST_DAY=31                  # Final end day of your simulation

FIRST_DATE=${START_YEAR}${START_MONTH}${START_DAY}

# Start of the loop (first day simulation, usually you do not need to change this)    
LOOP_START_DAY=01

#Calculation of the end loop (calculates total number of days that will be simulated)
LOOP_END_DAY=` expr $"(( $(date --date="$LAST_YEAR$LAST_MONTH$LAST_DAY" +%s) - $(date --date="$START_YEAR$START_MONTH$START_DAY" +%s) ))/(60*60*24) + 1"|bc ` 


########################################################################################
#
# create start and stop dates for the WRF NWP simulation
#
######################################################################################

## Now loop over days to automatise the work##

while [ ${LOOP_START_DAY} -le ${LOOP_END_DAY} ] 
 do

INITIAL_DATE=${START_YEAR}${START_MONTH}${START_DAY}   # Necessary afterward for organizing and naming folders for your outputs
INITIAL_HOUR=${START_HOUR}                             # Necessary afterward for organizing and naming folders for your outputs


# Calculate STOP time (STOP_YEAR, STOP_DAY, STOP_MONTH, STOP_HOUR) after running one cycle (e.g. 30 hours)
# if you have e.g. 30 forecast length, then STOP DATE will be the following day and STOP HOUR will be 6 UTC


INITIAL_DATE=${START_YEAR}${START_MONTH}                                # Initial date necessary for organising folders where you will put your outputs

MONTH_DAYS=` cal $START_MONTH $START_YEAR | xargs | awk '{print $NF}' ` #Calculates number of days per selected month

STOP_HOUR=0`expr $FORECAST_LENGTH - 24`            #Calculates the hour at which the forecast stops after one forecast cycle

if [ ${START_DAY} -lt ${MONTH_DAYS} ]              #If a day is within a month
 then
  STOP_DAY=`expr $START_DAY + 1`
  STOP_MONTH=$START_MONTH
  STOP_YEAR=$START_YEAR
elif [ ${START_MONTH} -eq 12 ] && [ ${START_DAY} -eq ${MONTH_DAYS} ]   #If a day is the last day in a year
 then
  STOP_DAY=1
  STOP_MONTH=01
  STOP_YEAR=`expr $START_YEAR + 1` 
elif [ ${START_DAY} -eq ${MONTH_DAYS} ]            #If a day is the last day in a month
 then
  STOP_DAY=1
  STOP_MONTH=0`expr $START_MONTH + 1`
  STOP_YEAR=$START_YEAR
fi


 #Adding zero before number 

if [ ${STOP_DAY} -lt 10 ]                  
  then
    STOP_DAY=0${STOP_DAY}
  fi

#####################################################################################
#  Define variables used to fill the namelist file "namelist.input" 
#
#   ***************** READ THIS CAREFULLY BEFORE YOU START!!!!!*********************
#
#####################################################################################

MAX_DOM=1                        # Number of WRF model domains

################################################################################
#The entries were calculated above for the namelist.input
################################################################################

S_YEAR="${START_YEAR}, ${START_YEAR}"       # This is an example for 2 domains. If you have
S_MONTH="${START_MONTH}, ${START_MONTH}"    # more domains, you have to adjust this:
S_DAY="${START_DAY}, ${START_DAY}"          # Insert comma separated list for the different
S_HOUR="${START_HOUR}, ${START_HOUR}"       # domains. The variables has to be replaced 
E_YEAR="${STOP_YEAR}, ${STOP_YEAR}"         # by numbers when start and stop shall be 
E_MONTH="${STOP_MONTH}, ${STOP_MONTH}"      # different for the different domains.
E_DAY="${STOP_DAY}, ${STOP_DAY}"            # 
E_HOUR="${STOP_HOUR}, ${STOP_HOUR}"         # 


################################################################################
# Create data directory and  working directory
################################################################################

 WRKDIR=/lustre/cray/ws7/ws/ipmspa-SABLE-0/NWP_MODE_WRF371/  # Your working directory (usually it is WRFV3/run where you run WRF)
DATADIR=/lustre/cray/ws7/ws/ipmspa-SABLE-0/MET_EM_NWP_MODE/  # Directory where you have MET_EM files 
 OUTPUT=/lustre/cray/ws7/ws/ipmspa-SABLE-0/NWP_MODE_WRF371/${INITIAL_DATE}${INITIAL_HOUR} # Directory where you want to put your output files

# Test whether the directories exist. Create if not the case. This will be changed in 
# a way, that an existing directory is automatically deleted and recreated when 
# everything is working.

#test -d ${WRKDIR}  || mkdir ${WRKDIR}
#test -d ${DATADIR} || mkdir ${DATADIR}
 test -d ${OUTPUT}  || mkdir ${OUTPUT}

#############################################################################
## Create namelist     
## Adjust the namelist as you want                                                    
#############################################################################

cd ${WRKDIR}   # Enter the working directory

cat > namelist.input <<EOF
 &time_controly
 run_days                            = 0,
 run_hours                           = 30,
 run_minutes                         = 0,
 run_seconds                         = 0,
 start_year                          = ${S_YEAR},
 start_month                         = ${S_MONTH},
 start_day                           = ${S_DAY},
 start_hour                          = ${S_HOUR},
 start_minute                        = 00, 00, 
 start_second                        = 00, 00,
 end_year                            = ${E_YEAR},
 end_month                           = ${E_MONTH},
 end_day                             = ${E_DAY},
 end_hour                            = ${E_HOUR},
 end_minute                          = 00, 00, 
 end_second                          = 00, 00, 
 interval_seconds                    = ${INTERVAL_SECONDS},
 input_from_file                     = .true., .true.,
 history_interval                    = 60, 30,
 frames_per_outfile                  = 6, 6,
 restart                             = .false.,
 restart_interval                    = 1440,
 io_form_history                     = 2,
 io_form_restart                     = 2,
 io_form_input                       = 2,
 io_form_boundary                    = 2,
 debug_level                         = 0,
 inputout_interval                   = 360,
 auxinput4_inname                    = 'wrflowinp_d<domain>',
 auxinput4_interval                  = 360,
 io_form_auxinput4                   = 2
 /
 
 &domains
 time_step                           = 36,
 max_dom                             = 2,
 e_we                                = 194, 271,
 e_sn                                = 217, 271,
 e_vert                              = 89, 89,
 p_top_requested                     = 5000,
 num_metgrid_levels                  = 92,
 eta_levels                          = 1.0,0.9987381,0.996218,0.992447,0.987437,0.9812,0.9737,0.965,
                       0.9552,0.9442,0.9321,0.919,0.9049,0.8898,0.8737,0.8567,0.8389,0.8203,0.8009,0.7809,0.7602,0.7389,
                       0.7171,0.69489,0.6722,0.6501,0.62856,0.60759,0.5871,0.5671,0.54768,0.5287,0.5102,0.4922,0.47465,
                       0.45755,0.4409,0.4247,0.4089,0.39355,0.3786,0.36402,0.34989,0.3361,0.32267,0.30961,0.29695,0.2846,
                       0.2726,0.261001,0.24969,0.2387,0.228,0.2176,0.2075,0.1977,0.1882,0.17898,0.17,0.1613,0.15285,0.14465,
                       0.1367,0.129,0.12155,0.11433,0.107321,0.10053,0.09395,0.0876,0.08145,0.0755,0.06974,0.06416,0.05876,0.05355,
                       0.048501,0.04364,0.03894,0.0344,0.03001,0.02578,0.0217,0.01776,0.01396,0.0103,0.00677,0.00332,0.0,
 num_metgrid_soil_levels             = 4,
 dx                                  = 6000, 2000,
 dy                                  = 6000, 2000,
 grid_id                             = 1, 2,
 parent_id                           = 0, 1,
 i_parent_start                      = 1, 50,
 j_parent_start                      = 1, 80,
 parent_grid_ratio                   = 1, 3,
 parent_time_step_ratio              = 1, 3,
 feedback                            = 1,
 smooth_option                       = 0,
 /

 &physics
 sst_update                          = 1, 
 mp_physics                          = 10, 10,
 ra_lw_physics                       = 4, 4,
 ra_sw_physics                       = 4, 4,
 radt                                = 6, 2,
 sf_sfclay_physics                   = 2, 2,
 sf_surface_physics                  = 2, 2,
 bl_pbl_physics                      = 2, 2,
 bldt                                = 0, 0,
 topo_wind                           = 0, 0,
 cu_physics                          = 3, 0,
 cudt                                = 5, 0,
 isfflx                              = 1,
 ifsnow                              = 1,
 icloud                              = 1,
 surface_input_source                = 1,
 num_soil_layers                     = 4,
 sf_urban_physics                    = 0,
 num_land_cat                        = 21,
 /

 &fdda
 /

 &dynamics
 w_damping                           = 0,
 diff_opt                            = 1,
 km_opt                              = 4,
 diff_6th_opt                        = 0,      0,      
 diff_6th_factor                     = 0.12,   0.12,  
 base_temp                           = 290.,
 damp_opt                            = 0,
 zdamp                               = 5000.,  5000., 
 dampcoef                            = 0.2,    0.2,  
 khdif                               = 0,      0,   
 kvdif                               = 0,      0,   
 non_hydrostatic                     = .true., .true.,
 moist_adv_opt                       = 1,      1,         
 scalar_adv_opt                      = 1,      1,         
 /


 &bdy_control
 spec_bdy_width                      = 10,
 spec_zone                           = 1,
 relax_zone                          = 4,
 specified                           = .true., .false.,
 nested                              = .false., .true., 
 /

 &grib2
 /

 &namelist_quilt
 nio_tasks_per_group = 0,
 nio_groups = 1,
 /
EOF

#######################################
## run REAL.EXE  
#######################################

cd ${WRKDIR}   # Enter the working directory

  ln -sf ${DATADIR}/met_em* ${WRKDIR}   # Linking the met_em files

# Starting real using start_real.sh script that you need to create for HRLS
    REAL_job_pid_orig=`qsub -q test start_real.sh` 
    REAL_job_pid=${REAL_job_pid_orig%.hornet-batch.hww.de}


# Checking if the job is still running
 sleep 60   
  while [ 1 = 1 ] 
  do
   sleep 30
       qout=`qstat | grep $REAL_job_pid` || break
       echo $qout | grep -q " C " && break
   done


# Checking if the job is finished with success or not
  if grep "SUCCESS" rsl.error.0000
   then
   echo "real at beginning ok"
   cp wrfinput* ${OUTPUT}    # If all good, input files copied into the OUTPUT folder
  else
   echo "REAL failed, exiting"
   echo "REAL failed" > mail_message   # If failed message sent to your email
   /usr/bin/mail -s "NWP MODE REAL failed" j.milovac@uni-hohenheim.de < mail_message  # Send an info to your mail
   exit 1
  fi

# Change SOIL data in the WRF input file to keep it continuous
 if [ ${INITIAL_DATE} -ne ${FIRST_DATE} ]  # If it is not the first date with which you intialise the NWP simulation
   then
   ncl change_wrfinput.ncl
   mv wrfout_wrfinput_d01 ${OUTPUT}
   mv wrfout_wrfinput_d02 ${OUTPUT}
 fi

# remove old files
 rm -f rsl.*


#######################################
## run WRF.EXE once at the beginning 
#######################################
 
 cd ${WRKDIR}

# Starting real using start_real.sh script that you need to create for HRLS
  WRF_job_pid_orig=`qsub start_wrf.sh`
  WRF_job_pid=${WRF_job_pid_orig%.hornet-batch.hww.de}


#check if the job is still running

  echo "Job WRF ID= " $WRF_job_pid
 sleep 60
  while [ 1 = 1 ] 
  do
   sleep 30
       qout=`qstat | grep $WRF_job_pid` || break
       echo $qout | grep -q " C " && break
   done

# Checking if the job is finished with success or not
  if grep "SUCCESS COMPLETE WRF" rsl.error.0000
  then
   echo "wrf final ok"
# If the job finished successfully, rename wrfout file at 00 UTC next day to wrfout_date_wrfinput_d0x necessary for keeping the soil vailables continuous!
# Notice, the number of these files corresponds to the number of domains!!!
   cp wrfout_d01_${STOP_YEAR}-${STOP_MONTH}-${STOP_DAY}_00_00_00 wrfout_wrfinput_d01
   cp wrfout_d02_${STOP_YEAR}-${STOP_MONTH}-${STOP_DAY}_00_00_00 wrfout_wrfinput_d02
 else
   echo "RUN_WRF_EXE failed, exiting"
   echo "RUN_WRF_EXE failed" > mail_message  
   /usr/bin/mail -s "MYNN WRF.EXE failed for "${START_YEAR}${START_MONTH}${START_DAY} jmilovac@uni-hohenheim.de < mail_message
   exit 1
 fi

# Moving all necessary files to your OUTPUT folder and removing the nonnecessary ones

  mv wrfout_d0* ${OUTPUT}
  mv wrfinput_d0* ${OUTPUT}
  mv wrflowinp_d0* ${OUTPUT}
  mv wrfbdy_d0* ${OUTPUT}
  mv wrfrst_d0* ${OUTPUT}
  rm -f rsl.*
  rm -f met_em*  

##########################################
# Change to the next day
##########################################

LOOP_START_DAY=`expr $LOOP_START_DAY + 1 `

if [ ${START_DAY} -lt ${MONTH_DAYS} ]              #If a day is within a month
 then
  START_DAY=`expr $START_DAY + 1`
  START_MONTH=$START_MONTH
  START_YEAR=$START_YEAR
elif [ ${START_MONTH} -eq 12 ] && [ ${START_DAY} -eq ${MONTH_DAYS} ]   #If a day is the last day in a year
 then
  START_DAY=1
  START_MONTH=01
  START_YEAR=`expr $START_YEAR + 1` 
elif [ ${START_DAY} -eq ${MONTH_DAYS} ]            #If a day is the last day in a month
 then
  START_DAY=1
  START_MONTH=0`expr $START_MONTH + 1`
  START_YEAR=$START_YEAR
fi


 if [ ${START_DAY} -lt 10 ]
    then
    START_DAY=0${START_DAY}
 fi


done