#!/bin/bash
#---------------------------------------
#
# Script for creating single point CLM5.0-FATES cases on Lawrencium with user-defined climate and surfdat
#
# Polly Buotte; March 6, 2019
#
# Runs from the cime/scripts/ directory
#---------------------------------------

#-Paths and file names.  Change for different site as necessary--
export CASE_ROOT=/global/home/users/pcbuotte/fates_cases
export TAG=CZ2_PPine_hydro
#export GIT_HASH=`git log -n 1 --pretty=%h`
export CASE_NAME=${CASE_ROOT}/${TAG}
export DOMAIN_DIR=/global/scratch/pcbuotte/ca_fates_input_data/domains
export SURFDAT_DIR=/global/scratch/pcbuotte/ca_fates_input_data/surfdat
export DOMAIN_FILE=domain.lnd.cz2.nc
export SURFDAT_FILE=surfdat_CZ2_190314.nc
export PARAM_FILE=fates_params_PPINE_BDT-190314.nc
export PARAM_DIR=/global/scratch/pcbuotte/ca_fates_input_data/param

./create_newcase --case=${CASE_NAME} --compset I2000Clm50FatesGs --res CLM_USRDAT --mach lawrencium-lr3 --project pc_cafates --run-unsupported

cd ${CASE_NAME}

#----Force run to start from a cold start---
./xmlchange --id CLM_FORCE_COLDSTART --val on

# -Set paths to land and atm domain files-
./xmlchange ATM_DOMAIN_FILE=${DOMAIN_FILE}
./xmlchange ATM_DOMAIN_PATH=${DOMAIN_DIR}
./xmlchange LND_DOMAIN_FILE=${DOMAIN_FILE}
./xmlchange LND_DOMAIN_PATH=${DOMAIN_DIR}

#--Set PE layout for single point run----
./xmlchange NTASKS_ATM=1
./xmlchange NTASKS_CPL=1
./xmlchange NTASKS_GLC=1
./xmlchange NTASKS_OCN=1
./xmlchange NTASKS_WAV=1
./xmlchange NTASKS_ICE=1
./xmlchange NTASKS_LND=1
./xmlchange NTASKS_ROF=1
./xmlchange ROOTPE_ATM=0
./xmlchange ROOTPE_CPL=0
./xmlchange ROOTPE_GLC=0
./xmlchange ROOTPE_OCN=0
./xmlchange ROOTPE_WAV=0
./xmlchange ROOTPE_ICE=0
./xmlchange ROOTPE_LND=0
./xmlchange ROOTPE_ROF=0
./xmlchange ROOTPE_ESP=0
./xmlchange NTHRDS_ATM=1
./xmlchange NTHRDS_CPL=1
./xmlchange NTHRDS_GLC=1
./xmlchange NTHRDS_OCN=1
./xmlchange NTHRDS_WAV=1
./xmlchange NTHRDS_ICE=1
./xmlchange NTHRDS_LND=1
./xmlchange NTHRDS_ROF=1
./xmlchange NTHRDS_ESP=1

#----Set run type preferences-------
./xmlchange DEBUG=TRUE
./xmlchange STOP_N=1
./xmlchange RUN_STARTDATE='1979-01-01'
./xmlchange STOP_OPTION=nyears
./xmlchange REST_N=1
./xmlchange DATM_CLMNCEP_YR_START=1979
./xmlchange DATM_CLMNCEP_YR_END=2009
./xmlchange DATM_MODE=CLMCRUNCEP

./case.setup

#---------change namelist options in user_nl_clm----------
cat >> user_nl_clm <<EOF
hist_empty_htapes = .true.
fsurdat = '${SURFDAT_DIR}/${SURFDAT_FILE}'
hist_fincl1='NEP','NPP','GPP','TLAI','TSOI_10CM','QVEGT','EFLX_LH_TOT','AR','HR','ED_biomass','ED_bleaf','ED_balive','DDBH_SCPF','BA_SCPF','NPLANT_SCPF','M1_SCPF','M2_SCPF','M3_SCPF','M4_SCPF','M5_SCPF','M6_SCPF','SMP','RAIN','NPP_SEED','LEAF_MD_CANOPY_SCLS','ROOT_MD_CANOPY_SCLS','BSTORE_MD_CANOPY_SCLS','BDEAD_MD_CANOPY_SCLS','BSW_MD_CANOPY_SCLS','LEAF_MD_UNDERSTORY_SCLS','ROOT_MD_UNDERSTORY_SCLS','BSTORE_MD_UNDERSTORY_SCLS','BDEAD_MD_UNDERSTORY_SCLS','BSW_MD_UNDERSTORY_SCLS','PARPROF_DIR_CNLF','PARPROF_DIF_CNLF','RECRUITMENT'
hist_nhtfrq = -8760:
use_fates = .true.
fates_paramfile = '${PARAM_DIR}/${PARAM_FILE}'
use_fates_spitfire = .false.
use_fates_planthydro = .true.
use_fates_ed_st3 = .false.
use_fates_inventory_init = .false.
use_fates_ed_prescribed_phys = .false.
use_fates_logging = .false.
fates_parteh_mode = 1
EOF

#fates_inventory_ctrl_filename = 'path to inventory file'

#--------Need to edit user_datm.streams files--------
#have to point to our climate forcing data
#I don't know how to do that in a script, only manually
# can do once and then copy those files to the new cases
# files are at /global/scratch/pcbuotte/streams_files/for_1979-2009

cp /global/scratch/pcbuotte/streams_files/for_1979-2009/*.* .
./case.build