#!/bin/bash
set -x

plots="FINNMARK"
res="1x1"

copy_phase="T"	     # Copy all files to the right place
first_phase="F"      # Simulate for 5 days
second_phase="F"     # Interpolate with existing data, then spin up
archive="F"

#module load nco
module load cesm

indir=/usit/abel/u1/jennybj
outdir=/work/users/jennybj


for plotn in $plots; do

 if [ ${copy_phase} = "T" ]
 then
## copy surface data and domain files
  cd /work/users/jennybj
  mkdir -p inputdata/share/domains/domain.clm/
  cp ${indir}/domain_file/domain.lnd.${plotn}.${res}.nc ${outdir}/inputdata/share/domains/domain.clm/domain.lnd.${res}_${plotn}_navy.nc

#!! need to modify "namelist_defaults_usr_files.xml" to set up the correct file name and directory for "fpftdyn"
#!! requirement: lnd/clm2/surfdata_map/surfdata.pftdyn_${clm_usr_name}_simyr1850-2005.nc 
#!!              lnd/clm2/surfdata_map/surfdata.pftdyn_rcp${rcp}_${clm_usr_name}_simyr${sim_year_range}.nc

## for constant pft cover, 2000 or 1850 simulation
  mkdir -p inputdata/lnd/clm2/surfdata_map
  cp ${indir}/inputdata/lnd/clm2/surfdata_map/surfdata_${res}_${plots}_simyr2000.nc ${outdir}/inputdata/lnd/clm2/surfdata_map/surfdata_${res}_${plotn}_simyr2000_cesm1_2_x_clm4_5.nc


## for constant 2000 or 1850 simulation
# mkdir -p inputdata/atm/cam/chem/trop_mozart_aero/aero
# cp ${indir}/mkmapdata/aerdep/aerosoldep_monthly_2000_mean_${plotn}_1x1.nc ${outdir}/inputdata/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_2000_mean_1x1_${plotn}.nc
 mkdir -p inputdata/lnd/clm2/snicardata
 cp ${indir}/mkmapdata/aerdep/aerosoldep_monthly_1849-2006_${plotn}_${res}.nc ${outdir}/inputdata/lnd/clm2/snicardata/aerosoldep_monthly_1849-2006_${res}_${plotn}.nc
  
  if [ ${res} = "1x1" ]
  then                           
    mkdir -p /work/users/jennybj/inputdata/atm/datm7/CLM1PT_data/1x1_${plotn}
    cp ${indir}/inputdata/atm/1x1_${plotn}/clm1pt_${plotn}_* ${outdir}/inputdata/atm/datm7/CLM1PT_data/1x1_${plotn}/
#    rename clm1pt_FINNMARK_1 1 *
#    rename clm1pt_FINNMARK_2 2 *
  fi

 fi


 if [ ${first_phase} = "T" ]
 then
     
  cd ${indir}/cesm/cesm1_2_2/scripts
  ./create_newcase -case ${indir}/cesm_case/1x1_${plotn} -user_compset 2000_DATM%1PT_CLM45%BGC_SICE_SOCN_RTM_SGLC_SWAV -mach abel -res CLM_USRDAT #-mpilib mpich2
                                                          
  cd ${indir}/cesm_case/1x1_${plotn}
# NEED TO DO THIS?
#  sed -i -e 's/12.1.2/12.1.3/g' env_mach_specific  ##
#  sed -i -e 's/2.2.1/2.4.2/g' env_mach_specific     ##
#  sed -i "34i module unload craype-interlagos" env_mach_specific
  
# default 20TR run, RUN_STARTDATE=1850-01-01; RCP8 run, RUN_STARTDATE=2005-01-01
  ./xmlchange -file env_run.xml -id RUN_STARTDATE -val 0001-01-01
#  xmlchange -file env_run.xml -id PIO_BUFFER_SIZE_LIMIT -val 0
  ./xmlchange -file env_run.xml -id DIN_LOC_ROOT -val /work/users/jennybj/inputdata
  ./xmlchange -file env_run.xml -id DATM_PRESAERO -val pt1_pt1
  ./xmlchange -file env_run.xml -id DATM_CLMNCEP_YR_ALIGN -val 0001
  ./xmlchange -file env_run.xml -id DATM_CLMNCEP_YR_START -val 1981 
  ./xmlchange -file env_run.xml -id DATM_CLMNCEP_YR_END -val 2010
  ./xmlchange -file env_run.xml -id CLM_USRDAT_NAME -val 1x1_${plotn}
  
  ./cesm_setup

# CHECK IF NEED TO ADD -mkl in SLIBS in the Macros file


# TO INCLUDE MODIFIED CODE
#  cp /home/uio/huit/noresm/cases/norway_plot405/SourceMods/src.clm/CNDVMod.F90 ./SourceMods/src.clm/

  ./1x1_${plotn}.build

# create user_datm.streams.txt.CLM1PT.CLM_USRDAT
  cp ${indir}/user_datm.streams.txt.CLM1PT.CLM_USRDAT ${indir}/cesm_case/1x1_${plotn}/
  ./preview_namelist
   
## modify run file
# CHANGE time, cpu=1, project... can be done in the file directly
#  sed -i -e 's/#PBS -A/#PBS -A nn2806k/g' 1x1_${plotn}.run
#  sed -i -e 's/#PBS -l walltime=05:00:00/#PBS -l walltime=00:15:00/g' 1x1_${plotn}.run

## modify user_nl_clm
  sed -i "21i ndepmapalgo = 'nn'" user_nl_clm
  sed -i "22i popdensmapalgo = 'nn'" user_nl_clm
#  sed -i "23i stream_year_first_popdens = 2000" user_nl_clm
#  sed -i "24i stream_year_last_popdens = 2000" user_nl_clm
  sed -i "23i lightngmapalgo = 'nn'" user_nl_clm

## modify user_nl_datm
  sed -i "14i taxmode = 'cycle'" user_nl_datm

#  ./1x1_${plotn}.submit

  fi


  if [ ${second_phase} = "T" ]
  then
#### second phase
  
    module switch PrgEnv-cray/5.2.40 PrgEnv-intel
    module load cray-netcdf

## prepare initial files for CLM run
    cp /work/users/jennybj/1x1_${plotn}/run/1x1_${plotn}.clm2.r.0001-01-06-00000.nc /usit/abel/u1/jennybj/cesm/cesm1_2_2/models/lnd/clm/tools/clm4_5/interpinic/
    cd /usit/abel/u1/jennybj/cesm/cesm1_2_2/models/lnd/clm/tools/clm4_5/interpinic
    cp 1x1_${plotn}.clm2.r.0001-01-06-00000.nc initial_1x1_${plotn}.clm2.r.0001-01-06-00000.nc 
    ./interpinic -i clmi.I2000CLM45CRUBGC.2000-01-01.0.9x1.25_gx1v6_simyr2000_c130517.nc -o initial_1x1_${plotn}.clm2.r.0001-01-06-00000.nc
    cp initial_1x1_${plotn}.clm2.r.0001-01-06-00000.nc /work/users/jennybj/1x1_${plotn}/run/
#    cd /work/huit/noresm/norway_plot${plotn}/run

## modify use_clm_nl 
    cd /usit/abel/u1/jennybj/cesm_case/1x1_${plotn}
    sed -i "24i finidat = '/work/users/jennybj/1x1_${plotn}/run/initial_1x1_${plotn}.clm2.r.0001-01-06-00000.nc'" user_nl_clm
 
## modify run file
# CHANGE again time, cpu etc...
    sed -i -e 's/#PBS -l walltime=05:00:00/#PBS -l walltime=00:45:00/g' 1x1_${plotn}.run
   
# CHANGE this
    ./xmlchange -file env_run.xml -id STOP_OPTION -val nyears
    ./xmlchange -file env_run.xml -id STOP_N -val 20
#    xmlchange -file env_run.xml -id REST_OPTION -val nyears
    ./xmlchange -file env_run.xml -id RESUBMIT -val 2

#    ./1x1_${plotn}.submit

  fi
  
  if [ ${archive} = "T" ]
  then
     cd /work/huit/archive
     scp -r 1x1_${plotn} huit@norstore.uio.no:/projects/NS2806K/huit/noresm/archive/    
  fi

done