#!/bin/bash

# ICON
#
# ------------------------------------------
# Copyright (C) 2004-2026, DWD, MPI-M, DKRZ, KIT, ETH, MeteoSwiss
# Contact information: icon-model.org
# See AUTHORS.TXT for a list of authors
# See LICENSES/ for license information
# SPDX-License-Identifier: BSD-3-Clause
# ------------------------------------------

# ----------------------------------------------------------------------------
#
# SCM run script for GOAmazon case on NEC
#
# ----------------------------------------------------------------------------
#PBS -q sx_norm
#PBS -v NE=1,CPE=1,NMPI_ROOT=/opt/nec/ve/mpi/2.3.1
#PBS -l elapstim_req=00:20:00
#PBS --venode=${NE}
#PBS --venum-lhost=1     # Number of VE per logical host
#PBS --cpunum-lhost=2    # Number of VH-x86-Cores per log. host
#PBS -T necmpi           # necessary for parallel jobs with NEC-MPI
##PBS -N icon-scm-real
#PBS -o /hpc/uwork/${USER}/wq/iconSCM.%s
#PBS -j o
# ----------------------------------------------------------------------------

source ${NMPI_ROOT}/bin/necmpivars.sh

set -x

# OpenMP settings
export OMP_SCHEDULE="static"
export OMP_DYNAMIC="false"
export OMP_NUM_THREADS=1   # check total number of requested cores!

# Run information
let PPN=${CPE}*${NE}/${OMP_NUM_THREADS}         # no. of MPI procs. per NQS job

ID=`echo $PBS_JOBID | cut -d: -f2 | cut -d. -f1`
ulimit -s unlimited

# ----------------------------------------------------------------------------
# specifiy experiment (idealized simulation)
# ----------------------------------------------------------------------------
   EXPNAME=SCM_GASS_DCP_SGP

#YYYY='2004'
#YYYY=`cat ${WORK}/run-icon/scm/${EXPNAME}/YYYY`
YYYY=`cat ${PBS_O_WORKDIR}/YYYY`
#YYYY=$1
echo 'Year: ' $YYYY


# ----------------------------------------------------------------------------
# path definitions
# ----------------------------------------------------------------------------

# base directory for ICON sources and binary:
#ICONDIR=${PBS_O_WORKDIR%/*}       # local icon directory (up from SCM-ideal)
ICONDIR=$HOME/icon/icon-nwp-test1

# SCM data directory (grids, init data, extpar)
SCMDATA=/hpc/uwork/mkoehler/scm/data       # at DWD on NEC

# directory with input grids:
GRIDDIR=${SCMDATA}/grid

# directory with init files:
INITDIR=${SCMDATA}/init_data

# absolute path to output directory for results:
EXPDIR=${WORK}/run-icon/scm/${EXPNAME}/${YYYY}

# path to model binary, including the executable:
MODEL=${ICONDIR}/build/VE/bin/icon

# debug traceback
export ATP_ENABLED=1

# ----------------------------------------------------------------------------
# copy input data: grids, external parameters, model
# ----------------------------------------------------------------------------

# the directory for the experiment will be created, if not already there
if [ ! -d $EXPDIR ]; then
    mkdir -p $EXPDIR
fi
cd ${EXPDIR}

# files needed for radiation
ln -sf ${ICONDIR}/data/ECHAM6_CldOptProps.nc .
ln -sf ${ICONDIR}/data/rrtmg_lw.nc .
ln -sf ${ICONDIR}/data/rrtmg_sw.nc .

ecRad_data_path=${ICONDIR}'/externals/ecrad/data'

# link binary
ln -sf $MODEL icon

# ----------------------------------------------------------------------------
# model timing
# ----------------------------------------------------------------------------

# 0.4 s for 70 m res., 0.5 for 100 m; 30 s for 2.5 km?
#dtime=60
dtime=120
ndyn_substeps=3
dt_checkpoint=`expr 100 \* 86400`  # write restart file every hours (when lrestart = TRUE)
#nhours=480
nhours=72
#nhours=1
nsteps=`expr ${nhours} \* 3600 / ${dtime}`

# ----------------------------------------------------------------------------
# loop 5day forecasts from every day 00UTC
# ----------------------------------------------------------------------------
#for gridfile in ${atmo_dyn_grids}; do

start_date=`cat start_date`
end_date=`cat end_date`

#start_date="2014-02-20T00:00:00Z"    # 5day case study
#end_date="2014-02-25T00:00:00Z"      # ...

#start_date="2014-02-15T00:00:00Z"    # 5day from start
#end_date="2014-02-20T00:00:00Z"      # ...

#start_date="2014-02-15T00:00:00Z"   # official start time
#end_date="2014-03-23T21:00:00Z"     # official end time
#end_date="2014-02-20T01:00:00Z"
#end_date="2014-02-15T00:02:00Z"     # one time step

# ----------------------------------------------------------------------------
# output
# ----------------------------------------------------------------------------
DT_DATA=`expr 1 \* 3600`      # output each n hours
DT_DATA=${dtime}              # output every time step
#n_in_ofile=60                # number of time steps per output file
n_in_ofile=10000              # number of time steps per output file

# ----------------------------------------------------------------------------
# grid namelist settings
# ----------------------------------------------------------------------------

# the grid parameters
atmo_dyn_grids="Torus_Triangles_4x4_2500m.nc"
atmo_rad_grids=""

# reconstruct the grid parameters in namelist form
dynamics_grid_filename=""
for gridfile in ${atmo_dyn_grids}; do
  dynamics_grid_filename="${dynamics_grid_filename} '${gridfile}',"
done
radiation_grid_filename=""
for gridfile in ${atmo_rad_grids}; do
  radiation_grid_filename="${radiation_grid_filename} '${gridfile}',"
done

ln -sf ${GRIDDIR}/${atmo_dyn_grids} .

#forcings
#ln -sf ${INITDIR}/init_SCM_GASS_DCP_GoAmazon.nc init_SCM.nc
#ln -sf ${INITDIR}/init_SCM_GASS_DCP_GoAmazon_IOP1.nc init_SCM.nc

# cut period from input (on lce or rcl)
#  cdodir=/hpc/sw/cdo/1.9.8/x86/gnu/bin
#  ncodir=/usr/bin
#  $cdodir/cdo seldate,`echo ${start_date} | cut -c 1-19`,`echo ${end_date} | cut -c 1-19` \
#    ${INITDIR}/init_SCM_GASS_DCP_GoAmazon_IOP1.nc init_SCM.nc
#  $ncodir/ncks -v longitude,latitude,FR_LAND,PLCOV_MX,LAI_MX,ROOTDP,RSMIN,SOILTYP,Z0,EMIS_RAD,TOPO \
#    ${INITDIR}/init_SCM_GASS_DCP_GoAmazon_IOP1.nc init_SCM_2.nc
#  $ncodir/ncks -A init_SCM_2.nc init_SCM.nc
#  $ncodir/ncks -d time,0,360 init_SCM.nc init_SCM.nc
#  $ncodir/ncks -3 init_SCM.nc out.nc
#  $ncodir/ncrename -d time,nt out.nc
#  $ncodir/ncks -4 out.nc init_SCM.nc
#  $ncodir/ncatted -O -a units,time,a,c,'seconds since 2014-2-15 0:00:00 0:00' init_SCM.nc

# ----------------------------------------------------------------------------
# create ICON master namelist
# ----------------------------------------------------------------------------

cat > icon_master.namelist << EOF

&master_nml
 lrestart                    =                     .FALSE.        ! .TRUE.=current experiment is resumed
/
&master_model_nml
 model_type                  =                          1         ! identifies which component to run (atmosphere,ocean,...)
 model_name                  =                      "ATMO"        ! character string for naming this component.
 model_namelist_filename     =       "NAMELIST_${EXPNAME}"        ! file name containing the model namelists
 model_min_rank              =                          1         ! start MPI rank for this model
 model_max_rank              =                      65536         ! end MPI rank for this model
 model_inc_rank              =                          1         ! stride of MPI ranks
/

! time_nml: specification of date and time------------------------------------
&time_nml
 ini_datetime_string         =               "$start_date"        ! initial date and time of the simulation
 end_datetime_string         =                 "$end_date"        ! initial date and time of the simulation
/

EOF

# ----------------------------------------------------------------------------
# model namelists
# ----------------------------------------------------------------------------
# For a complete list see Namelist_overview.pdf

cat > NAMELIST_${EXPNAME} << EOF

&parallel_nml
 nproma         =  32
 p_test_run     = .false.
 num_io_procs   =  1         ! number of I/O processors
 l_test_openmp  = .false.
 l_log_checks   = .false.
/

&grid_nml
 dynamics_grid_filename = "${atmo_dyn_grids}",
 corio_lat              = -3.11         ! Manaus 3.11S, 60.02W
 is_plane_torus         = .TRUE.
 l_scm_mode = .TRUE.       ! main logical to turn on SCM mode
/


&SCM_nml
 i_scm_netcdf = 1            ! read initial profiles and forcings from netcdf
 lscm_read_tke = .FALSE.    ! read initial tke from netcdf
 lscm_read_z0  = .TRUE.     ! read initial z0 from netcdf
 scm_sfc_mom   = 2          ! 2: prescribed u*
 scm_sfc_temp  = 2          ! 2: prescribed sensible heat flux at surface
 scm_sfc_qv    = 2          ! 2: prescribed latent heat flux at surface
!scm_sfc_mom   = 0          ! 0: TURBTRANS: no prescribed u*
!scm_sfc_temp  = 0          ! 0: TERRA:     no prescribed sensible heat flux at surface
!scm_sfc_qv    = 0          ! 0: TERRA:     no prescribed latent heat flux at surface
/

&io_nml
 dt_checkpoint  = ${dt_checkpoint}
 lkeep_in_sync  = .true.
 lflux_avg      = .FALSE.     ! false: accumulated fluxes
/

&run_nml
 num_lev        = 90           ! number of full levels of vertical grid
 dtime          = ${dtime}     ! timestep in seconds
 nsteps         = ${nsteps}
 ldynamics      = .FALSE.      ! compute adiabatic dynamic tendencies
 ltransport     = .FALSE.
 ntracer        = 5            ! default: 0
 iforcing       = 3            ! 3: NWP forcing; 6:inhecham forcing
 ltestcase      = .TRUE.       ! run testcase
 ltimer         = .FALSE.      !
 msg_level      = 12           ! detailed report during integration
 output         = 'nml','totint'
/

&nwp_phy_nml
 inwp_gscp       = 1
 inwp_convection = 1 ! 1:Tiedtke/Bechtold, 0:off
 inwp_radiation  = 4 ! 1:RRTM radiation, 4:ecRad
 inwp_cldcover   = 1 ! 3: clouds from COSMO SGS cloud scheme 0: no cloud 5: grid-scale clouds
 inwp_turb       = 1 ! 1: TKE diffusion and transfer
 inwp_satad      = 1
 inwp_sso        = 0
 inwp_gwd        = 0
 inwp_surface    = 0 ! 0: none; 1: TERRA   (0: simple ocean, sea-ice albedo!)
!icapdcycl       = 3 ! apply CAPE modification to improve diurnalcycle over tropical land (optimizes NWP scores)
 icapdcycl       = 0 ! apply CAPE modification to improve diurnalcycle over tropical land (optimizes NWP scores)
 latm_above_top  = .TRUE.  ! needed for radiation routine
 itype_z0        = 2
!dt_rad	         = 1800.        ! Default: 1800   ! M. Koehler: 1440
 dt_rad	         = 3600.        ! Default: 1800   ! M. Koehler: 1440
 dt_conv         = 600.         ! Default: 600    ! M. Koehler: 360
 dt_sso	         = 600.         ! Default: 1200   ! M. Koehler: 720
 dt_gwd	         = 600.         ! Default: 1200   ! M. Koehler: 720
/

&nwp_tuning_nml
 itune_albedo                 = 0       ! somewhat reduced albedo (w.r.t. MODIS data) over Sahara in order to reduce cold bias
 tune_zceff_min               = 0.01    ! ** default value to be used for R3B7; use 0.025 for R2B6 in order to get similar temperature biases in upper troposphere **
 tune_gkdrag                  = 0.075   ! R2B6: 0.075
 tune_gkwake                  = 1.5     ! R2B6: 1.5
 tune_gfrcrit                 = 0.425   ! R2B6: 0.425
 tune_dust_abs                = 0.
 tune_zvz0i                   = 0.85
 tune_box_liq_asy             = 3.25    ! oper global: 3.0 , oper D2: 3.25, default: 2.5
 tune_box_liq                 = 0.05
 tune_rcucov                  = 0.075
 tune_rhebc_land              = 0.825
 tune_gust_factor             = 7.0
 icpl_turb_clc                = 1
 lcalib_clcov                 = .false. ! turn off TCC, HCC, MCC, LCC tuning
/

&turbdiff_nml
 tkhmin                       = 0.6
 tkhmin_strat                 = 1.0
 tkmmin                       = 0.75
 tkmmin_strat                 = 4
 alpha0                       = 0.0123
 alpha0_max                   = 0.0335
 alpha1                       = 0.125
 pat_len                      = 750.
 c_diff                       = 0.2
 rlam_heat                    = 10.0
 rat_sea                      = 0.8
 ltkesso                      = .true.  ! SSO dissipation energy used in TKE equation
 frcsmot                      = 0.2     ! these 2 switches together apply vertical smoothing of the TKE source terms
 imode_frcsmot                = 2       ! in the tropics (only), which reduces the moist bias in the tropical lower troposphere
 itype_sher                   = 3       ! use horizontal shear production terms with 1/SQRT(Ri) scaling to prevent unwanted side effects
 ltkeshs                      = .true.
 a_hshr                       = 2.0
 icldm_turb                   = 1       ! 2: Gauss clouds for turbulence    1: grid scale clouds
 icldm_tran                   = 2       ! 2: Gauss clouds for surface layer 1: grid scale clouds
/

&lnd_nml
  ntiles         = 1
  nlev_snow      = 3
  lmulti_snow    = .false.
  itype_heatcond = 3
  idiag_snowfrac = 20
  lsnowtile      = .true.
  lseaice        = .true.
  llake          = .true.
  itype_lndtbl   = 4
  itype_evsl     = 4
  itype_trvg     = 3
  itype_root     = 2
  cwimax_ml      = 5.e-4
  c_soil         = 1.25
  c_soil_urb     = 0.5
  sstice_mode    = 2
! lprog_albsi    = .true.
  itype_snowevap = 2
/

&radiation_nml
 irad_o3                      = 9
! izenith                      = 4           ! 4: NWP default, 3: no annual cycle
! albedo_type                  = 2 ! Modis albedo
! vmr_co2                      = 390.e-06 ! values representative for 2012
! vmr_ch4                      = 1800.e-09
! vmr_n2o                      = 322.0e-09
! vmr_o2                       = 0.20946
! vmr_cfc11                    = 240.e-12
! vmr_cfc12                    = 532.e-12
! direct_albedo                = 4
! direct_albedo_water          = 3
! albedo_whitecap              = 1
 llw_cloud_scat               = .true.
 ecRad_data_path              = '${ecRad_data_path}'
/

&ls_forcing_nml
 is_subsidence_moment         = .FALSE.
 is_subsidence_heat           = .TRUE.
!is_subsidence_heat           = .FALSE.
 is_advection                 = .TRUE.
 is_advection_uv              = .FALSE.
 is_advection_tq              = .TRUE.
!is_advection_tq              = .FALSE.
 is_geowind                   = .FALSE.
 is_rad_forcing               = .FALSE.
 is_nudging                   = .TRUE.
 is_nudging_uv                = .TRUE.
 is_nudging_t                 = .FALSE.
 is_nudging_q                 = .FALSE.
/

&nonhydrostatic_nml
 iadv_rhotheta                = 2
 ivctype                      = 2
 itime_scheme                 = 4
 exner_expol                  = 0.333
 vwind_offctr                 = 0.2         ! 0.2 for R2B6 and higher resolution, 0.3 for lower resolution
 damp_height                  = 44000.
 rayleigh_coeff               = 0.5
 divdamp_order                = 24          ! 2 ass, 24 fc
 divdamp_type                 = 32          ! optional: 2 assimilation cycle, 32 forecast
 divdamp_fac                  = 0.004       ! 0.004 for R2B6; recommendation for R3B7: 0.003
 divdamp_trans_start          = 12500
 divdamp_trans_end            = 17500
 igradp_method                = 3
 l_zdiffu_t                   = .true.
 thslp_zdiffu                 = 0.02
 thhgtd_zdiffu                = 125.
 htop_moist_proc              = 22500.
 hbot_qvsubstep               = 16000.
/

&sleve_nml
 min_lay_thckn                = 20.         ! lowest level thickness (between half-levels)
 max_lay_thckn                = 400.        ! maximum layer thickness below htop_thcknlimit
 htop_thcknlimit              = 14000.
!top_height                   = 75000.
 top_height                   = 30000.
 stretch_fac                  = 0.9
 decay_scale_1                = 4000.
 decay_scale_2                = 2500.
 decay_exp                    = 1.2
 flat_height                  = 16000.
/

&dynamics_nml
 divavg_cntrwgt               = 0.50
 lcoriolis                    = .false.   ! SCM attention: .TRUE. distroys U-profile!!
/

&transport_nml
 ivadv_tracer                 = 3,3,3,3,3
 itype_hlimit                 = 3,4,4,4,4,0
 ihadv_tracer                 = 52,2,2,2,2,0
/

&diffusion_nml
 hdiff_order                  = 5
 itype_vn_diffu               = 1
 itype_t_diffu                = 2
 hdiff_efdt_ratio             = 24.0   ! for R2B6; recommendation for R3B7: 30.0
 hdiff_smag_fac               = 0.025  ! for R2B6; recommendation for R3B7: 0.02
 lhdiff_vn                    = .true.
 lhdiff_temp                  = .true.
/

&extpar_nml
 itopo                        = 0   ! 0: analytical topo; 1: topography/ext. data read from file - if TERRA is on!!!
/

&output_nml
 output_time_unit =  1                        ! 1: seconds
 output_bounds    =  0., 10000000., 21600.    ! start, end, increment
 mode             =  1                        ! 1: forecast
 filetype         =  4                        ! test nc4-output with 5
 steps_per_file   = ${n_in_ofile}
 include_last     = .TRUE.
 output_filename  = 'scm_out'
 filename_format  = "<output_filename>_<levtype>_<datetime2>"
 ml_varlist       = 'group:all'
 output_grid      = .TRUE.
/
&output_nml
 output_start     = "${start_date}"
 output_end       = "${end_date}"
 output_interval  = "PT01H"
!output_interval  = "PT60S"
!file_interval    = "P01H"
 mode             =  1                         ! 1: forecast
 output_time_unit =  1                         ! 1: seconds
 steps_per_file   = ${n_in_ofile}
 include_last     = .TRUE.
 output_filename  = 'scm_GASS_out'
 filename_format  = "<output_filename>_<levtype>_<datetime2>"
!ml_varlist       = 'group:all'
 ml_varlist       = 'pres_sfc','accshfl_s','acclhfl_s','accthb_s','accthb_t','accsob_s','accsob_t',
                    'accthd_s', 'accthu_s', 'accsod_s', 'accsod_t', 'accsou_t', 'accsou_t',
                    'accumfl_s','accvmfl_s','cape','rain_gsp','rain_con','snow_gsp','snow_con',
                    'u_10m','v_10m','t_2m','td_2m','t_g','qv_s','tot_prec',
                    'clct','clch','clcm','clcl','tqv_dia','tqc_dia','tqi_dia','tqr','tqs'
 pl_varlist       = 'u','v','w','temp','rho','geopot','rh','clc','tot_qv_dia','tot_qc_dia','tot_qi_dia',
                    'ddt_temp_dyn', 'ddt_temp_radsw', 'ddt_temp_radlw', 'ddt_temp_turb', 'ddt_temp_drag',
                    'ddt_temp_pconv','ddt_qv_turb', 'ddt_qc_turb', 'ddt_qi_turb', 'ddt_qv_conv',
                    'ddt_temp_gscp','ddt_qv_gscp','ddt_qc_gscp','ddt_qi_gscp'
 p_levels         =  2500, 5000, 7500,10000,12500,15000,17500,20000,22500,25000,27500,30000,
                    32500,35000,37500,40000,42500,45000,47500,50000,52500,55000,57500,60000,
                    62500,65000,67500,70000,72500,75000,77500,80000,82500,85000,87500,90000,
                    92500,95000,97500,100000
 output_grid      = .TRUE.
/
&output_nml
 output_start     = "${start_date}"
 output_end       = "${end_date}"
 output_interval  = "PT30M"
 mode             =  1                         ! 1: forecast
 output_time_unit =  1                         ! 1: seconds
 steps_per_file   = ${n_in_ofile}
 include_last     = .TRUE.
 output_filename  = 'scm_GASS_flx'
 filename_format  = "<output_filename>_<levtype>_<datetime2>"
 ml_varlist       = 'accshfl_s','acclhfl_s','accthb_s','accthb_t','accsob_s','accsob_t',
                    'accthd_s', 'accthu_s', 'accsod_t', 'accsou_t', 'accsou_t','accsod_s'
                    'accumfl_s','accvmfl_s','rain_gsp','rain_con','snow_gsp','snow_con','tot_prec'
 output_grid      = .TRUE.
/

EOF

#                   !'z_ifc','z_mc','u','v','w','temp','pres','rho','theta_v','pres_sfc','div',
#                   !'qv','qc','qi','qs','qr','rh',
#                   !'ashfl_s', 'alhfl_s', 'athb_s', 'athb_t', 'asob_s', 'asob_t',
#                   !'ddt_temp_radsw', 'ddt_temp_radlw', 'ddt_temp_turb', 'ddt_temp_drag', 'ddt_temp_pconv',
#                   !'ddt_qv_turb','ddt_qc_turb','ddt_qv_conv','ddt_qc_conv','u_10m', 'v_10m', 't_2m', 't_g',
#                   !'qv_s','z_mc','lhfl_s','shfl_s','umfl_s','vmfl_s','tcm','tch','clc','tke','rcld','qhfl_s',
#                   !'sob_s', 'thb_s','sob_t'

# ----------------------------------------------------------------------------
# run the model!
# ----------------------------------------------------------------------------

ls -l $MODEL

# VE with openMP only (PPN = 1!)
date1=`date`
mpiexec -v -x -venode -np ${PPN} ${MODEL}
echo $date1 ; date


# SCM mean over columns:

#cdo fldavg scm_out_ML_`echo ${inidate} |cut -c 1-8`*Z.nc scm_out_ML_${EXPNAME}_${inidate}_${location}_mean.nc
