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run_cable.sh
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run_cable.sh
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#!/usr/bin/env bash
# Gadi
# https://opus.nci.org.au/display/Help/How+to+submit+a+job
#PBS -N S0
#PBS -P rp23
#PBS -q normal
#PBS -p 600
#PBS -l walltime=10:30:00
#PBS -l mem=4GB
#PBS -l ncpus=1
#PBS -l storage=gdata/rp23+scratch/rp23+scratch/hh5
#PBS -l software=netCDF:MPI:Intel:GNU
#PBS -r y
#PBS -l wd
#PBS -j oe
#PBS -S /bin/bash
# --------------------------------------------------------------------
#
# Full Cable run with biomass spinup, POP, land-use change, etc.
#
# The run sequence is as follows:
# 1. Create a climate restart file using Cable's default vegetation distribution.
# 2. First phase of spinup with static land use, fixed atmospheric CO2 and
# N deposition from 1700, and 30 years of repeated meteorology.
# Zero initial biomass stocks, POP and climate.
# 3. Bring biomass stocks into equilibrium without restricting labile P and mineral N pools.
# Repeat a and b several times.
# a) Start from restart files.
# b) Use dump files for the biophysics. Quasi-equilibrium of soil and litter pools
# using an analytic steady-state solution.
# 4. Same as 3 but with limited labile P and mineral N pools.
# Repeat a and b several times.
# 5. Final spinup for 200 years (necessary because step 4 does not give equilibrium in all cases)
# 6. Second phase of spinup with dynamic land use, atmospheric CO2 and N deposition.
# a) Dynamic land use from 1580 to 1699, using still fixed atmospheric CO2 and
# N deposition from 1700, and 30 years of repeated meteorology.
# b) Run from 1700 to 1899 with dynmic land use, varying atmospheric CO2 and N deposition,
# but still with 30 years of repeated meteorology.
# 7. Final historical run, everything dynamic from 1900 to 2020.
#
# Written, Matthias Cuntz, Aug 2019, following the run scripts and namelists provided by Vanessa Haverd
# Modified, Jurgen Knauer, 2020 - gm_explicit, coordination, acclimation
# - bios, plume, future runs
# Matthias Cuntz, Mar 2021 - functions into run_cable-pop_lib.sh
# Jurgen Knauer, Mar 2023 - modified to run CABLE in serial mode using pseudo-parallelisation
#
# --------------------------------------------------------------------
# --------------------------------------------------------------------
# Load Modules
# --------------------------------------------------------------------
pdir=${isdir}
. /etc/bashrc
module purge
module load intel-compiler/2021.5.0
module load intel-mpi/2021.5.1
module load netcdf/4.8.0
export mpiexecdir=/apps/intel-mpi/2021.5.1/bin
if [[ ! -z ${mpiexecdir} ]] ; then export mpiexecdir="${mpiexecdir}/" ; fi
## ------------------------------------------------------------------
## Basic settings (parsed through from wrapper script)
## ------------------------------------------------------------------
# TRENDY experiment (S0, S1, S2, S3, S4, S5, S6):
experiment='S0'
# Name of the experiment (= name of output folder)
experiment_name='S0'
# Code directory
cablecode='/home/564/lw5085/CABLE'
# Script directory
rundir='/g/data/rp23/experiments/2024-03-12_CABLE4-dev/lw5085/TRENDY_MCUNTZ'
# Data directory
datadir='/g/data/rp23/data/no_provenance/'
# Cable executable
exe='/home/564/lw5085/CABLE/offline/cable'
# Global Meteorology
MetPath='/g/data/rp23/experiments/2024-03-12_CABLE4-dev/lw5085/data_links/'
# MetVersion
MetVersion=''
# Global LUC
TransitionFilePath='/g/data/rp23/data/no_provenance//luc/LUH2_GCB_1x1/v2023'
# Global Surface file
SurfaceFile='/g/data/rp23/data/no_provenance//gridinfo/gridinfo_CSIRO_1x1.nc'
# Output directory of the run
runpath='/g/data/rp23/experiments/2024-03-12_CABLE4-dev/lw5085/TRENDY_MCUNTZ/S0/run4'
# Land Mask used for this run
LandMaskFile='/g/data/rp23/experiments/2024-03-12_CABLE4-dev/lw5085/TRENDY_MCUNTZ/S0/run4/landmask/landmask4.nc'
## ----------------------------------------------------------------
## Run Sequence
## ----------------------------------------------------------------
doclimate=1 # 1/0: Do/Do not create climate restart file
dofromzero=1 # 1/0 Do/Do not first spinup phase from zero biomass stocks
doequi1=1 # 1/0: Do/Do not bring biomass stocks into quasi-equilibrium with unrestricted P and N pools
nequi1=3 # number of times to repeat steps in doequi1 4
doequi2=1 # 1/0: Do/Do not bring biomass stocks into quasi-equilibrium with restricted P and N pools
nequi2=15 # number of times to repeat steps in doequi2 14
nequi2a=5 # number of times to repeat analytic spinup in this step 5
if [[ "${experiment}" == "S3" ]] ; then
doiniluc=1 # 1/0: Do/Do not spinup with dynamic land use (initialise land use)
else
doiniluc=0
fi
doinidyn=1 # 1/0: Do/Do not full dynamic spinup (transient run) from 1701 to 1900
dofinal=1 # 1/0: Do/Do not final run from 1901 to 2022
purge_restart=0 # Delete all restart files?
## ----------------------------------------------------------------
## CABLE Settings
## ----------------------------------------------------------------
# MetType
mettype="cru" # "cru", "plume", "bios"
# Cable
read_fdiff=1 # 1/0: do/do not read in diffuse radiation fraction
call_blaze=0 # 1/0: do/do not call BLAZE
explicit_gm=0 # 1/0: explicit (finite) or implicit mesophyll conductance
Rubisco_params="Bernacchi_2002" # "Bernacchi_2002" or "Walker_2013"
coordinate_photosyn=1 # 1/0: Do/Do not coordinate photosynthesis
coord=F # T/F: version of photosyn. optimisation (optimised(F) or forced (T))
acclimate_photosyn=1 # 1/0: Do/Do not acclimate photosynthesis
call_pop=1 # 1/0: Do/Do not use POP population dynamics model, coupled to CASA
doc13o2=0 # 1/0: Do/Do not calculate 13C
c13o2_simple_disc=0 # 1/0: simple or full 13C leaf discrimination
# Parameter files
namelistpath="${rundir}/namelists"
filename_veg='${datadir}/parameter/def_veg_params.txt'
filename_soil='${datadir}/parameter/def_soil_params.txt'
casafile_cnpbiome='${datadir}/parameter/pftlookup.csv'
# Climate restart file
# changes for TRENDY >= v11: ClimateFile always created!
# ClimateFile="/g/data/x45/ipbes/cable_climate/ipsl_climate_rst_glob_1deg.nc"
#ClimateFile="$(dirname ${runpath})/climate_restart/cru_climate_rst.nc"
ClimateFile="${runpath}/cru_climate_rst.nc"
# gm lookup tables
gm_lut_bernacchi_2002='${datadir}/parameter/gm_LUT_351x3601x7_1pt8245_Bernacchi2002.nc'
gm_lut_walker_2013='${datadir}/parameter/gm_LUT_351x3601x7_1pt8245_Walker2013.nc'
# 13C
filename_d13c_atm='${datadir}/parameter/gm_LUT_351x3601x7_1pt8245_Bernacchi2002.nc'
# --------------------------------------------------------------------
# Setup and Functions
# --------------------------------------------------------------------
set -e
trap cleanup 1 2 3 6
pid=$$
isdir="${PWD}"
prog=$0
pprog=$(basename ${prog})
pdir=$(dirname ${prog})
tmp=${TMPDIR:-"/tmp"}
# Helper functions, most functions are in run_cable-pop_lib.sh
source ${isdir}/run_cable-pop_lib.sh
# usage of script
function usage()
{
printf "${pprog} [-h]\n"
printf "Runs Cable on a single grid cell with spinup, POP, land-use change, etc.\n"
printf "Behaviour of the script is controlled by switches at the top of the script (ca. line 101ff).\n"
printf "\n"
printf "Options\n"
printf " -h Prints this help screen.\n"
}
# cleanup at end or at trap
function cleanup()
{
\rm -f ${tmp}/*.${pid}*
exit 1
}
# ---------------------------------------------------------------------------------
# Preparation
# ---------------------------------------------------------------------------------
# Get options
while getopts "h" option ; do
case ${option} in
h) usage; exit;;
*) printf "Error ${pprog}: unimplemented option.\n\n" 1>&2; usage 1>&2; exit 1;;
esac
done
shift $((${OPTIND} - 1))
# get directories
pdir=$(abspath ${pdir})
cd ${pdir}
mkdir -p ${runpath}
rdir=$(abspath ${runpath})
ndir=$(abspath ${namelistpath})
# prepare run directory
cd ${rdir}
mkdir -p logs
mkdir -p outputs
mkdir -p restart
cp ${exe} ./
iexe=$(basename ${exe})
cd ${pdir}
# OS and Workload manager
ised='sed --in-place=.old'
# --------------------------------------------------------------------
# Print Info
# --------------------------------------------------------------------
t1=$(date +%s)
printf "Started at %s\n" "$(date)"
printf "\nSetup\n"
printf " Sequence\n"
printf " experiment=${experiment}\n"
printf " doclimate=${doclimate}\n"
printf " dofromzero=${dofromzero}\n"
printf " doequi1=${doequi1}\n"
printf " nequi1=${nequi1}\n"
printf " doequi2=${doequi2}\n"
printf " nequi2=${nequi2}\n"
printf " doiniluc=${doiniluc}\n"
printf " doinidyn=${doinidyn}\n"
printf " dofinal=${dofinal}\n"
printf "\n"
printf " Options\n"
printf " mettype=${mettype}\n"
printf " explicit_gm=${explicit_gm}\n"
printf " Rubisco_params=${Rubisco_params}\n"
printf " coordinate_photosyn=${coordinate_photosyn}\n"
printf " coord=${coord}\n"
printf " acclimate_photosyn=${acclimate_photosyn}\n"
printf " call_pop=${call_pop}\n"
printf " doc13o2=${doc13o2}\n"
printf " c13o2_simple_disc=${c13o2_simple_disc}\n"
printf "\n"
printf " Directories\n"
printf " rundir=${rundir}\n"
printf " runpath=${runpath}\n"
printf " exe=${exe}\n"
printf " LandMaskFile=${LandMaskFile}\n"
printf " SurfaceFile=${SurfaceFile}\n"
printf " namelistpath=${namelistpath}\n"
printf " filename_veg=${filename_veg}\n"
printf " filename_soil=${filename_soil}\n"
printf " casafile_cnpbiome=${casafile_cnpbiome}\n"
printf " MetPath=${MetPath}\n"
printf " MetVersion=${MetVersion}\n"
printf " ClimateFile=${ClimateFile}\n"
printf " TransitionFilePath=${TransitionFilePath}\n"
printf " gm_lut_bernacchi_2002=${gm_lut_bernacchi_2002}\n"
printf " gm_lut_walker_2013=${gm_lut_walker_2013}\n"
printf " filename_d13c_atm=${filename_d13c_atm}\n"
printf "\n"
# ------------------------------------------------------------------------------------
# Write global namelists
# ------------------------------------------------------------------------------------
# Write standard namelists with options that are common to all steps of the sequence.
# They can, however, be overwritten in later steps.
# global met namelist file
if [[ ${read_fdiff} -eq 1 ]] ; then
fdiff_bool=.true.
else
fdiff_bool=.false.
fi
cat > ${tmp}/sedtmp.${pid} << EOF
rainFile = "${MetPath}/pre/pre_<startdate>_<enddate>.nc"
lwdnFile = "${MetPath}/dlwrf/dlwrf_<startdate>_<enddate>.nc"
swdnFile = "${MetPath}/tswrf/tswrf_<startdate>_<enddate>.nc"
presFile = "${MetPath}/pres/pres_<startdate>_<enddate>.nc"
qairFile = "${MetPath}/spfh/spfh_<startdate>_<enddate>.nc"
TmaxFile = "${MetPath}/tmax/tmax_<startdate>_<enddate>.nc"
TminFile = "${MetPath}/tmin/tmin_<startdate>_<enddate>.nc"
uwindFile = "${MetPath}/ugrd/ugrd_<startdate>_<enddate>.nc"
vwindFile = "${MetPath}/vgrd/vgrd_<startdate>_<enddate>.nc"
fDiffFile = "${MetPath}/fd/fd_<startdate>_<enddate>.nc"
CO2File = "${MetPath}/co2/co2_17000101_20221231.txt"
NDepFile = "${MetPath}/ndep/NDep_<startdate>_<enddate>.nc"
LandMaskFile = "${LandMaskFile}"
rainRecycle = T
lwdnRecycle = T
swdnRecycle = T
presRecycle = T
qairRecycle = T
TmaxRecycle = T
TminRecycle = T
uWindRecycle = T
vWindRecycle = T
fDiffRecycle = T
CO2Method = "1700"
NDepMethod = "1850"
ReadDiffFrac = ${fdiff_bool}
DThrs = 3.0 ! **CABLE** timestep hours (not the met timestep)
EOF
applysed ${tmp}/sedtmp.${pid} ${ndir}/cru.nml ${rdir}/cru_${experiment}.nml
cp ${ndir}/met_names.nml ${rdir}
# global landuse change namelist
cat > ${tmp}/sedtmp.${pid} << EOF
TransitionFilePath = "${TransitionFilePath}"
ClimateFile = "${ClimateFile}"
YearStart = 1700
YearEnd = 2022
EOF
applysed ${tmp}/sedtmp.${pid} ${ndir}/luc.nml ${rdir}/luc_${experiment}.nml
# global Cable namelist
if [[ "${Rubisco_params}" == "Bernacchi_2002" ]] ; then
filename_gm_lut=${gm_lut_bernacchi_2002}
elif [[ "${Rubisco_params}" == "Walker_2013" ]] ; then
filename_gm_lut=${gm_lut_walker_2013}
else
filename_gm_lut=""
fi
cat > ${tmp}/sedtmp.${pid} << EOF
filename%met = ""
filename%veg = "${filename_veg}"
filename%soil = "${filename_soil}"
filename%type = "${SurfaceFile}"
filename%out = "outputs/${mettype}_out_cable.nc"
filename%restart_in = "restart/${mettype}_cable_rst.nc"
filename%restart_out = "restart/${mettype}_cable_rst.nc"
casafile%cnpbiome = "${casafile_cnpbiome}"
casafile%out = "outputs/${mettype}_out_casa.nc"
casafile%cnpipool = "restart/${mettype}_casa"
casafile%cnpepool = "restart/${mettype}_casa"
cable_user%CASA_OUT_FREQ = "monthly"
cable_user%POP_restart_in = "restart/pop_${mettype}_ini.nc"
cable_user%POP_restart_out = "restart/pop_${mettype}_ini.nc"
cable_user%LUC_restart_in = "restart/${mettype}_LUC_rst.nc"
cable_user%LUC_restart_out = "restart/${mettype}_LUC_rst.nc"
cable_user%LUC_outfile = "outputs/${mettype}_out_LUC.nc"
cable_user%climate_restart_in = "restart/${mettype}_climate_rst.nc"
cable_user%climate_restart_out = "restart/${mettype}_climate_rst.nc"
cable_user%RunIden = "${mettype}"
cable_user%MetType = "${mettype}"
output%averaging = "monthly"
output%grid = "land"
output%vars5D = .FALSE.
leaps = .false.
cable_user%SOIL_STRUC = "default"
cable_user%Rubisco_parameters = "${Rubisco_params}"
cable_user%CALL_POP = .false.
cable_user%coordinate_photosyn = .false.
cable_user%acclimate_photosyn = .false.
cable_user%explicit_gm = .false.
cable_user%gm_LUT_file = "${filename_gm_lut}"
cable_user%CALL_BLAZE = .false.
cable_user%c13o2 = .false.
cable_user%c13o2_simple_disc = .false.
cable_user%c13o2_delta_atm_file = "${filename_d13c_atm}"
cable_user%c13o2_outfile = "outputs/${mettype}_out_casa_c13o2.nc"
cable_user%c13o2_restart_in_flux = "restart/${mettype}_c13o2_flux_rst.nc"
cable_user%c13o2_restart_out_flux = "restart/${mettype}_c13o2_flux_rst.nc"
cable_user%c13o2_restart_in_pools = "restart/${mettype}_c13o2_pools_rst.nc"
cable_user%c13o2_restart_out_pools = "restart/${mettype}_c13o2_pools_rst.nc"
cable_user%c13o2_restart_in_luc = "restart/${mettype}_c13o2_luc_rst.nc"
cable_user%c13o2_restart_out_luc = "restart/${mettype}_c13o2_luc_rst.nc"
EOF
if [[ ${call_pop} -eq 1 ]] ; then
${ised} -e "/cable_user%CALL_POP/s|=.*|= .true.|" ${tmp}/sedtmp.${pid}
fi
if [[ ${coordinate_photosyn} -eq 1 ]] ; then
${ised} -e "/cable_user%coordinate_photosyn/s|=.*|= .true.|" ${tmp}/sedtmp.${pid}
fi
if [[ ${acclimate_photosyn} -eq 1 ]] ; then
${ised} -e "/cable_user%acclimate_photosyn/s|=.*|= .true.|" ${tmp}/sedtmp.${pid}
fi
if [[ ${explicit_gm} -eq 1 ]] ; then
${ised} -e "/cable_user%explicit_gm/s|=.*|= .true.|" ${tmp}/sedtmp.${pid}
fi
if [[ ${doc13o2} -eq 1 ]] ; then
${ised} -e "/cable_user%c13o2/s|=.*|= .true.|" ${tmp}/sedtmp.${pid}
if [[ ${c13o2_simple_disc} -eq 1 ]] ; then
${ised} -e "/cable_user%c13o2_simple_disc/s|=.*|= .true.|" ${tmp}/sedtmp.${pid}
fi
fi
if [[ ${call_blaze} -eq 1 ]] ; then
${ised} -e "/cable_user%CALL_BLAZE/s|=.*|= .true.|" ${tmp}/sedtmp.${pid}
fi
applysed ${tmp}/sedtmp.${pid} ${ndir}/cable.nml ${rdir}/cable_${experiment}.nml
irm ${tmp}/sedtmp.${pid}.old
# BLAZE (no changes at the moment)
if [[ ${call_blaze} -eq 1 ]] ; then
cp ${ndir}/blaze.nml ${rdir}/blaze.nml
fi
# -----------------------------------------------------------------------
# -----------------------------------------------------------------------
# Start Runs according to sequence specified above
# -----------------------------------------------------------------------
# -----------------------------------------------------------------------
# delete all restart files if required
if [[ ${purge_restart} -eq 1 ]] ; then
rm -f ${rdir}/restart/*
# rm -f ${ClimateFile}
fi
# --------------------------------------------------------------------
# 1. Create climate restart file
# --------------------------------------------------------------------
if [[ ${doclimate} -eq 1 ]] ; then
echo "1. Create climate restart file"
rid="climate_restart"
# Met forcing
cp ${rdir}/cru_${experiment}.nml ${rdir}/cru.nml
# LUC
cp ${rdir}/luc_${experiment}.nml ${rdir}/luc.nml
# Cable
cat > ${tmp}/sedtmp.${pid} << EOF
filename%restart_in = ""
cable_user%CLIMATE_fromZero = .true.
cable_user%YearStart = 1841
cable_user%YearEnd = 1860
icycle = 2
spincasa = .false.
cable_user%CASA_fromZero = .true.
cable_user%CASA_DUMP_READ = .false.
cable_user%CASA_DUMP_WRITE = .true.
cable_user%CASA_SPIN_STARTYEAR = 1850
cable_user%CASA_SPIN_ENDYEAR = 1859
cable_user%limit_labile = .true.
casafile%cnpipool = ""
cable_user%POP_fromZero = .true.
cable_user%POP_out = "ini"
cable_user%POP_restart_in = ""
cable_user%POPLUC = .false.
cable_user%POPLUC_RunType = "static"
cable_user%c13o2 = .false.
EOF
applysed ${tmp}/sedtmp.${pid} ${rdir}/cable_${experiment}.nml ${rdir}/cable.nml
# run model
cd ${rdir}
irm logs/log_cable.txt logs/log_out_cable.txt
#valgrind --tool=massif --xtree-memory=full --pages-as-heap=yes ./${iexe} > logs/log_out_cable.txt
./${iexe} > logs/log_out_cable.txt
# save output
renameid ${rid} ${mettype}.nml luc.nml cable.nml
imv *_${rid}.nml restart/
cd logs
renameid ${rid} log_cable.txt log_out_cable.txt
cd ../restart
copyid ${rid} ${mettype}_climate_rst.nc
cp ${mettype}_climate_rst.nc ${ClimateFile} # new for TRENDY >= v11
cd ../outputs
renameid ${rid} ${mettype}_out_cable.nc ${mettype}_out_casa.nc
cd ..
cd ${pdir}
fi
echo "Finish stage 1"
# --------------------------------------------------------------------
# 2. First spinup phase from zero biomass
# --------------------------------------------------------------------
if [[ ${dofromzero} -eq 1 ]] ; then
echo "2. First spinup from zero biomass"
rid="zero_biomass"
# Met forcing
cp ${rdir}/cru_${experiment}.nml ${rdir}/cru.nml
# LUC
cp ${rdir}/luc_${experiment}.nml ${rdir}/luc.nml
# Cable
cat > ${tmp}/sedtmp.${pid} << EOF
filename%restart_in = ""
cable_user%CLIMATE_fromZero = .true.
cable_user%YearStart = 1841
cable_user%YearEnd = 1870
icycle = 2
spincasa = .false.
cable_user%CASA_OUT_FREQ = "monthly"
cable_user%CASA_fromZero = .true.
cable_user%CASA_DUMP_READ = .false.
cable_user%CASA_DUMP_WRITE = .false.
cable_user%CASA_SPIN_STARTYEAR = 1850
cable_user%CASA_SPIN_ENDYEAR = 1859
cable_user%limit_labile = .true.
casafile%cnpipool = ""
cable_user%POP_fromZero = .true.
cable_user%POP_out = "ini"
cable_user%POP_restart_in = ""
cable_user%POPLUC = .true.
cable_user%POPLUC_RunType = "static"
cable_user%c13o2_restart_in_flux = ""
cable_user%c13o2_restart_in_pools = ""
EOF
applysed ${tmp}/sedtmp.${pid} ${rdir}/cable_${experiment}.nml ${rdir}/cable.nml
# run model
cd ${rdir}
irm logs/log_cable.txt logs/log_out_cable.txt
# valgrind --tool=massif --xtree-memory=full --pages-as-heap=yes ./${iexe} > logs/log_out_cable.txt
./${iexe} > logs/log_out_cable.txt
saveid ${rid} ${mettype} ${doc13o2}
cd ${pdir}
fi
# --------------------------------------------------------------------
# 3. Biomass into quasi-equilibrium with restricted N and P pools
# --------------------------------------------------------------------
if [[ ${doequi1} -eq 1 ]] ; then
echo "3. Bring biomass into quasi-equilibrium with unrestricted N and P pools"
for ((iequi1=1; iequi1<=${nequi1}; iequi1++)) ; do
# 3a. 30 year run starting from restart files
echo " 3a. 30 year spinup from accumulated biomass; iequi1=${iequi1}/${nequi1}"
rid="spinup_limit_labile_${iequi1}"
# rid="spinup_limit_labile${iequi}"
# Met forcing
cp ${rdir}/cru_${experiment}.nml ${rdir}/cru.nml
# LUC
cp ${rdir}/luc_${experiment}.nml ${rdir}/luc.nml
# Cable
cat > ${tmp}/sedtmp.${pid} << EOF
cable_user%CLIMATE_fromZero = .false.
cable_user%YearStart = 1841
cable_user%YearEnd = 1860
icycle = 2
spincasa = .false.
cable_user%CASA_fromZero = .false.
cable_user%CASA_DUMP_READ = .false.
cable_user%CASA_DUMP_WRITE = .true.
cable_user%CASA_SPIN_STARTYEAR = 1850
cable_user%CASA_SPIN_ENDYEAR = 1859
cable_user%limit_labile = .true.
cable_user%POP_fromZero = .false.
cable_user%POP_out = "ini"
cable_user%POPLUC = .true.
cable_user%POPLUC_RunType = "static"
EOF
applysed ${tmp}/sedtmp.${pid} ${rdir}/cable_${experiment}.nml ${rdir}/cable.nml
# run model
cd ${rdir}
irm logs/log_cable.txt logs/log_out_cable.txt
./${iexe} > logs/log_out_cable.txt
saveid ${rid} ${mettype} ${doc13o2}
cd ${pdir}
#
# 3b. analytic quasi-equilibrium of biomass pools
echo " 3b. Analytic solution of biomass pools"
rid="spinup_analytic_limit_labile"
# rid="spin_casa_limit_labile${iequi}"
# Met forcing
cp ${rdir}/cru_${experiment}.nml ${rdir}/cru.nml
# LUC
cp ${rdir}/luc_${experiment}.nml ${rdir}/luc.nml
# Cable
cat > ${tmp}/sedtmp.${pid} << EOF
cable_user%CLIMATE_fromZero = .false.
cable_user%YearStart = 1841
cable_user%YearEnd = 1860
icycle = 12
spincasa = .true.
cable_user%CASA_fromZero = .false.
cable_user%CASA_DUMP_READ = .true.
cable_user%CASA_DUMP_WRITE = .false.
cable_user%CASA_SPIN_STARTYEAR = 1841
cable_user%CASA_SPIN_ENDYEAR = 1860
cable_user%limit_labile = .true.
cable_user%POP_fromZero = .false.
cable_user%POP_out = "ini"
cable_user%POPLUC = .true.
cable_user%POPLUC_RunType = "static"
EOF
applysed ${tmp}/sedtmp.${pid} ${rdir}/cable_${experiment}.nml ${rdir}/cable.nml
# run model
cd ${rdir}
irm logs/log_cable.txt logs/log_out_cable.txt
./${iexe} > logs/log_out_cable.txt
saveid ${rid} ${mettype} ${doc13o2}
cd ${pdir}
done
fi
# --------------------------------------------------------------------
# 4. Biomass into quasi-equilibrium without restricted N and P pools
# --------------------------------------------------------------------
if [[ ${doequi2} -eq 1 ]] ; then
echo "4. Bring biomass into quasi-equilibrium with restricted N and P pools"
for ((iequi2=1; iequi2<=${nequi2}; iequi2++)) ; do
# 4a. 30 year run starting from restart files
echo " 4a. 30 year spinup from accumulated biomass; iequi2=${iequi2}/${nequi2}"
# rid="spinup_nutrient_limited"
rid="spinup_nutrient_limited_${iequi2}"
# Met forcing
cp ${rdir}/cru_${experiment}.nml ${rdir}/cru.nml
# LUC
cp ${rdir}/luc_${experiment}.nml ${rdir}/luc.nml
# Cable
cat > ${tmp}/sedtmp.${pid} << EOF
cable_user%CLIMATE_fromZero = .false.
cable_user%YearStart = 1841
cable_user%YearEnd = 1860
icycle = 2
spincasa = .false.
cable_user%CASA_fromZero = .false.
cable_user%CASA_DUMP_READ = .false.
cable_user%CASA_DUMP_WRITE = .true.
cable_user%CASA_SPIN_STARTYEAR = 1850
cable_user%CASA_SPIN_ENDYEAR = 1859
cable_user%limit_labile = .false.
cable_user%POP_fromZero = .false.
cable_user%POP_out = "ini"
cable_user%POPLUC = .true.
cable_user%POPLUC_RunType = "static"
EOF
applysed ${tmp}/sedtmp.${pid} ${rdir}/cable_${experiment}.nml ${rdir}/cable.nml
# run model
cd ${rdir}
irm logs/log_cable.txt logs/log_out_cable.txt
./${iexe} > logs/log_out_cable.txt
saveid ${rid} ${mettype} ${doc13o2}
cd ${pdir}
#
# 4b. analytic quasi-equilibrium of biomass pools
if [[ ${iequi2} -le ${nequi2a} ]] ; then
echo " 4b. Analytic solution of biomass pools"
# rid="spinup_analytic"
rid="spinup_analytic_${iequi2}"
# Met forcing
cp ${rdir}/cru_${experiment}.nml ${rdir}/cru.nml
# LUC
cp ${rdir}/luc_${experiment}.nml ${rdir}/luc.nml
# applysed ${tmp}/sedtmp.${pid} ${rdir}/LUC_${experiment}.nml ${rdir}/LUC.nml
# Cable
cat > ${tmp}/sedtmp.${pid} << EOF
cable_user%CLIMATE_fromZero = .false.
cable_user%YearStart = 1841
cable_user%YearEnd = 1860
icycle = 12
spincasa = .true.
cable_user%CASA_fromZero = .false.
cable_user%CASA_DUMP_READ = .true.
cable_user%CASA_DUMP_WRITE = .false.
cable_user%CASA_SPIN_STARTYEAR = 1841
cable_user%CASA_SPIN_ENDYEAR = 1860
cable_user%limit_labile = .false.
cable_user%POP_fromZero = .false.
cable_user%POP_out = "ini"
cable_user%POPLUC = .true.
cable_user%POPLUC_RunType = "static"
EOF
applysed ${tmp}/sedtmp.${pid} ${rdir}/cable_${experiment}.nml ${rdir}/cable.nml
# run model
cd ${rdir}
irm logs/log_cable.txt logs/log_out_cable.txt
./${iexe} > logs/log_out_cable.txt
saveid ${rid} ${mettype} ${doc13o2}
cd ${pdir}
fi
done
fi
# --------------------------------------------------------------------
# 5. First dynamic land use (Initialise land use)
# --------------------------------------------------------------------
if [[ ${doiniluc} -eq 1 ]] ; then
echo "5. First dynamic land use (initialise land use)"
rid="init_land_use"
# Met forcing
YearStart=1580 # should be the same as in the global luc.nml file!
YearEnd=1699
cp ${rdir}/cru_${experiment}.nml ${rdir}/cru.nml
# LUC
cat > ${tmp}/sedtmp.${pid} << EOF
YearStart = ${YearStart}
YearEnd = ${YearEnd}
EOF
applysed ${tmp}/sedtmp.${pid} ${rdir}/luc_${experiment}.nml ${rdir}/luc.nml
# Cable
cat > ${tmp}/sedtmp.${pid} << EOF
cable_user%CLIMATE_fromZero = .false.
cable_user%YearStart = ${YearStart}
cable_user%YearEnd = ${YearEnd}
icycle = 12
spincasa = .false.
cable_user%CASA_OUT_FREQ = "annually"
cable_user%CASA_fromZero = .false.
cable_user%CASA_DUMP_READ = .true.
cable_user%CASA_DUMP_WRITE = .false.
cable_user%CASA_SPIN_STARTYEAR = 1841
cable_user%CASA_SPIN_ENDYEAR = 1860
cable_user%limit_labile = .false.
cable_user%POP_fromZero = .false.
cable_user%POP_out = "ini"
cable_user%POPLUC = .true.
cable_user%POPLUC_RunType = "init"
cable_user%LUC_restart_in = ""
cable_user%c13o2_restart_in_luc = ""
EOF
applysed ${tmp}/sedtmp.${pid} ${rdir}/cable_${experiment}.nml ${rdir}/cable.nml
# run model
cd ${rdir}
irm logs/log_cable.txt logs/log_out_cable.txt
./${iexe} > logs/log_out_cable.txt
saveid ${rid} ${mettype} ${doc13o2}
cd ${pdir}
fi
# --------------------------------------------------------------------
# 6. Transient run
# --------------------------------------------------------------------
if [[ ${doinidyn} -eq 1 ]] ; then
echo "6. Transient run (full dynamic spinup)"
# Met forcing
YearStart=1700
YearEnd=1900
rid=${YearStart}_${YearEnd}
if [[ "${experiment}" == "S1" || "${experiment}" == "S2" || "${experiment}" == "S3" ]] ; then
cat > ${tmp}/sedtmp.${pid} << EOF
CO2Method = "Yearly"
NDepMethod = "Yearly"
EOF
else
cat > ${tmp}/sedtmp.${pid} << EOF
CO2Method = "1700"
NDepMethod = "1850"
EOF
fi
# if [[ "${experiment}" == "S0" ]] ; then
# cat > ${tmp}/sedtmp.${pid} << EOF
# Run = "S0_TRENDY"
#EOF
# elif [[ "${experiment}" == "S1" || "${experiment}" == "S2" || "${experiment}" == "S3" ]] ; then
# cat > ${tmp}/sedtmp.${pid} << EOF
# Run = "S1_TRENDY"
#EOF
# fi
applysed ${tmp}/sedtmp.${pid} ${rdir}/cru_${experiment}.nml ${rdir}/cru.nml
# LUC
if [[ "${experiment}" == "S3" ]] ; then
cat > ${tmp}/sedtmp.${pid} << EOF
YearStart = ${YearStart}
YearEnd = ${YearEnd}
EOF
else
cat > ${tmp}/sedtmp.${pid} << EOF
YearStart = 1700
YearEnd = ${YearEnd}
EOF
fi
applysed ${tmp}/sedtmp.${pid} ${rdir}/luc_${experiment}.nml ${rdir}/luc.nml
# Cable
if [[ "${experiment}" == "S3" ]] ; then
POPLUC_RunType="restart"
else
POPLUC_RunType="static"
fi
cat > ${tmp}/sedtmp.${pid} << EOF
cable_user%CLIMATE_fromZero = .false.
cable_user%YearStart = ${YearStart}
cable_user%YearEnd = ${YearEnd}
icycle = 2
spincasa = .false.
cable_user%CASA_fromZero = .false.
cable_user%CASA_DUMP_READ = .false.
cable_user%CASA_DUMP_WRITE = .false.
cable_user%CASA_SPIN_STARTYEAR = 1850
cable_user%CASA_SPIN_ENDYEAR = 1859
cable_user%limit_labile = .false.
cable_user%POP_fromZero = .false.
cable_user%POP_out = "ini"
cable_user%POPLUC = .true.
cable_user%POPLUC_RunType = "${POPLUC_RunType}"
EOF
applysed ${tmp}/sedtmp.${pid} ${rdir}/cable_${experiment}.nml ${rdir}/cable.nml
# run model
cd ${rdir}
irm logs/log_cable.txt logs/log_out_cable.txt
./${iexe} > logs/log_out_cable.txt
saveid ${rid} ${mettype} ${doc13o2}
cd ${pdir}
fi
# --------------------------------------------------------------------
# 7. Final centennial run
# --------------------------------------------------------------------
if [[ ${dofinal} -eq 1 ]] ; then
echo "7. Final centennial run"
# Met forcing
YearStart=1901
YearEnd=2022
rid=${YearStart}_${YearEnd}
if [[ "${experiment}" == "S1" ]] ; then
cat > ${tmp}/sedtmp.${pid} << EOF
CO2Method = "Yearly"
NDepMethod = "Yearly"
EOF
elif [[ "${experiment}" == "S2" || "${experiment}" == "S3" ]] ; then
cat > ${tmp}/sedtmp.${pid} << EOF
CO2Method = "Yearly"
NDepMethod = "Yearly"
rainRecycle = F
lwdnRecycle = F
swdnRecycle = F
presRecycle = F
qairRecycle = F
TmaxRecycle = F
TminRecycle = F
uWindRecycle = F
vWindRecycle = F
fDiffRecycle = F
EOF
else
cat > ${tmp}/sedtmp.${pid} << EOF
CO2Method = "1700"
NDepMethod = "1850"
EOF
fi
# if [[ "${experiment}" == "S0" ]] ; then
# cat > ${tmp}/sedtmp.${pid} << EOF
# Run = "S0_TRENDY"
#EOF
# elif [[ "${experiment}" == "S1" ]] ; then
# cat > ${tmp}/sedtmp.${pid} << EOF
# Run = "S1_TRENDY"
#EOF
# elif [[ "${experiment}" == "S2" || "${experiment}" == "S3" ]] ; then
# cat > ${tmp}/sedtmp.${pid} << EOF
# Run = "S2_TRENDY"
#EOF
# fi
applysed ${tmp}/sedtmp.${pid} ${rdir}/cru_${experiment}.nml ${rdir}/cru.nml
# LUC
if [[ "${experiment}" == "S3" ]] ; then
cat > ${tmp}/sedtmp.${pid} << EOF
YearStart = ${YearStart}
YearEnd = ${YearEnd}
EOF
else
cat > ${tmp}/sedtmp.${pid} << EOF
YearStart = 1700
YearEnd = ${YearEnd}
EOF
fi
applysed ${tmp}/sedtmp.${pid} ${rdir}/luc_${experiment}.nml ${rdir}/luc.nml
# Cable
if [[ "${experiment}" == "S3" ]] ; then
POPLUC_RunType="restart"
else
POPLUC_RunType="static"
fi
cat > ${tmp}/sedtmp.${pid} << EOF
cable_user%CLIMATE_fromZero = .false.
cable_user%YearStart = ${YearStart}
cable_user%YearEnd = ${YearEnd}
icycle = 2
spincasa = .false.
cable_user%CASA_fromZero = .false.
cable_user%CASA_DUMP_READ = .false.
cable_user%CASA_DUMP_WRITE = .false.
cable_user%CASA_SPIN_STARTYEAR = 1850
cable_user%CASA_SPIN_ENDYEAR = 1859
cable_user%limit_labile = .false.
cable_user%POP_fromZero = .false.
cable_user%POP_out = "ini"
cable_user%POPLUC = .true.
cable_user%POPLUC_RunType = "${POPLUC_RunType}"
EOF
applysed ${tmp}/sedtmp.${pid} ${rdir}/cable_${experiment}.nml ${rdir}/cable.nml
# run model
cd ${rdir}
irm logs/log_cable.txt logs/log_out_cable.txt
./${iexe} > logs/log_out_cable.txt
saveid ${rid} ${mettype} ${doc13o2}
cd ${pdir}
fi
# --------------------------------------------------------------------
# Finish
# --------------------------------------------------------------------
cd ${isdir}
t2=$(date +%s)
dt=$((t2-t1))
printf "\n"
if [[ ${dt} -lt 60 ]] ; then
printf "Finished at %s in %i seconds.\n" "$(date)" ${dt}
else
dm=$(echo "(${t2}-${t1})/60." | bc -l)
printf "Finished at %s in %.2f minutes.\n" "$(date)" ${dm}
fi
exit