#! /bin/ksh
#=============================================================================
# mistral cpu batch job parameters
# --------------------------------
# #SBATCH --account=bm1021
#SBATCH --account=mh0287
# #SBATCH --qos=mh0287
#SBATCH --job-name=slo1325
#SBATCH --partition=compute2
#SBATCH --chdir=/work/mh0287/m211032/Icon/Git_Icon/icon.oes.20200506/run
# #SBATCH --nodes=60
#SBATCH --nodes=120
#SBATCH --threads-per-core=2
# the following is needed to work around a bug that otherwise leads to
# a too low number of ranks when using compute,compute2 as queue
#SBATCH --mem=0
#SBATCH --output=LOG.slo1325.%j.o
#SBATCH --error=LOG.slo1325.%j.o
#SBATCH --exclusive
# #SBATCH --time=00:30:00
# #SBATCH --time=01:00:00
# #SBATCH --time=00:10:00
#SBATCH --time=04:00:00
#=============================================================================
##### R2B4/R2B6 coupled runs on equatorial symmetric grids - setup at icon.oes.20191216, #7a1f82559 #####
# 17.12.2019: slo1236: - production run on 20191217 from ocean_omip_long_tke_r2b6_19346-PCA-2101y
# 04.03.2020: slo1266: upd.GMcorr as jkr0025/reduced albedo, corrected hdpara, rest-slo1236-1200y, GM/Redi=0
# 23.03.2020: slo1268: upd.QVsubst as jkr0034/correcded substepping, rest-jkr0034-1400y, GM/Redi=0
# 08.04.2020: slo1271: upd.GMcorr as jkr0042 (reduc.alb, crs/crt) warm albedos +7%, rest-jkr0042-1500y
##### R2B4/R2B6 coupled runs on equatorial symmetric grids - setup at icon.oes.dev1merge, #00729c4a5
# 05.03.2020: slo1267: production run corrected/new hdpara, rest-omipPCA-2101y, GM/Redi=0
##### R2B4/R2B6 coupled runs on equatorial symmetric grids - setup at icon.oes.dev2merge, #0b2a9e90b
# 27.03.2020: slo1269: production run (#7aee65879) as slo1267 new hdpara, rest-omipPCA-2101y, GM/Redi=0
# 01.04.2020: slo1270: production run (#6370da467) as slo1269 new hdpara, rest-omipPCA-2101y, GM/Redi=0
# 09.04.2020: slo1273: test run (#6ed84b844) as slo1270
# 23.04.2020: slo1277: 1y run (#6e8625a0c) as slo1273/1270/1264/1236-GM=0, rest-jkr0042-1500y
# 23.04.2020: slo1278: 100y run (#6e8625a0c) as slo1273/1270/1264/1236-GM=0, rest-jkr0042-1500y, no log-saltfix
# 24.04.2020: slo1279: 100y run (#6e8625a0c) tuning as jkr0042, rest-jkr0042-1500y, no log-saltfix
# 28.04.2020: slo1280: 200y run (#734c5361c) tuning as jkr0042/slo1279, rest-omipPCA-2101y, merge rc262 - nbuild2
# 24.04.2020: slo1281: 30y run (#6e8625a0c) as slo1279, rest-slo1279-1570y, no saltfix - nbuild
# 24.04.2020: slo1282: 30y run (#6e8625a0c) as slo1279, rest-slo1279-1570y, old ice-limiter, with saltfix
##### R2B4/R2B6 coupled runs on equatorial symmetric grids - setup at (mh0469) icon.oes.20200506, branch rubydev2
# 06.05.2020: slo1283: 100y run (oes-rubydev2 #95869e4f6, icon.oes.20200506) tuning as slo1271
# rest-jkr0042-1500y: abort, since atm-restart contains old namelist! - initialization of atmos necessary
# 2020-05-06 - restart-oce-jkr0042-1500y (init atmos)
# 07.05.2020: slo1284: 100y run #95869e4f6, as slo1283/slo1271, rest-slo1283-1550y, tuning crt=0.8 (colder)
# 04.06.2020: slo1285: #95869e4f6, new bathy/sill depths, grid=35, rest-omipCIQ-2200y, as slo1284/hel1284-TOP
# 04.06.2020: slo1286: #95869e4f6, new bathy/sill depths, grid=35, rest-omipCIQ-2200y, as slo1285 with kpp-scheme
# 09.06.2020: slo1287: #95869e4f6, rest-omipCIQ-2200y, as slo1285, pr0=1.0
# 09.06.2020: slo1288: #95869e4f6, rest-slo1286-1770y, as slo1286, kpp, warmer tuning crs/crt=0.99/0.82
# 11.06.2020: slo1289: #95869e4f6, rest-omipCIQ-2200y, tuning as dap7023 (gkdrag/wake/lift, fsl) GM/Redi on/800
# 11.06.2020: slo1290: #95869e4f6, rest-omipCIQ-2200y, as slo1289/GM/Redi on/800, def.albedos 85/70/75/70
# 12.06.2020: slo1291: #95869e4f6, rest-omipCIQ-2200y, as slo1290/GM/Redi 400, def.albedos 85/70/75/70
# 14.06.2020: slo1292: #95869e4f6, rest-omipCIQ-2200y, as slo1291/GM/Redi 400, def.albedos, gkdrag/wake=0.03
# 15.06.2020: slo1293: #95869e4f6, rest-omipCIQ-2200y, as slo1292/dap7027: gkdrag/wake=0.03/pr0=1/crs=0.968
# 15.06.2020: slo1294: #95869e4f6, rest-dap7023-1800y, as slo1289/dap7023: GMR=100/100
# gkdrag/wake=0.01/pr0=0.8/crs=0.978/alb=80/72/60/57/GMRedi=100/100
# 15.06.2020: slo1295: #95869e4f6, rest-dap7023-1800y, as slo1294/dap7023: GMR=400/0
# 15.06.2020: slo1296: #95869e4f6, rest-slo1293-1570y, as slo1293, leadclose1=0.5
# 17.06.2020: slo1297: #95869e4f6.ks0.7, rest-slo1293-1570y, as slo1293, snow conductivity ks=0.71 (def=0.31), lc1=0.25
# 18.06.2020: slo1298: #95869e4f6.ks0.7, rest-slo1293-1570y, as slo1297, lcl1=0.6, GMRedi=300/0 (colder?)
# 19.06.2020: slo1299: #95869e4f6, rest-omipCIQ-2200y, as slo1293, test landuse year 1850
# 19.06.2020: slo1300: #e0e6ab563, rest-slo1293-1570y, as slo1293, ks/ki/emiss=0.7/2.4/0.97, lcl1=0.6, GMRedi=400/400
# 21.06.2020: slo1301: #c17fc149e, rest-slo1293-1570y, as slo1300, lcl2=0.8
# 22.06.2020: slo1302: #c17fc149e, rest-slo1293-1570y, as slo1296/97, ks/ki/emiss=0.7/def/def, lcl1=0.5, crs=0.948
# 22.06.2020: slo1303: #c17fc149e, rest-slo1293-1570y, as slo1296/97, ks/ki/emiss=0.7/def/def, lcl1=0.5, alb=85/75/80/75
# 22.06.2020: slo1304: #c17fc149e, rest-omipCIQ-2200y, as slo1303, landuse year 1850 - spinup production run!
# gkdrag/wake=0.03/gklift=0.7/fsl=0.5, pr0/crs/crt/ki/emiss=def, ks=0.7, lcl1=0.5, alb=85/75/80/75
# 26.06.2020: slo1306: #65f5b0a13.ks07 (ks=0.7), rest-slo1304-1650y, as slo1304, irad_aero=19, background Kinne aerosol
# 06.07.2020: slo1307: #c17fc149e, rest-slo1304-1650y, as slo1304, irad_aero=13, alb=def., crs=0.978
# gkdrag/wake=0.03/gklift=0.7/fsl=0.5, pr0/alb/crt/ki/emiss=def, ks=0.7, lcl1=0.5 (alb=85/70/75/70)
# 07.07.2020: slo1308: #c17fc149e, rest-slo1304-1650y, as slo1307, irad_aero=13, alb=def., crs=0.988
# 10.07.2020: slo1309: #c17fc149e.iaero12, rest-slo1304-1650y, as slo1308, irad_aero=12, no TSI file, crs=0.995
# 12.07.2020: slo1310: #c17fc149e, rest-slo1304-1650y, as slo1307, irad_aero=13, alb=def., crs=0.995 (test response)
# 14.07.2020: slo1311: #c17fc149e.iaero12, rest-slo1307-2060y, as slo1307, irad_aero=12, alb=80/65/60/50 (crs=0.978)
# 14.07.2020: slo1312: #c17fc149e.iaero12, rest-slo1307-1950y, as slo1307, csecfrl=2.5e-6
# lookup after 3 days, repeat rayl=0.1001 in 1950y - same abort with other values! - budget issue!
# 3rd attempt: csecfrl=3.0e-6/4th: csec=4.0e-6 - same instability due to start_date<restart_date!
# again: csecfrl=2.5e-6
# 14.07.2020: slo1313: #c17fc149e.iaero12, rest-slo1307-1950y, as slo1307, alb=85/72/70/65 (cold snow untouched)
# 15.07.2020: slo1314: #c17fc149e.iaero12, rest-slo1307-1950y, as slo1307/1312, csecfrl=4.0e-6
# 16.07.2020: slo1315: #c17fc149e.iaero12, rest-slo1307-1700y, as slo1312, csecfrl=4.5e-6 (warmer)
# 17.07.2020: slo1316: #c17fc149e.iaero12, rest-slo1307-1700y, as slo1307, crt=0.85 (warmer; csec=def=1.5e-5)
# 17.07.2020: slo1317: #c17fc149e.iaero12, rest-slo1307-1700y, as slo1307, entrpen=0.00015 (warmer; csec=def=1.5e-5)
# 17.07.2020: slo1318: #c17fc149e.iaero12, rest-slo1307-1700y, as slo1307, entrpen=0.0003, entrscv=0.00015
# 17.07.2020: slo1319: #c17fc149e.iaero12, rest-slo1307-1700y, as slo1307, csecfrl=4.0e-6 (warmer), crt=0.77 (colder)
# 20.07.2020: slo1320: #c17fc149e.iaero12, rest-slo1307-1700y, as slo1307, csecfrl=4.5e-6 (warmer), entrpen=0.00045 (colder)
# 20.07.2020: slo1321: #c17fc149e.iaero12, rest-slo1307-1700y, as slo1307, csecfrl=5.0e-6, entrpen=0.00045 (colder)
# 23.07.2020: slo1322: #c17fc149e.iaero12, rest-slo1307-1700y, as slo1307, csecfrl=10.e-6 (warmer)
# 23.07.2020: slo1323: #c17fc149e.iaero12, rest-slo1307-1950y, as slo1322, csecfrl=10.e-6 (warmer)
# 30.07.2020: slo1324: #c17fc149e.iaero12, rest-slo1317-2100y, mixed, csecfrl=10.e-6; entrpen=0.00025
# 18.08.2020: slo1325: #c17fc149e.snowfix, rest-slo1317-3500y/atmos-init, pstar=27500 (csecfrl=10.e-6; entrpen=0.00025)
# 28.08.20 - 4400y: new path changed from mh0469 to mh0287
# 01.09.20 - 4870y: l_fast_sum=F/stay at compute2 for reproducibility
# 01.09.20 - 4900y: stopped
#=============================================================================
#=============================================================================
set -x
ulimit -s unlimited
#=============================================================================
#
# ICON run script:
# !ATTENTION! Do not change the format of the following lines.
# They are evaluated by checksuite scripts.
# created by ./run/make_target_runscript
# target machine is bullx_cpu
# target use_compiler is intel
# with_mpi=yes
# with_openmp=no
# memory_model=large
# submit with sbatch
#
#=============================================================================
#
# OpenMP environment variables
# ----------------------------
export OMP_NUM_THREADS=1
export ICON_THREADS=1
export OMP_SCHEDULE=dynamic,1
export OMP_DYNAMIC="false"
export OMP_STACKSIZE=200M
#
# MPI variables
# -------------
no_of_nodes=${SLURM_JOB_NUM_NODES:=1}
mpi_procs_pernode=$((${SLURM_JOB_CPUS_PER_NODE%%\(*} / 2))
((mpi_total_procs=no_of_nodes * mpi_procs_pernode))
#
# blocking length
# ---------------
nproma=16
#
#=============================================================================
# load local setting, if existing
# -------------------------------
if [ -a ../setting ]
then
echo "Load Setting"
. ../setting
fi
# environment variables for the experiment and the target system
# --------------------------------------------------------------
#export EXPNAME="icon.oes.20200506.intel.95869e4f6"
export EXPNAME=slo1325
export KMP_AFFINITY="verbose,granularity=core,compact,1,1"
export KMP_LIBRARY="turnaround"
export KMP_KMP_SETTINGS="1"
export OMP_WAIT_POLICY="active"
export OMPI_MCA_pml="cm"
export OMPI_MCA_mtl="mxm"
export OMPI_MCA_coll="^fca"
export MXM_RDMA_PORTS="mlx5_0:1"
export HCOLL_MAIN_IB="mlx5_0:1"
export HCOLL_ML_DISABLE_BARRIER="1"
export HCOLL_ML_DISABLE_IBARRIER="1"
export HCOLL_ML_DISABLE_BCAST="1"
export HCOLL_ENABLE_MCAST_ALL="1"
export HCOLL_ENABLE_MCAST="1"
export OMPI_MCA_coll_sync_barrier_after_alltoallv="1"
export OMPI_MCA_coll_sync_barrier_after_alltoallw="1"
export MXM_HANDLE_ERRORS="bt"
export UCX_HANDLE_ERRORS="bt"
export MALLOC_TRIM_THRESHOLD_="-1"
export KMP_AFFINITY="verbose,granularity=core,compact,1,1"
export KMP_LIBRARY="turnaround"
export KMP_KMP_SETTINGS="1"
export OMP_WAIT_POLICY="active"
export OMPI_MCA_pml="cm"
export OMPI_MCA_mtl="mxm"
export OMPI_MCA_coll="^fca"
export MXM_RDMA_PORTS="mlx5_0:1"
export HCOLL_MAIN_IB="mlx5_0:1"
export HCOLL_ML_DISABLE_BARRIER="1"
export HCOLL_ML_DISABLE_IBARRIER="1"
export HCOLL_ML_DISABLE_BCAST="0"
export HCOLL_ENABLE_MCAST_ALL="1"
export HCOLL_ENABLE_MCAST="1"
export OMPI_MCA_coll_sync_barrier_after_alltoallv="1"
export OMPI_MCA_coll_sync_barrier_after_alltoallw="1"
export MXM_HANDLE_ERRORS="bt"
export UCX_HANDLE_ERRORS="bt"
# load profile
# ------------
if [[ -a /etc/profile ]]
then
. /etc/profile
fi
#=============================================================================
# directories with absolute paths
# -------------------------------
thisdir=$(pwd)
basedir=${thisdir%/*}
export basedir
icon_data_rootFolder="/pool/data/ICON"
# how to start the icon model
# ---------------------------
export START="srun --cpu-freq=HighM1 --kill-on-bad-exit=1 --nodes=${SLURM_JOB_NUM_NODES:-1} --cpu_bind=verbose,cores --distribution=block:block --ntasks=$((no_of_nodes * mpi_procs_pernode)) --ntasks-per-node=${mpi_procs_pernode} --cpus-per-task=$((2 * OMP_NUM_THREADS)) --propagate=STACK,CORE"
#export MODEL="${basedir}/bin/icon"
#export MODEL="${basedir}/bin/icon.x.95869e4f6"
#export MODEL="${basedir}/bin/icon.x.95869e4f6.ks0.7"
#export MODEL="${basedir}/bin/icon.x.e0e6ab563"
#export MODEL="${basedir}/bin/icon.x.c17fc149e"
#export MODEL="${basedir}/bin/icon.x.c17fc149e.iaero12"
export MODEL="${basedir}/bin/icon.x.c17fc149e.snowfix"
# how to submit the next job
# --------------------------
submit="sbatch"
#job_name="exp.icon.oes.20200506.intel.95869e4f6.run"
job_name="exp.slo1325.run"
# cdo for post-processing
# -----------------------
cdo="cdo"
cdo_diff="cdo diffn"
# constants for time calculations
# -------------------------------
second=1 # [s] 1 second
minute=60 # [s] 1 minute
hour=3600 # [s] 1 hour
day=86400 # [s] 1 day
month=2592000 # [s] 30 days
year360=31104000 # [s] 360 days
year=31556900 # [s] 1 earth year
# define script functions used in the experiment run script
# ---------------------------------------------------------
. ./add_run_routines
#=============================================================================
ulimit -s 2097152
ulimit -c 0
#!/bin/bash
#--------------------------------------------------------------------------------------------------
#
# ICON-ESM R2B4 atmosphere including jsbach coupled to R2B6 ocean on equatorial-symmetric grids
# Atmosphere-Land-Ocean YAC Coupled Experiment:
# - atmosphere-soil-ocean (aso) spinup script without HAMOCC biogeochemistry
#
author_list="Monika Esch, Rene Redler, Stephan Lorenz"
#
#--------------------------------------------------------------------------------------------------
#
# This file describes a coupled experiment setup on a R2B4 grid based on the non-hydrostatic
# atmosphere with ECHAM physics and the hydrostatic ocean running on a R2B6 grid. The atmosphere
# is intialized from analysis files and using transient boundary conditions (1850) for:
# - spectral solar irradiation
# - well mixed greenhouse gases CO2, CH4, N2O, no CFCs
# - O3 concentration
# - SST and sea ice are transferred via YAC from the ocean.
# - and no (!) aerosols
#
# Here, the ocean is already spun up from PHC3.0 (Levitus) climatology for several centuries
# initialiseOcean="fromRestart"
# initialiseOcean="fromClimatology" is possible, see below.
#
# The coupling:
#
# atmosphere -> ocean:
# . surface_downward_eastward_stress
# . surface_downward_northward_stress
# . surface_fresh_water_flux
# . total_heat_flux
# . atmosphere_sea_ice_bundle
# . river_runoff
#
# ocean -> atmosphere:
# . sea_surface_temperature
# . eastward_sea_water_velocity
# . northward_sea_water_velocity
# . ocean_sea_ice_bundle
# . 10m_wind_speed
#
# currently not activated for coupling:
# . co2_mixing_ratio
# . co2_flux
#
#--------------------------------------------------------------------------------------------------
# (0) Basic model configuration
# -----------------------------
atmos_gridID="0013"
atmos_refinement="R02B04"
ocean_gridID="0035"
ocean_refinement="R02B06"
# use alternatively: full restart, init from (ocean) restart, init from climatology or false
# - set to false if ocean was already initialised
# initialiseOcean="fromRestart"
# initialiseOcean="fromClimatology"
# initialiseOcean="FALSE"
restart=.true.
# variables for restart:
restart_dir=/work/mh0287/m211032/Icon/Git_Icon/icon.oes.20200506/experiments
restart_exp=slo1317
#restart_dir=/work/mh0033/m300466/icon-ruby/icon-ruby2b/experiments
#restart_exp=dap7032-r0
restart_yea=3500
# Directory for Setup
Setupdir=/work/mh0287/m211032/Icon/Git_Icon/icon.oes.20200506/experiments/Setup
#mpi_oce_nodes=34 # this is a suitable value for 60 nodes = 26 atm + 34 oce nodes
mpi_oce_nodes=74
mpi_oce_nodes=${mpi_oce_nodes:=((no_of_nodes/2))} # default: half of requested nodes
((mpi_oce_procs=mpi_oce_nodes * mpi_procs_pernode))
# do not read namelists from ocean restart-file
read_restart_namelists=".false."
#--------------------------------------------------------------------------------------------------
# (1) Define the model time stepping
# ----------------------------------
radTimeStep="PT90M" # radiation time step: 18 time steps per day
atmTimeStep="PT15M" # atmosphere time step: 96 time steps per day
atm_substeps=8 # atmosphere dynamics substeps, ca. 2 min for atm-dyn-stepping
oceTimeStep="PT30M" # ocean time step: 48 time steps per day
couplingTimeStep="PT30M" # coupling time step: 3 time steps per radTimeStep
#--------------------------------------------------------------------------------------------------
# (2) unset some setting of create_target_header for mistral
unset OMPI_MCA_coll_fca_enable
unset OMPI_MCA_coll_fca_priority
#--------------------------------------------------------------------------------------------------
# (3) icon_data_poolFolder
# Variables provided by the scripting mechanism
# EXPNAME = name of exp. in 'exp.<name>'
# basedir = base directory, where src/, run/ etc exist
# icon_data_poolFolder = base directory, where grids/, input/ and setup/ exist
# nproma = blocking length for array dimensioning and inner loop lengths
# -> deprecated. nproma_atm and nproma_ocn are used here.
nproma_atm=16
nproma_oce=16
# overwrite the default setting with the new path and handle daint (CSCS)
if [ -d /users/icontest ]
then
poolFolder_prefix=/users/icontest
else
poolFolder_prefix=
fi
#icon_data_poolFolder="$poolFolder_prefix/work/mh0287/users/rene/public/mpim"
icon_data_poolFolder="$poolFolder_prefix/pool/data/ICON/grids/private/rene/mpim"
# horizontal grid(s)
# ------------------
atm_grid_name=icon_grid_${atmos_gridID}_${atmos_refinement}_G # global grid incl. land
atmo_grid_folder=/pool/data/ICON/grids/private/rene/mpim/${atmos_gridID} # still some private path!
atmo_data_InputFolder=${icon_data_poolFolder}/${atmos_gridID}
atmo_dyn_grid=${atm_grid_name}.nc
#--------------------------------------------------------------------------------------------------
# (4) Set variables to configure the experiment:
# ----------------------------------------------
# start and end date+time of experiment
# -------------------------------------
start_date=${start_date:="4700-01-01T00:00:00Z"}
end_date=${end_date:="4900-01-01T00:00:00Z"}
# restart/checkpoint/output intervals
# -----------------
#restart_interval="P1D" # test run 30 min
#restart_interval="P1Y" # production run
restart_interval="P10Y" # production run
#restart_interval="P30Y" # production run
# restart and output files are written once per job
checkpoint_interval="P20Y"
atm_file_interval="P20Y"
oce_file_interval="P20Y"
lnd_file_interval="P20Y"
# output interval: test run - 6-hourly; production run - monthly
atm_output_interval="P1M"
oce_output_interval="P1M"
lnd_output_interval="P1M"
#atm_output_interval="PT6H"
#oce_output_interval="PT6H"
#lnd_output_interval="PT6H"
# asynchronous diagnostic output processes
# ----------------------------------------
# Note that "mpi_atm_io_procs" must match the number of output files
mpi_atm_io_procs=0 # >0 for atmosphere plus land (not working for monitoring)
mpi_oce_io_procs=0 # >0 for ocean is not working yet
# output file selection
# ---------------------
#
# output_<xyz>=yes : yes --> output files for <xyz>, any other value --> no files for <xyz>
# monitoring output switches
output_atm_mon=yes
output_oce_mon=yes
output_oce_moc=yes # calc_moc is called every timestep - switch off for high resolutions
# sea ice, snow, SST and some deeper levels ocean output
output_oce_ice=yes
# standard debug-flux arrays at surface
output_atm_dbg=yes
output_oce_dbg=yes
output_lnd_dbg=yes
# land masks
output_lnd_msk=no
# default output files for atm/oce needed for standard quickplots
output_atm_3d=yes
output_atm_2d=yes
output_oce_def=yes # annual mean output is sufficient
# output interval for default atm/oce files, normally set to general atmos interval:
atm_output_interval_3d="$atm_output_interval"
atm_output_interval_2d="$atm_output_interval"
# annual mean output for deep ocean, since monthly output increases cpu-time!
oce_output_interval_def="P1Y"
# output switches for large atm/oce files - set to "yes" if needed for additional analysis
output_atm_cgrid=no # produces 1 atm file
output_lnd_amip=no # land output for atm_amip experiment
output_phy_3d=no # atmosphere physics, note: "yes" increases the output volume significantly!
#--------------------------------------------------------------------------------------------------
# (5) Define the model configuration
#-----------------------------------
# JSBACH settings
run_jsbach=yes
jsbach_usecase=jsbach_pfts # jsbach_lite or jsbach_pfts
jsbach_with_lakes=yes
jsbach_check_wbal=yes # check water balance
jsbach_with_carbon=no # yes needs jsbach_pfts usecase
# Some further processing for land configuration
# ----------------------------------------------
ljsbach=$([ "${run_jsbach:=no}" == yes ] && echo .TRUE. || echo .FALSE. )
llake=$([ "${jsbach_with_lakes:=yes}" == yes ] && echo .TRUE. || echo .FALSE. )
lcarbon=$([ "${jsbach_with_carbon:=yes}" == yes ] && echo .TRUE. || echo .FALSE. )
if [[ $jsbach_usecase == *pfts* ]]
then
pft_file_tag="11pfts_"
else
pft_file_tag=""
fi
# namelist files
# --------------
atm_namelist=NAMELIST_${EXPNAME}_atm
lnd_namelist=NAMELIST_${EXPNAME}_lnd
oce_namelist=NAMELIST_${EXPNAME}_oce
#--------------------------------------------------------------------------------------------------
# I. coupling section
#--------------------------------------------------------------------------------------------------
if [ $mpi_total_procs -lt 2 ] ; then
check_error 0 "This setup requires at least 2 mpi processes. Exit"
fi
# I.1 Split the number of total procs and assign to each component
# ----------------------------------------------------------------
oce_min_rank=`expr ${mpi_total_procs} - ${mpi_oce_procs}`
oce_max_rank=`expr ${oce_min_rank} + ${mpi_oce_procs} - 1`
oce_inc_rank=1
atm_min_rank=0
atm_max_rank=`expr ${oce_min_rank} - 1`
atm_inc_rank=1
#
# I.2 Fill model list
# -------------------
#
namelist_list[0]="$atm_namelist"
modelname_list[0]="atmo"
modeltype_list[0]=1
minrank_list[0]=$atm_min_rank
maxrank_list[0]=$atm_max_rank
incrank_list[0]=$atm_inc_rank
#
namelist_list[1]="$oce_namelist"
modelname_list[1]="ocean"
modeltype_list[1]=2
minrank_list[1]=$oce_min_rank
maxrank_list[1]=$oce_max_rank
incrank_list[1]=$oce_inc_rank
# I.3 YAC coupling library configuration
#-----------------------------------------------------------------------------
# Mapping parameter for coupling:
# in order to enforce errors if unmapped grid-cells are found:
# - for conservative remapping use: user_value=-999.9 as second method only
# - for method bernstein_bezier use: (2) n-nearest_neighbor and (3) user_value=-999.9
#
atm_lag=1
oce_lag=1
# write weights for runoff-coupling (source_to_target mapping) into file
runoffweightfile=runoff_$EXPNAME
# co2_flux and co2_mixing_ratio are listed as transients
# below but are not configured for coupling in the couples
# section. There fields are therefore not considered for
# the search not for the data exchange even if yac_fget and
# yac_fput are called for these fields.
#
# component names in coupling.xml must (!) match with modelname_list[*]
#
cat > coupling_${EXPNAME}.xml << EOF
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<coupling xmlns="http://www.w3schools.com"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.w3schools.com coupling.xsd">
<redirect redirect_of_root="false" redirect_stdout="false"/>
<components>
<component id="1">
<name>${modelname_list[0]}</name>
<model>ICON</model>
<simulated>atmosphere</simulated>
<transient_grid_refs>
<transient_grid_ref collection_size="2" grid_ref="1" id="1" transient_ref="1"/>
<transient_grid_ref collection_size="2" grid_ref="1" id="2" transient_ref="2"/>
<transient_grid_ref collection_size="3" grid_ref="1" id="3" transient_ref="3"/>
<transient_grid_ref collection_size="4" grid_ref="1" id="4" transient_ref="4"/>
<transient_grid_ref collection_size="2" grid_ref="1" id="5" transient_ref="5"/>
<transient_grid_ref collection_size="1" grid_ref="1" id="6" transient_ref="6"/>
<transient_grid_ref collection_size="1" grid_ref="1" id="7" transient_ref="7"/>
<transient_grid_ref collection_size="1" grid_ref="1" id="8" transient_ref="8"/>
<transient_grid_ref collection_size="3" grid_ref="1" id="9" transient_ref="9"/>
<transient_grid_ref collection_size="1" grid_ref="1" id="10" transient_ref="10"/>
<transient_grid_ref collection_size="1" grid_ref="1" id="11" transient_ref="11"/>
<transient_grid_ref collection_size="1" grid_ref="1" id="12" transient_ref="12"/>
<transient_grid_ref collection_size="1" grid_ref="1" id="13" transient_ref="13"/>
</transient_grid_refs>
</component>
<component id="2">
<name>${modelname_list[1]}</name>
<model>ICON</model>
<simulated>ocean</simulated>
<transient_grid_refs>
<transient_grid_ref collection_size="2" grid_ref="1" id="1" transient_ref="1"/>
<transient_grid_ref collection_size="2" grid_ref="1" id="2" transient_ref="2"/>
<transient_grid_ref collection_size="3" grid_ref="1" id="3" transient_ref="3"/>
<transient_grid_ref collection_size="4" grid_ref="1" id="4" transient_ref="4"/>
<transient_grid_ref collection_size="2" grid_ref="1" id="5" transient_ref="5"/>
<transient_grid_ref collection_size="1" grid_ref="1" id="6" transient_ref="6"/>
<transient_grid_ref collection_size="1" grid_ref="1" id="7" transient_ref="7"/>
<transient_grid_ref collection_size="1" grid_ref="1" id="8" transient_ref="8"/>
<transient_grid_ref collection_size="3" grid_ref="1" id="9" transient_ref="9"/>
<transient_grid_ref collection_size="1" grid_ref="1" id="10" transient_ref="10"/>
<transient_grid_ref collection_size="1" grid_ref="1" id="11" transient_ref="11"/>
<transient_grid_ref collection_size="1" grid_ref="1" id="12" transient_ref="12"/>
<transient_grid_ref collection_size="1" grid_ref="1" id="13" transient_ref="13"/>
</transient_grid_refs>
</component>
<component id="3">
<name>name_list_io</name>
<model>ICON</model>
<simulated>IO</simulated>
</component>
</components>
<transients>
<transient id="1" transient_standard_name="surface_downward_eastward_stress"/>
<transient id="2" transient_standard_name="surface_downward_northward_stress"/>
<transient id="3" transient_standard_name="surface_fresh_water_flux"/>
<transient id="4" transient_standard_name="total_heat_flux"/>
<transient id="5" transient_standard_name="atmosphere_sea_ice_bundle"/>
<transient id="6" transient_standard_name="sea_surface_temperature"/>
<transient id="7" transient_standard_name="eastward_sea_water_velocity"/>
<transient id="8" transient_standard_name="northward_sea_water_velocity"/>
<transient id="9" transient_standard_name="ocean_sea_ice_bundle"/>
<transient id="10" transient_standard_name="10m_wind_speed"/>
<transient id="11" transient_standard_name="river_runoff"/>
<transient id="12" transient_standard_name="co2_mixing_ratio"/>
<transient id="13" transient_standard_name="co2_flux"/>
</transients>
<grids>
<grid alias_name="grid1" id="1"/>
</grids>
<dates>
<start_date>+1800-01-01T00:00:00.000</start_date>
<end_date>+2100-01-01T00:00:00.000</end_date>
<calendar>proleptic-gregorian</calendar>
</dates>
<timestep_unit>ISO_format</timestep_unit>
<couples>
<couple>
<component1 component_id="1"/>
<component2 component_id="2"/>
<transient_couple transient_id="1">
<source component_ref="1" transient_grid_ref="1"/>
<target transient_grid_ref="1"/>
<timestep>
<source>${atmTimeStep}</source>
<target>${oceTimeStep}</target>
<coupling_period operation="average">${couplingTimeStep}</coupling_period>
<source_timelag>${atm_lag}</source_timelag>
<target_timelag>${oce_lag}</target_timelag>
</timestep>
<mapping_on_source>true</mapping_on_source>
<interpolation_requirements use_source_mask="true" use_target_mask="true">
<interpolation method="bernstein_bezier"/>
<interpolation method="n-nearest_neighbor" n="4" weighted="ARITHMETIC_AVERAGE"/>
<interpolation method="fixed_value" user_value="-999.9"/>
</interpolation_requirements>
<debug_mode at_source_after_interpolation="false" at_source_before_interpolation="false" at_target="false"/>
<enforce_write_restart>false</enforce_write_restart>
<enforce_write_weight_file filename="">false</enforce_write_weight_file>
</transient_couple>
<transient_couple transient_id="2">
<source component_ref="1" transient_grid_ref="2"/>
<target transient_grid_ref="2"/>
<timestep>
<source>${atmTimeStep}</source>
<target>${oceTimeStep}</target>
<coupling_period operation="average">${couplingTimeStep}</coupling_period>
<source_timelag>${atm_lag}</source_timelag>
<target_timelag>${oce_lag}</target_timelag>
</timestep>
<mapping_on_source>true</mapping_on_source>
<interpolation_requirements use_source_mask="true" use_target_mask="true">
<interpolation method="bernstein_bezier"/>
<interpolation method="n-nearest_neighbor" n="4" weighted="ARITHMETIC_AVERAGE"/>
<interpolation method="fixed_value" user_value="-999.9"/>
</interpolation_requirements>
<debug_mode at_source_after_interpolation="false" at_source_before_interpolation="false" at_target="false"/>
<enforce_write_restart>false</enforce_write_restart>
<enforce_write_weight_file filename="">false</enforce_write_weight_file>
</transient_couple>
<transient_couple transient_id="3">
<source component_ref="1" transient_grid_ref="3"/>
<target transient_grid_ref="3"/>
<timestep>
<source>${atmTimeStep}</source>
<target>${oceTimeStep}</target>
<coupling_period operation="average">${couplingTimeStep}</coupling_period>
<source_timelag>${atm_lag}</source_timelag>
<target_timelag>${oce_lag}</target_timelag>
</timestep>
<mapping_on_source>true</mapping_on_source>
<interpolation_requirements use_source_mask="true" use_target_mask="true">
<interpolation enforced_conservation="false" method="conservative" normalisation="FRACAREA" order="1" partial_coverage="true"/>
<interpolation method="fixed_value" user_value="-999.9"/>
</interpolation_requirements>
<debug_mode at_source_after_interpolation="false" at_source_before_interpolation="false" at_target="false"/>
<enforce_write_restart>false</enforce_write_restart>
<enforce_write_weight_file filename="">false</enforce_write_weight_file>
</transient_couple>
<transient_couple transient_id="4">
<source component_ref="1" transient_grid_ref="4"/>
<target transient_grid_ref="4"/>
<timestep>
<source>${atmTimeStep}</source>
<target>${oceTimeStep}</target>
<coupling_period operation="average">${couplingTimeStep}</coupling_period>
<source_timelag>${atm_lag}</source_timelag>
<target_timelag>${oce_lag}</target_timelag>
</timestep>
<mapping_on_source>true</mapping_on_source>
<interpolation_requirements use_source_mask="true" use_target_mask="true">
<interpolation enforced_conservation="false" method="conservative" normalisation="FRACAREA" order="1" partial_coverage="true"/>
<interpolation method="fixed_value" user_value="-999.9"/>
</interpolation_requirements>
<debug_mode at_source_after_interpolation="false" at_source_before_interpolation="false" at_target="false"/>
<enforce_write_restart>false</enforce_write_restart>
<enforce_write_weight_file filename="">false</enforce_write_weight_file>
</transient_couple>
<transient_couple transient_id="5">
<source component_ref="1" transient_grid_ref="5"/>
<target transient_grid_ref="5"/>
<timestep>
<source>${atmTimeStep}</source>
<target>${oceTimeStep}</target>
<coupling_period operation="average">${couplingTimeStep}</coupling_period>
<source_timelag>${atm_lag}</source_timelag>
<target_timelag>${oce_lag}</target_timelag>
</timestep>
<mapping_on_source>true</mapping_on_source>
<interpolation_requirements use_source_mask="true" use_target_mask="true">
<interpolation enforced_conservation="false" method="conservative" normalisation="FRACAREA" order="1" partial_coverage="true"/>
<interpolation method="fixed_value" user_value="-999.9"/>
</interpolation_requirements>
<debug_mode at_source_after_interpolation="false" at_source_before_interpolation="false" at_target="false"/>
<enforce_write_restart>false</enforce_write_restart>
<enforce_write_weight_file filename="">false</enforce_write_weight_file>
</transient_couple>
<transient_couple transient_id="6">
<source component_ref="2" transient_grid_ref="6"/>
<target transient_grid_ref="6"/>
<timestep>
<source>${oceTimeStep}</source>
<target>${atmTimeStep}</target>
<coupling_period operation="average">${couplingTimeStep}</coupling_period>
<source_timelag>${oce_lag}</source_timelag>
<target_timelag>${atm_lag}</target_timelag>
</timestep>
<mapping_on_source>true</mapping_on_source>
<interpolation_requirements use_source_mask="true" use_target_mask="true">
<interpolation enforced_conservation="false" method="conservative" normalisation="FRACAREA" order="1" partial_coverage="true"/>
<interpolation method="fixed_value" user_value="-999.9"/>
</interpolation_requirements>
<debug_mode at_source_after_interpolation="false" at_source_before_interpolation="false" at_target="false"/>
<enforce_write_restart>false</enforce_write_restart>
<enforce_write_weight_file filename="">false</enforce_write_weight_file>
</transient_couple>
<transient_couple transient_id="7">
<source component_ref="2" transient_grid_ref="7"/>
<target transient_grid_ref="7"/>
<timestep>
<source>${oceTimeStep}</source>
<target>${atmTimeStep}</target>
<coupling_period operation="average">${couplingTimeStep}</coupling_period>
<source_timelag>${oce_lag}</source_timelag>
<target_timelag>${atm_lag}</target_timelag>
</timestep>
<mapping_on_source>true</mapping_on_source>
<interpolation_requirements use_source_mask="true" use_target_mask="true">
<interpolation enforced_conservation="false" method="conservative" normalisation="FRACAREA" order="1" partial_coverage="true"/>
<interpolation method="fixed_value" user_value="-999.9"/>
</interpolation_requirements>
<debug_mode at_source_after_interpolation="false" at_source_before_interpolation="false" at_target="false"/>
<enforce_write_restart>false</enforce_write_restart>
<enforce_write_weight_file filename="">false</enforce_write_weight_file>
</transient_couple>
<transient_couple transient_id="8">
<source component_ref="2" transient_grid_ref="8"/>
<target transient_grid_ref="8"/>
<timestep>
<source>${oceTimeStep}</source>
<target>${atmTimeStep}</target>
<coupling_period operation="average">${couplingTimeStep}</coupling_period>
<source_timelag>${oce_lag}</source_timelag>
<target_timelag>${atm_lag}</target_timelag>
</timestep>
<mapping_on_source>true</mapping_on_source>
<interpolation_requirements use_source_mask="true" use_target_mask="true">
<interpolation enforced_conservation="false" method="conservative" normalisation="FRACAREA" order="1" partial_coverage="true"/>
<interpolation method="fixed_value" user_value="-999.9"/>
</interpolation_requirements>
<debug_mode at_source_after_interpolation="false" at_source_before_interpolation="false" at_target="false"/>
<enforce_write_restart>false</enforce_write_restart>
<enforce_write_weight_file filename="">false</enforce_write_weight_file>
</transient_couple>
<transient_couple transient_id="9">
<source component_ref="2" transient_grid_ref="9"/>
<target transient_grid_ref="9"/>
<timestep>
<source>${oceTimeStep}</source>
<target>${atmTimeStep}</target>
<coupling_period operation="average">${couplingTimeStep}</coupling_period>
<source_timelag>${oce_lag}</source_timelag>
<target_timelag>${atm_lag}</target_timelag>
</timestep>
<mapping_on_source>true</mapping_on_source>
<interpolation_requirements use_source_mask="true" use_target_mask="true">
<interpolation enforced_conservation="false" method="conservative" normalisation="FRACAREA" order="1" partial_coverage="true"/>
<interpolation method="fixed_value" user_value="-999.9"/>
</interpolation_requirements>
<debug_mode at_source_after_interpolation="false" at_source_before_interpolation="false" at_target="false"/>
<enforce_write_restart>false</enforce_write_restart>
<enforce_write_weight_file filename="">false</enforce_write_weight_file>
</transient_couple>
<transient_couple transient_id="10">
<source component_ref="1" transient_grid_ref="10"/>
<target transient_grid_ref="10"/>
<timestep>
<source>${atmTimeStep}</source>
<target>${oceTimeStep}</target>
<coupling_period operation="average">${couplingTimeStep}</coupling_period>
<source_timelag>${atm_lag}</source_timelag>
<target_timelag>${oce_lag}</target_timelag>
</timestep>
<mapping_on_source>true</mapping_on_source>
<interpolation_requirements use_source_mask="true" use_target_mask="true">
<interpolation method="bernstein_bezier"/>
<interpolation method="n-nearest_neighbor" n="4" weighted="ARITHMETIC_AVERAGE"/>
<interpolation method="fixed_value" user_value="-999.9"/>
</interpolation_requirements>
<debug_mode at_source_after_interpolation="false" at_source_before_interpolation="false" at_target="false"/>
<enforce_write_restart>false</enforce_write_restart>
<enforce_write_weight_file filename="">false</enforce_write_weight_file>
</transient_couple>
<transient_couple transient_id="11">
<source component_ref="1" transient_grid_ref="11"/>
<target transient_grid_ref="11"/>
<timestep>
<source>${atmTimeStep}</source>
<target>${oceTimeStep}</target>
<coupling_period operation="average">${couplingTimeStep}</coupling_period>
<source_timelag>${atm_lag}</source_timelag>
<target_timelag>${oce_lag}</target_timelag>
</timestep>
<mapping_on_source>true</mapping_on_source>
<interpolation_requirements use_source_mask="true" use_target_mask="true">
<interpolation method="source_to_target_map"/>
</interpolation_requirements>
<debug_mode at_source_after_interpolation="false" at_source_before_interpolation="false" at_target="false"/>
<enforce_write_restart>false</enforce_write_restart>
<enforce_write_weight_file filename="$runoffweightfile">true</enforce_write_weight_file>
</transient_couple>
</couple>
</couples>
<created date="16-04-2019 15:49" tool="YAC-CouplingGUI v.1.5"/>
</coupling>
EOF
# xsd and xml files for yac
# -------------------------
#
add_required_file ${basedir}/run/coupling_${EXPNAME}.xml ./coupling.xml
add_required_file ${basedir}/externals/yac/input/coupling.xsd ./coupling.xsd
#-----------------------------------------------------------------------------
# II. ATMOSPHERE and LAND
#-----------------------------------------------------------------------------
#
# atmosphere namelist
# -------------------
cat > ${atm_namelist} << EOF
!
&coupling_mode_nml
coupled_mode = .TRUE.
/
¶llel_nml
nproma = ${nproma_atm}
num_io_procs = ${mpi_atm_io_procs}
num_prefetch_proc = 0
pio_type = 0
/
&grid_nml
dynamics_grid_filename = "${atmo_dyn_grid}"
/
&run_nml
num_lev = 47 ! number of full levels
modelTimeStep = "${atmTimeStep}" ! model time step in ISO-format
ltestcase = .FALSE. ! run testcase
ldynamics = .TRUE. ! dynamics
ltransport = .TRUE. ! transport
iforcing = 2 ! 0: none, 1: HS, 2: ECHAM, 3: NWP
output = 'nml'
msg_level = 12 ! level of details report during integration
restart_filename = "${EXPNAME}_restart_atm_<rsttime>.nc"
activate_sync_timers = .TRUE.
profiling_output = 1 ! aggregated: 1; detailed: 2; in files: 3
/
&extpar_nml
itopo = 1 ! 1: read topography from the grid file
itype_lwemiss = 0
/
&initicon_nml
init_mode = 2 ! 2: initialize from IFS analysis
ifs2icon_filename= "ifs2icon.nc"
/
&nonhydrostatic_nml
ndyn_substeps = $atm_substeps ! dtime/dt_dyn
damp_height = 50000. ! [m]
rayleigh_coeff = 0.1000 ! set to 0.1001 for rerun with little change
vwind_offctr = 0.2
divdamp_fac = 0.004
/
&interpol_nml
rbf_scale_mode_ll = 1
/
&sleve_nml
min_lay_thckn = 40. ! [m]
top_height = 83000. ! [m]
stretch_fac = 0.9
decay_scale_1 = 4000. ! [m]
decay_scale_2 = 2500. ! [m]
decay_exp = 1.2
flat_height = 16000. ! [m]
/
&diffusion_nml
/
&transport_nml
tracer_names = 'hus','clw','cli'
ivadv_tracer = 3 , 3 , 3
itype_hlimit = 3 , 4 , 4
ihadv_tracer = 52 , 2 , 2
/
&echam_phy_nml
!
! domain 1
! --------
!
! atmospheric phyiscs (""=never)
echam_phy_config(1)%dt_rad = "${radTimeStep}"
echam_phy_config(1)%dt_vdf = "${atmTimeStep}"
echam_phy_config(1)%dt_cnv = "${atmTimeStep}"
echam_phy_config(1)%dt_cld = "${atmTimeStep}"
echam_phy_config(1)%dt_gwd = "${atmTimeStep}"
echam_phy_config(1)%dt_sso = "${atmTimeStep}"
!
! atmospheric chemistry (""=never)
echam_phy_config(1)%dt_mox = "${atmTimeStep}"
echam_phy_config(1)%dt_car = ""
echam_phy_config(1)%dt_art = ""
!
! surface (.TRUE. or .FALSE.)
echam_phy_config(1)%ljsb = ${ljsbach}
echam_phy_config(1)%lamip = .FALSE.
echam_phy_config(1)%lice = .TRUE.
echam_phy_config(1)%lmlo = .FALSE.
echam_phy_config(1)%llake = ${llake}
!
! fix negative humidity (default=0, no correction)
! echam_phy_config(1)%iqneg_d2p = 0
! echam_phy_config(1)%iqneg_p2d = 0
/
&echam_rad_nml
!
! domain 1
! --------
!
echam_rad_config(1)%isolrad = 6
echam_rad_config(1)%irad_h2o = 1
echam_rad_config(1)%irad_co2 = 2
echam_rad_config(1)%irad_ch4 = 2
echam_rad_config(1)%irad_n2o = 2
echam_rad_config(1)%irad_o3 = 2 ! constant annual cycle climatology
echam_rad_config(1)%irad_o2 = 2
echam_rad_config(1)%irad_cfc11 = 0
echam_rad_config(1)%irad_cfc12 = 0
echam_rad_config(1)%irad_aero = 12
echam_rad_config(1)%vmr_co2 = 284.317e-6 ! constant volume mixing ration
echam_rad_config(1)%vmr_ch4 = 808.249e-9 ! constant volume mixing ration
echam_rad_config(1)%vmr_n2o = 273.021e-9 ! constant volume mixing ration
echam_rad_config(1)%lyr_perp = .TRUE.
echam_rad_config(1)%yr_perp = 1850
/
&echam_gwd_nml
!echam_gwd_config(:)%emiss_lev = 10
!echam_gwd_config(:)%rmscon = 0.87
!echam_gwd_config(:)%kstar = 5.0e-5
!echam_gwd_config(:)%m_min = 0.0
/
&echam_sso_nml
echam_sso_config(1)%gkdrag = 0.03 ! default: 0.05
echam_sso_config(1)%gkwake = 0.03 ! default: 0.05
echam_sso_config(:)%gklift = 0.7 ! default: 0.
/
&echam_vdf_nml
!echam_vdf_config(1)%pr0 = 0.8 ! neutral limit Prandtl no - default: 1.0
echam_vdf_config(1)%fsl = 0.5 ! default: 0.4
/
&echam_cnv_nml
echam_cnv_config(1)%entrpen = 0.00015 ! default: 0.0003 (old default: 0.0002)
!echam_cnv_config(1)%cmfctop = 0.1 ! default: 0.1 (old default: 0.2)
!echam_cnv_config(1)%entrscv = 0.0003 ! default: 0.0003 (old default: 0.003)
/
&echam_cld_nml
!echam_cld_config(1)%csecfrl = 1.0e-5
! threshold for ice and water in clouds default: 1.5e-5 (default was 5e-6)
!echam_cld_config(1)%ccraut = 2.0 ! default: 2.0 (default was 15.0)
!echam_cld_config(1)%ccsaut = 2.0 ! default: 2.0 (default was 95.0)
!echam_cld_config(1)%cauloc = 1.0 ! default: 1.0 (default was 10.0)
/
&echam_cov_nml
echam_cov_config(1)%crs = 0.978 ! Critical relative humidity at surface, default 0.968
!echam_cov_config(1)%crt = 0.85 ! Critical relative humidity at toa, default 0.8
/
&sea_ice_nml
!albs = 0.8 ! Albedo of snow (not melting) ! def: 0.85
!albsm = 0.65 ! Albedo of snow (melting) ! def: 0.70
!albi = 0.60 ! Albedo of ice (not melting) ! def: 0.75
!albim = 0.50 ! Albedo of ice (melting) ! def: 0.70
/
EOF
# jsbach namelist
# ---------------
cat > ${lnd_namelist} << EOF
&jsb_model_nml
usecase = "${jsbach_usecase}"
use_lakes = ${llake}
fract_filename = "bc_land_frac.nc"
output_tiles = ${output_tiles} ! List of tiles to output
/
&jsb_seb_nml
bc_filename = 'bc_land_phys.nc'
ic_filename = 'ic_land_soil.nc'
/
&jsb_rad_nml
use_alb_veg_simple = .FALSE. ! Use TRUE for jsbach_lite, FALSE for jsbach_pfts
bc_filename = 'bc_land_phys.nc'
ic_filename = 'ic_land_soil.nc'
/
&jsb_turb_nml
bc_filename = 'bc_land_phys.nc'
ic_filename = 'ic_land_soil.nc'
/
&jsb_sse_nml
l_heat_cap_map = .FALSE.
l_heat_cond_map = .FALSE.
l_heat_cap_dyn = .FALSE.
l_heat_cond_dyn = .FALSE.
l_snow = .TRUE.
l_dynsnow = .TRUE.
l_freeze = .TRUE.
l_supercool = .TRUE.
bc_filename = 'bc_land_soil.nc'
ic_filename = 'ic_land_soil.nc'
/
&jsb_hydro_nml
l_organic = .FALSE.
bc_filename = 'bc_land_soil.nc'
ic_filename = 'ic_land_soil.nc'
bc_sso_filename = 'bc_land_sso.nc'
/
&jsb_assimi_nml
active = .TRUE. ! Use FALSE for jsbach_lite, TRUE for jsbach_pfts
/
&jsb_pheno_nml
scheme = 'logrop' ! scheme = climatology for jsbach_lite / scheme = logrop for jsbach_pfts
bc_filename = 'bc_land_phys.nc'
ic_filename = 'ic_land_soil.nc'
/
&jsb_carbon_nml
active = ${lcarbon}
bc_filename = 'bc_land_carbon.nc'
ic_filename = 'ic_land_carbon.nc'
read_cpools = .FALSE.
/
&jsb_fuel_nml
active = ${lcarbon}
fuel_algorithm = 1
/
&jsb_disturb_nml
active = .FALSE.
ic_filename = 'ic_land_soil.nc'
bc_filename = 'bc_land_phys.nc'
fire_algorithm = 1
windbreak_algorithm = 1
lburn_pasture = .FALSE.
/
&jsb_hd_nml
active = .TRUE.
routing_scheme = 'full' ! 'zero' no HD, runoff=0; 'full' incl. full HD model; 'weighted_to_coast'
bc_filename = 'bc_land_hd.nc'
diag_water_budget = .TRUE.
debug_hd = .FALSE.
enforce_water_budget = .FALSE. ! TRUE: stop in case of water conservation problem
/
EOF
#--------------------------------------------------------------------------------------------------
# Define the atmosphere and land input
# ------------------------------------
# model files
#
add_link_file ${basedir}/data/lsdata.nc ./
add_link_file ${basedir}/data/ECHAM6_CldOptProps.nc ./
# namelist files
# --------------
add_required_file ${basedir}/run/${atm_namelist} ./
add_required_file ${basedir}/run/${lnd_namelist} ./
# dictionary file for output variable names
#
dict_file="dict.${EXPNAME}"
cat dict.iconam.mpim > ${dict_file}
add_required_file ${basedir}/run/${dict_file} ./
# initial conditions
#
# - atmosphere: ECMWF analysis, 1979-01-01T00:00:00Z
datadir=${atmo_data_InputFolder}/initial_condition/r0002
add_link_file ${datadir}/ifs2icon_1979010100_${atmos_refinement}_G.nc ./ifs2icon.nc
#
# - land: source?, date+time? - not yet set to 1850!
#datadir=${atmo_data_InputFolder}/land/r0006
#add_link_file ${datadir}/ic_land_soil_1992.nc ./ic_land_soil.nc
# preliminary path for land data at 1850 / pre-industrial (2020-06-19)
#datadir=/work/mj0060/m212005/data/icon/ruby/0013-0031/land/r0001
datadir=$Setupdir/land
add_link_file ${datadir}/ic_land_soil_1850.nc ./ic_land_soil.nc
# boundary conditions
#
# - ozone
# -- for irad_o3=8
#
datadir=${atmo_data_InputFolder}/ozone/r0002
#
add_link_file ${datadir}/bc_ozone_picontrol.nc ./bc_ozone.nc
#
# - tropospheric anthropogenic aerosols, simple plumes (irad_aero=19)
#
#add_link_file ${basedir}/data/MACv2.0-SP_v1.nc ./MACv2.0-SP_v1.nc
#
# Kinne background aerosols are needed for the year 1850 (irad_aero=13/18)
#
# Here we use revised data (r0002) based on work by Sebastian Rast
#
datadir=${atmo_data_InputFolder}/aerosol_kinne/r0002
#
add_link_file ${datadir}/bc_aeropt_kinne_lw_b16_coa.nc ./
add_link_file ${datadir}/bc_aeropt_kinne_sw_b14_coa.nc ./
#
# use exlcusively Kinne background aerosols for the year 1850, filename without year (irad_aero=12)
add_link_file ${datadir}/bc_aeropt_kinne_sw_b14_fin_1850.nc ./bc_aeropt_kinne_sw_b14_fin.nc
#
# Trick Kinne background aerosols to year 1850 (irad_aero=13)
# - from atm_amip - whole simulation range with links!
#
# range of years for yearly files
# assume start_date and end_date have the format yyyy-...
#start_year=$(( ${start_date%%-*} - 1 ))
#end_year=$(( ${end_date%%-*} + 1 ))
#year=$start_year
#while [[ $year -le $end_year ]]
#do
# add_link_file ${datadir}/bc_aeropt_kinne_sw_b14_fin_1850.nc ./bc_aeropt_kinne_sw_b14_fin_${year}.nc
# (( year = year+1 ))
#done
#
# - stratospheric aerosol constant for 1850 (irad_aero=15/18)
#
#datadir=${icon_data_poolFolder}/independent/aerosol_stenchikov
#year=1850
#add_link_file ${datadir}/bc_aeropt_stenchikov_lw_b16_sw_b14_${year}.nc ./bc_aeropt_stenchikov_lw_b16_sw_b14_${year}.nc
#
# - sst and sic
#
datadir=${atmo_data_InputFolder}/sst_and_seaice/r0002
#
add_link_file ${datadir}/bc_sic_1979_2016.nc ./bc_sic.nc
add_link_file ${datadir}/bc_sst_1979_2016.nc ./bc_sst.nc
#
# - ssi and tsi
#
#datadir=${icon_data_poolFolder}/independent/solar_radiation/3.2
#
#add_link_file ${datadir}/swflux_14band_cmip6_1850-2299-v3.2.nc ./bc_solar_irradiance_sw_b14.nc
#
# - land parameters
#
datadir=${atmo_data_InputFolder}/land/r0006
#
# - not yet set to 1850!
#add_link_file ${datadir}/bc_land_frac_${pft_file_tag}1992.nc ./bc_land_frac.nc
#add_link_file ${datadir}/bc_land_phys_1992.nc ./bc_land_phys.nc
#add_link_file ${datadir}/bc_land_soil_1992.nc ./bc_land_soil.nc
#add_link_file ${datadir}/bc_land_sso_1992.nc ./bc_land_sso.nc
#
# preliminary path for land data at 1850 / pre-industrial (2020-06-19)
#datadir=/work/mj0060/m212005/data/icon/ruby/0013-0031/land/r0001
datadir=$Setupdir/land
add_link_file ${datadir}/bc_land_frac_${pft_file_tag}1850.nc ./bc_land_frac.nc
add_link_file ${datadir}/bc_land_phys_1850.nc ./bc_land_phys.nc
add_link_file ${datadir}/bc_land_soil_1850.nc ./bc_land_soil.nc
add_link_file ${datadir}/bc_land_sso_1850.nc ./bc_land_sso.nc
#
# - HD model input by Tom Riddick
#
# prelinminary test version
datadir=/pool/data/ICON/grids/private/Stephan/mpim/${atmos_gridID}/land
#add_link_file $datadir/hdpara_icon_${atmos_gridID}_20190927.nc ./bc_land_hd.nc
#add_link_file $datadir/hdpara_icon_${atmos_gridID}_${atmos_refinement}_20200303_v2.nc ./bc_land_hd.nc
add_link_file $datadir/hdpara_icon_0013_R02B04_20200303_v2.nc ./bc_land_hd.nc
#
# - lctlib file for JSBACH
#
add_link_file ${basedir}/externals/jsbach/data/lctlib_nlct21.def ./lctlib_nlct21.def
#
# - HD mask for interpolation of runoff
#
add_required_file ${atmo_grid_folder}/${atmo_dyn_grid} ./hd_mask.nc
#
# - the atmosphere grid itself (the grid copy section below from $HGRIDDIR is ignored)
#
add_required_file ${atmo_grid_folder}/${atmo_dyn_grid} ./
#
#--------------------------------------------------------------------------------------------------
# (5) Define the output
# ---------------------
# Parameters for all output files
# -------------------------------
cat >> ${atm_namelist} << EOF
&io_nml
output_nml_dict = "${dict_file}"
netcdf_dict = "${dict_file}"
itype_pres_msl = 4
restart_file_type= 5
! restart_write_mode = "joint procs multifile" ! not necessary/useful in default r2b4 setup
! lnetcdf_flt64_output = .TRUE. ! 64 bit output in all files
lkeep_in_sync = .TRUE. ! sync after each timestep
! lkeep_in_sync = .FALSE.
/
&dbg_index_nml
idbg_mxmn = 0 ! initialize MIN/MAX debug output
idbg_val = 0 ! initialize one cell debug output
idbg_slev = 1 ! initialize start level for debug output
idbg_elev = 2 ! initialize end level for debug output
dbg_lat_in = 30.0 ! latitude location of one cell debug output
dbg_lon_in = -30.0 ! longitude location of one cell debug output
str_mod_tst ='InterFaceOce' ! define modules to print out in debug mode
/
EOF
# Define output files
# -------------------
#
# output_<xyz>=yes : yes --> output files for <xyz>, any other value --> no files for <xyz>
#
# 3-dimensional files include 'ps' and 'pfull' to allow the vertical
# interpolation to pressure levels by cdo ap2pl.
#
if [[ "$output_atm_cgrid" == "yes" ]]; then
#
cat >> ${atm_namelist} << EOF
&output_nml
output_filename = "${EXPNAME}_atm_cgrid"
filename_format = "<output_filename>_<levtype_l>"
filetype = 5
remap = 0
output_grid = .TRUE.
output_start = "${start_date}" ! output_start = output_end
output_end = "${start_date}" ! --> write once only irrespective of
output_interval = "${atm_output_interval}" ! the output interval and
file_interval = "${atm_file_interval}" ! the file interval
ml_varlist = 'clon', 'clat', 'areacella', 'zghalf', 'zg'
/
EOF
fi
# output atmospheric monitoring
if [[ "$output_atm_mon" == "yes" ]]; then
cat >> ${atm_namelist} << EOF
&output_nml
output_filename = "${EXPNAME}_atm_mon"
filename_format = "<output_filename>_<datetime2>"
filetype = 5 ! output format: 2=GRIB2, 4=NETCDFv2, 5=NETCDFv4
remap = 0
mode = 1 ! 1: forecast mode (relative t-axis), 2: climate mode (absolute t-axis)
operation = 'mean' ! mean over output interval
output_grid = .FALSE.
output_start = "${start_date}"
output_end = "${end_date}"
output_interval = "${atm_output_interval}"
file_interval = "${atm_file_interval}"
include_last = .FALSE.
ml_varlist = 'tas_gmean','rsdt_gmean','rsut_gmean','rlut_gmean','radtop_gmean',
'prec_gmean','evap_gmean','fwfoce_gmean'
/
EOF
fi
# interface debug output
if [[ "$output_atm_dbg" == "yes" ]]; then
cat >> ${atm_namelist} <<EOF
&output_nml
filetype = 5 ! output format: 2=GRIB2, 4=NETCDFv2, 5=NETCDFv4
output_filename = "${EXPNAME}_atm_dbg"
filename_format = "<output_filename>_<levtype_l>_<datetime2>"
remap = 0
operation = 'mean'
output_grid = .TRUE.
output_start = "${start_date}"
output_end = "${end_date}"
output_interval = "${atm_output_interval}"
file_interval = "${atm_file_interval}"
include_last = .FALSE.
ml_varlist = 'orog' , 'ps' ,
'frac_wtr', 'frac_ice', 'frac_lnd', 'alake', 'lake_ice_frc',
'hs_icecl', 'ts_icecl', 'qtop_icecl','qbot_icecl',
'sic' , 'sit' , 'sic_icecl', 'sit_icecl',
'clt' , 'psl' , 'tas' , 'ts' ,
'pr' , 'prw' , 'cllvi' , 'clivi' ,
'prlr' , 'prls' , 'prcr' , 'prcs' ,
'tauu' , 'tauv' , 'albedo' ,
'albedo_wtr', 'albedo_ice', 'albedo_lnd',
'albvisdir','albvisdif' , 'albnirdir' , 'albnirdif',
'albvisdir_ice', 'albvisdir_wtr', 'albvisdir_lnd',
'rvds_dir','rvds_dif','rnds_dir','rnds_dif','rvus','rnus',
'hfls' , 'hfss' , 'evspsbl' ,
'hfls_wtr', 'hfls_ice', 'hfls_lnd',
'hfss_wtr', 'hfss_ice', 'hfss_lnd',
'rsns_wtr', 'rsns_ice', 'rsns_lnd',
'rlns_wtr', 'rlns_ice', 'rlns_lnd',
'rsut' , 'rsutcs' , 'rlut' , 'rlutcs',
'rsds' , 'rsdscs' , 'rlds' , 'rldscs',
'rsus' , 'rsuscs' , 'rlus' , 'rsdt' ,
'evspsbl_wtr', 'evspsbl_ice', 'evspsbl_lnd',
'ts_wtr' , 'ts_ice' , 'ts_lnd' ,
'tauu_wtr', 'tauu_ice', 'tauu_lnd',
'tauv_wtr', 'tauv_ice', 'tauv_lnd',
'sfcwind' , 'uas' , 'vas'
/
EOF
fi
#
# Standard AMIP output...
#
#
if [[ "$output_atm_3d" == "yes" ]]; then
#
cat >> ${atm_namelist} << EOF
&output_nml
output_filename = "${EXPNAME}_atm_3d"
filename_format = "<output_filename>_<levtype_l>_<datetime2>"
filetype = 5
remap = 0
operation = 'mean'
output_grid = .FALSE.
output_start = "${start_date}"
output_end = "${end_date}"
output_interval = "${atm_output_interval}"
file_interval = "${atm_file_interval}"
include_last = .FALSE.
ml_varlist = 'zg' ,
'ps' , 'pfull' ,
'rho' , 'ta' ,
'ua' , 'va' , 'wap' ,
'hus' , 'clw' , 'cli' ,
'hur' , 'cl' ,
! 'qo3_phy' ,
/
EOF
fi
if [[ "$output_atm_2d" == "yes" ]]; then
#
cat >> ${atm_namelist} << EOF
&output_nml
output_filename = "${EXPNAME}_atm_2d"
filename_format = "<output_filename>_<levtype_l>_<datetime2>"
filetype = 5
remap = 0
operation = 'mean'
output_grid = .FALSE.
output_start = "${start_date}"
output_end = "${end_date}"
output_interval = "${atm_output_interval}"
file_interval = "${atm_file_interval}"
include_last = .FALSE.
ml_varlist = 'orog' ,
'ps' , 'psl' ,
'cosmu0' ,
'rsdt' ,
'rsut' , 'rsutcs' , 'rlut' , 'rlutcs' ,
'rsds' , 'rsdscs' , 'rlds' , 'rldscs' ,
'rsus' , 'rsuscs' , 'rlus' ,
'ts' ,
'sic' , 'sit' ,
'albedo' ,
'clt' ,
'prlr' , 'prls' , 'prcr' , 'prcs' ,
'pr' , 'prw' , 'cllvi' , 'clivi' ,
'hfls' , 'hfss' , 'evspsbl' ,
'tauu' , 'tauv' ,
'tauu_sso', 'tauv_sso', 'diss_sso',
'sfcwind' , 'uas' , 'vas' ,
'tas' , 'dew2' ,
'ptp'
/
EOF
fi
if [[ "$output_phy_3d" == "yes" ]]; then
#
cat >> ${atm_namelist} << EOF
&output_nml
output_filename = "${EXPNAME}_phy_3d"
filename_format = "<output_filename>_<levtype_l>_<datetime2>"
filetype = 5
remap = 0
operation = 'mean'
output_grid = .FALSE.
output_start = "${start_date}"
output_end = "${end_date}"
output_interval = "${atm_output_interval}"
file_interval = "${atm_file_interval}"
include_last = .FALSE.
ml_varlist = 'ps' , 'pfull' ,
'tend_ta' , 'tend_ta_dyn' , 'tend_ta_phy' ,
'tend_ta_vdf' , 'tend_ta_gwd' , 'tend_ta_sso' ,
'tend_ta_cnv' , 'tend_ta_cld' ,
'tend_ua' , 'tend_ua_dyn' , 'tend_ua_phy' ,
'tend_ua_vdf' , 'tend_ua_gwd' , 'tend_ua_sso' ,
'tend_ua_cnv' ,
'tend_va' , 'tend_va_dyn' , 'tend_va_phy' ,
'tend_va_vdf' , 'tend_va_gwd' , 'tend_va_sso' ,
'tend_va_cnv' ,
'tend_qhus' , 'tend_qhus_dyn', 'tend_qhus_phy',
'tend_qhus_cld', 'tend_qhus_cnv', 'tend_qhus_vdf'
/
EOF
fi
if [[ "$output_lnd_dbg" == "yes" ]]; then
cat >> ${atm_namelist} << EOF
&output_nml
filetype = 5 ! output format: 2=GRIB2, 4=NETCDFv2, 5=NETCDFv4
output_filename = "${EXPNAME}_lnd_dbg"
filename_format = "<output_filename>_<levtype_l>_<datetime2>"
remap = 0
operation = 'mean'
output_grid = .TRUE.
output_start = "${start_date}"
output_end = "${end_date}"
output_interval = "${lnd_output_interval}"
file_interval = "${lnd_file_interval}"
include_last = .FALSE.
ml_varlist = 'fract_box',
'seb_t_box' , 'seb_qsat_star_box' ,
'rad_alb_vis_box' , 'rad_alb_nir_box' ,
'rad_rad_srf_net_box' , 'rad_lw_srf_net_box' , 'rad_sw_srf_net_box',
'seb_latent_hflx_box' , 'seb_sensible_hflx_box' , 'pheno_lai_box' ,
'hydro_evapotrans_box' , 'hydro_w_soil_column_box',
'hydro_runoff_box' , 'hydro_drainage_box' ,
'hydro_discharge_ocean_box' , 'hydro_discharge_box' ,
/
EOF
# or using - like in exp.esm_R2B3_R2B4
# ml_varlist = 'group:jsb_all_basic','hd_water_error_box','hydro_discharge_ocean_box','hydro_discharge_box'
fi
if [[ "$output_lnd_msk" == "yes" ]]; then
cat >> ${atm_namelist} << EOF
&output_nml
filetype = 5 ! output format: 2=GRIB2, 4=NETCDFv2, 5=NETCDFv4
output_filename = "${EXPNAME}_lnd_msk"
filename_format = "<output_filename>_<levtype_l>_<datetime2>"
remap = 0
!operation = 'mean'
output_grid = .TRUE.
output_start = "${start_date}"
output_end = "${end_date}"
output_interval = "${lnd_output_interval}"
file_interval = "${lnd_file_interval}"
include_last = .FALSE.
ml_varlist = 'group:jsb_tile_fractions'
/
EOF
fi
# minimal jsbach output for running atm_amip experiment
# for more jsbach output see exp.atm_amip_les
#
if [[ "$output_lnd_amip" == "yes" ]]; then
cat >> ${atm_namelist} << EOF
&output_nml
output_filename = "${EXPNAME}_lnd"
filename_format = "<output_filename>_<levtype_l>_<datetime2>"
filetype = 5
remap = 0
operation = 'mean'
output_grid = .TRUE.
output_start = "${start_date}"
output_end = "${end_date}"
output_interval = "${lnd_output_interval}"
file_interval = "${lnd_file_interval}"
include_last = .FALSE.
ml_varlist = 'pheno_lai_box' , 'pheno_fract_fpc_veg' , 'hydro_fract_water_box' ,
'hydro_fract_snow_box' , 'hydro_w_skin_box' , 'hydro_w_snow_box' ,
'hydro_w_soil_column_box'
/
EOF
fi
#-----------------------------------------------------------------------------
# III. OCEAN and SEA-ICE (and HAMOCC)
#-----------------------------------------------------------------------------
ocean_vertical_levels=64
#ocean_grid="icon_grid_${ocean_gridID}_${ocean_refinement}_O.nc" # no land points
#ocean_grid="icon_grid_${ocean_gridID}_${ocean_refinement}_G.nc" # global ocean mask
ocean_data_InputFolder="${icon_data_poolFolder}/${ocean_gridID}"
#ocean_grid_folder="$ocean_data_InputFolder"
ocean_grid_folder="$Setupdir"
ocean_grid="icon_grid_${ocean_gridID}_modsills_${ocean_refinement}_O.nc" # no land points
#-----------------------------------------------------------------------------
#
# ocean namelist
# --------------
cat > ${oce_namelist} << EOF
!
&coupling_mode_nml
coupled_mode = .TRUE.
/
¶llel_nml
nproma = ${nproma_oce}
num_io_procs = ${mpi_oce_io_procs}
num_prefetch_proc = 0
pio_type = 0
p_test_run = .FALSE.
l_fast_sum = .FALSE.
/
&grid_nml
dynamics_grid_filename = "${ocean_grid}"
use_dummy_cell_closure = .TRUE.
use_duplicated_connectivity = .FALSE.
/
&dynamics_nml
iequations = -1 ! -1: hydrost. ocean model
/
&run_nml
modelTimeStep = "${oceTimeStep}"
output = 'nml' ! namelist controlled output scheme
activate_sync_timers = .TRUE.
profiling_output = 1 ! aggregated: 1; detailed: 2; in files: 3
msg_timestamp = .FALSE.
timers_level = 10
debug_check_level = 1
restart_filename = "${EXPNAME}_restart_oce_<rsttime>.nc"
/
EOF
# output of fixed geometry - at start of integration only
fx_date=${start_date:="1510-01-01T00:00:00Z"}
cat >> ${oce_namelist} << EOF
&output_nml
filetype = 5 ! output format: 2=GRIB2, 4=NETCDFv2, 5=NETCDFv4
output_filename = "${EXPNAME}_oce_fx"
filename_format = "<output_filename>_<datetime2>"
output_start = "${fx_date}" ! start date in ISO-format
output_end = "${fx_date}" ! end date in ISO-format
output_interval = "${oce_output_interval}" ! interval in ISO-format
file_interval = "${oce_file_interval}" ! interval in ISO-format
output_grid = .TRUE.
mode = 2 ! 1: forecast mode (relative t-axis); 2: climate mode
include_last = .false.
ml_varlist = 'wet_c','basin_c','regio_c','lsm_ctr_c'
/
EOF
#
if [[ "$output_oce_def" == "yes" ]]; then
#
cat >> ${oce_namelist} << EOF
&output_nml
filetype = 5
output_filename = "${EXPNAME}_oce_def"
filename_format = "<output_filename>_<datetime2>"
output_start = "${start_date}" ! start in ISO-format
output_end = "${end_date}" ! end in ISO-format
output_interval = "${oce_output_interval_def}" ! interval in ISO-format
file_interval = "${oce_file_interval}"
mode = 1 ! 1: forecast mode (relative t-axis)
! 2: climate mode (absolute t-axis)
include_last = .FALSE.
output_grid = .FALSE.
filename_format = "<output_filename>_<datetime2>"
operation = "mean"
ml_varlist = 'group:oce_default'
/
EOF
fi
if [[ "$output_oce_ice" == "yes" ]]; then
cat >> ${oce_namelist} <<EOF
&output_nml
output_start = "${start_date}" ! start date in ISO-format
output_end = "${end_date}" ! end date in ISO-format
output_interval = "${oce_output_interval}" ! interval in ISO-format
file_interval = "${oce_file_interval}" ! interval in ISO-format
mode = 1 ! 1: forecast mode (relative t-axis), 2: climate mode (absolute t-axis)
operation = 'mean' ! mean over output interval
output_grid = .TRUE.
output_filename = "${EXPNAME}_oce_ice"
filename_format = "<output_filename>_<datetime2>"
filetype = 5 ! output format: 2=GRIB2, 4=NETCDFv2, 5=NETCDFv4
m_levels = "1...28" ! upper 500m
ml_varlist = 'mld','condep','draftave','hi','hs','conc','to','so','ice_u','ice_v'
/
EOF
fi
if [[ "$output_oce_mon" == "yes" ]]; then
#
cat >> ${oce_namelist} << EOF
&output_nml
filetype = 4
output_filename = "${EXPNAME}_oce_mon"
filename_format = "<output_filename>_<datetime2>"
output_start = "${start_date}" ! start in ISO-format
output_end = "${end_date}" ! end in ISO-format
output_interval = "${oce_output_interval}"
file_interval = "${oce_file_interval}"
mode = 1 ! 1: forecast mode (relative t-axis)
! 2: climate mode (absolute t-axis)
include_last = .FALSE.
output_grid = .FALSE.
filename_format = "<output_filename>_<datetime2>"
operation = "mean"
ml_varlist = 'group:ocean_monitor'
/
EOF
fi
#
if [[ "$output_oce_moc" == "yes" ]]; then
#
cat >> ${oce_namelist} << EOF
&output_nml
filetype = 5
output_filename = "${EXPNAME}_oce_moc"
filename_format = "<output_filename>_<datetime2>"
output_start = "${start_date}" ! start in ISO-format
output_end = "${end_date}" ! end in ISO-format
output_interval = "${oce_output_interval}"
file_interval = "${oce_file_interval}"
mode = 1 ! 1: forecast mode (relative t-axis)
! 2: climate mode (absolute t-axis)
include_last = .FALSE.
output_grid = .FALSE.
filename_format = "<output_filename>_<datetime2>"
operation = "mean"
ml_varlist = 'group:ocean_moc'
/
EOF
fi
if [[ "$output_oce_dbg" == "yes" ]]; then
cat >> ${oce_namelist} <<EOF
&output_nml
filetype = 5 ! output format: 2=GRIB2, 4=NETCDFv2, 5=NETCDFv4
output_filename = "${EXPNAME}_oce_dbg"
filename_format = "<output_filename>_<datetime2>"
output_start = "${start_date}" ! start date in ISO-format
output_end = "${end_date}" ! end date in ISO-format
output_interval = "${oce_output_interval}" ! interval in ISO-format
file_interval = "${oce_file_interval}" ! interval in ISO-format
output_grid = .TRUE.
mode = 1 ! 1: forecast mode (relative t-axis); 2: climate mode
operation = 'mean' ! mean over output interval
include_last = .false.
m_levels = "1,2" ! surface and subsurface level only
filename_format = "<output_filename>_<datetime2>"
ml_varlist = 'Qtop', 'Qbot','Qbot_slow', 'zHeatOceI','heatOceI','heatOceW','draftave','zUnderIce',
'mld','condep','zos','u_vint','hi','hs','conc','to','so','u',
'HeatFlux_Total','atmos_fluxes_HeatFlux_ShortWave','atmos_fluxes_HeatFlux_LongWave',
'HeatFlux_ShortWave','HeatFlux_LongWave','HeatFlux_Sensible','HeatFlux_Latent',
'FrshFlux_Runoff','FrshFlux_Precipitation','FrshFlux_Evaporation','FrshFlux_SnowFall',
'FrshFlux_TotalOcean','FrshFlux_VolumeIce','totalsnowfall','Wind_Speed_10m',
'atmos_fluxes_stress_x','atmos_fluxes_stress_y',
'atmos_fluxes_stress_xw','atmos_fluxes_stress_yw'
/
EOF
fi
cat >> ${oce_namelist} << EOF
&dbg_index_nml
idbg_mxmn = 0 ! initialize MIN/MAX debug output
idbg_val = 0 ! initialize one cell debug output
idbg_slev = 1 ! initialize start level for debug output
idbg_elev = 2 ! initialize end level for debug output
dbg_lat_in = 30.0 ! latitude location of one cell debug output
dbg_lon_in = -30.0 ! longitude location of one cell debug output
str_mod_tst ='oceanCouplng' ! define modules to print out in debug mode
!str_mod_tst = 'all' ! define modules to print out in debug mode
/
&ocean_dynamics_nml
n_zlev = ${ocean_vertical_levels}
! 64 unevenly spaced levels, updated by Leonidas/Helmuth 201906
dzlev_m(1:64) = 12, 10, 10, 10, 10, 10, 10, 10, 10, 10,
11, 12, 13, 14, 15, 16, 17, 18, 20, 22,
24, 26, 28, 30, 32, 35, 38, 41, 45, 49,
53, 58, 62, 66, 71, 75, 80, 85, 91, 97,
104, 111, 118, 125, 132, 138, 145, 152, 160, 167,
175, 182, 188, 195, 201, 208, 213, 219, 224, 230,
235, 241, 250, 260
l_edge_based = .FALSE. ! edge- or cell-based mimetic discretization
! l_partial_cells = .FALSE. ! partial bottom cells=TRUE: local varying bottom depth
select_solver = 4 ! 1=gmres_oce_old; 2=ocean_restart_gmres, 3=mixed precisison restart
! 4=CG (default) 5=CGJ 6=BiCG 7=GMRES restart (legacy) 8=MINRES
use_absolute_solver_tolerance = .TRUE.
solver_tolerance = 1.0E-10 ! 1e-10 in omip-YVF - 1e-13 necessary?
l_lhs_direct = .TRUE. ! .true.= use lhs implementation directly .false.= matrix scanner (default)
solver_FirstGuess = 2 ! 0=start from zeros 1=last timestep smoothed 2=last timestep (default)
! solver_tolerance = 7.5E-14 ! old value
! solver_max_iter_per_restart = 19 ! old value
! solver_max_restart_iterations = 100 ! outer (restart solver)
fast_performance_level = 200 ! performance level 12: for cell-based; 5: default
use_continuity_correction = .TRUE. ! height adjustment according to vertical velocity in dynamics
cfl_check = .FALSE.
cfl_write = .FALSE.
i_bc_veloc_top = 1
i_bc_veloc_bot = 1 ! 0: (def) bottom friction off, 1: on
/
&ocean_tracer_transport_nml
flux_calculation_horz = 5 ! 1=upwind, 2=central, 3=Lax-Friedrichs,
! 4=Miura, 5=FCT with Zalesak limiter (default)
flux_calculation_vert = 7 ! 6=adpo; 7=upwind biased ppm (default); 8=FCT with zalesak limiter
! define low and high order methods to be used in
! horizontal flux corrected transport methods
! (flux_calculation_horz=4,5)
fct_low_order_flux = 1 ! horizontal low order method: 1=upwind (def), no other implemented
fct_high_order_flux = 5 ! horizontal high order method: 1=upwind, 2=central, 3=lax_friedrichs, 4=miura_order1
fct_limiter_horz = 100 ! zalesak
/
&ocean_horizontal_diffusion_nml
laplacian_form = 1 ! 1=curlcurl-graddiv
VelocityDiffusion_order = 2 ! 1=laplacian (def); 2=biharmonic; 21=biharmonic+laplacian (for the laplacian leith)
!
BiharmonicViscosity_scaling = 1
BiharmonicViscosity_reference = 3.5E12 ! enhanced value (old: 1e12, def: 0)
BiharmonicViscosity_background = 0.0 ! [m2/s] constant horizontal viscosity coefficient for velocity
HarmonicViscosity_scaling = 1
HarmonicViscosity_reference = 0.0 ! [m2/s] constant horizontal viscosity coefficient for velocity
HarmonicViscosity_background = 0.0
TracerHorizontalDiffusion_scaling = 1
Temperature_HorizontalDiffusion_Background = 0.0
Temperature_HorizontalDiffusion_Reference = 0
Salinity_HorizontalDiffusion_Background = 0.0
Salinity_HorizontalDiffusion_Reference = 0
/
&ocean_vertical_diffusion_nml
vert_mix_type = 2 ! 1: PP; 2: TKE
PPscheme_type = 0 ! 4: current PPscheme - 0: switched off
velocity_VerticalDiffusion_background = 5.0E-5 ! [m2/s] vertical background viscosity coefficient for velocity
temperature_VerticalDiffusion_background = 1.0E-5 ! [m2/s] vertical background diffusion coefficient for temperature
salinity_VerticalDiffusion_background = 1.0E-5 ! [m2/s] vertical background diffusion coefficient for salinity
tracer_convection_MixingCoefficient = 0.1 ! max vertical tracer diffusion for convection used in case of instability
convection_InstabilityThreshold = -1.0E-6 ! used in update_ho_params - default=-5e-8
richardsonDiffusion_threshold = 0.0 ! used in update_ho_params - default=+5e-8
tracer_RichardsonCoeff = 2.0E-3 ! factor for vertical diffusion coefficient in PP scheme
velocity_RichardsonCoeff = 2.0E-3 ! factor for vertical viscosity coefficient in PP scheme
bottom_drag_coeff = 3.0E-3 ! default=2.5E-3; active for i_bc_veloc_bot=1
use_wind_mixing = .TRUE. ! TRUE: use wind mixing scheme in MPIOM-type pp-scheme
lambda_wind = 0.03
! tracer_TopWindMixing = 1.0E-5
! velocity_TopWindMixing = 1.0E-5
tracer_TopWindMixing = 2.31480E-6 ! eqals 0.5e-3 m2s-1 (MPIOM)
velocity_TopWindMixing = 2.31480E-6
! cvmix/tke parameters
c_k = 0.1
c_eps = 0.7
alpha_tke = 30.0
mxl_min = 1.d-8
kappaM_min = 0.0
kappaM_max = 100.0
cd = 3.75
tke_min = 1.d-6
tke_mxl_choice = 2
tke_surf_min = 1.d-4
only_tke = .true.
use_ubound_dirichlet = .false.
use_lbound_dirichlet = .false.
/
&ocean_GentMcWilliamsRedi_nml
GMRedi_configuration = 1 ! 0=cartesian diffusion; 1=GM-Redi: bolus advection + isopycnal diffusion
tapering_scheme = 1
GMRedi_usesRelativeMaxSlopes = .FALSE.
S_max = 1.0e-3 ! 1.0
S_d = 1.0e-4 ! 5e-3 to 5e-4
!
k_tracer_GM_kappa_parameter = 400.0 !
k_tracer_isoneutral_parameter = 400.0 ! value for cell-based cartesian diffusion - mpiom: 1000/400km = 400/160km
k_tracer_dianeutral_parameter = 0.0 ! 1.0E-5 !
!
switch_off_diagonal_vert_expl = .TRUE.
gmredi_combined_diagnostic = .FALSE.
! switch_on_redi_balance_diagnostic = .FALSE. ! not yet available in icon-aes-dyamond++
revert_vertical_recon_and_transposed = .TRUE.
slope_calc_via_temperture_salinity = .TRUE.
include_slope_squared_implicit = .TRUE. ! think of l_with_vert_tracer_diffusion
switch_on_tapering_horizontal_diffusion = .TRUE.
/
&ocean_physics_nml
i_sea_ice = 1 ! 0 = no sea ice; 1 = sea ice model on; default=1
/
&sea_ice_nml
i_ice_therm = 1 ! 1=zero-layer (default), 2=Winton, 0/2: not allowed
i_ice_dyn = 1 ! 1/0=switch on/off AWI ice dynamics
! i_Qio_type = 3 ! 3 (default): energy of whole grid-area used for melting (MPIOM-type)
albedoW_sim = 0.10 ! albedo of the ocean used in sea ice model
leadclose_1 = 0.5 ! default: 0.5 - value of MPIOM: 0.25
leadclose_2n = 0.666 ! default: 0.0 - value of MPIOM: 2/3
!pstar = 40000. ! default: 27500.; MPIOM=20000.
therm_conduct_snow = 0.7 ! default: ks=0.31
!therm_conduct_ice = 2.4 ! default: ki=2.1656
!therm_emiss = 0.97 ! default: zemiss_def=0.996
/
&ocean_forcing_nml
iforc_oce = 14 ! ocean forcing: 14 from coupling via YAC
type_surfRelax_Temp = -1 ! -1: use net surface heat flux from atmosphere
! 0: no relaxation used
! 1: relaxation switched on for reading (init_oce_relax=1)
! or some testcases only
forcing_enable_freshwater = .TRUE. ! enable/disable freshwater flux
forcing_windstress_u_type = 2 ! 0: zero wind stress, 1: read from file, 2: none
forcing_windstress_v_type = 2 ! 0: zero wind stress, 1: read from file, 2: none
! salt-change due to internal fluxes only
limit_seaice = .TRUE. ! default: TRUE
seaice_limit = 0.8 ! hard limit set to 80% of upper layer for sea ice
limit_elevation = .FALSE. ! true: adjust daily to zero, default=false: free surface
lswr_jerlov = .TRUE. ! use jerlov water types for sw absorption (default=T)
jerlov_atten = 0.08 ! jerlov water type IB
jerlov_bluefrac = 0.36 ! jerlov water type IB
! parameters for salt content conservation
lfix_salt_content = .true. ! fix global ocean+ice salt content to constant (def=F)
!surface_flux_type = 1 ! 1: apply_surface_fluxes_slo (def), 2: apply_surface_fluxes (Vladimir L.)
!lcheck_salt_content = .false. ! diagnostic output of salt content (def=F)
!limit_seaice = .true. ! use seaice limiter
!limit_seaice_type = 1 ! 1: ice_thickness_limiter (def), 2: ice_thickness_limiter_hh (H. Haak)
/
EOF
#
if [[ "$initialiseOcean" == "fromRestart" ]]; then
#
cat >> ${oce_namelist} << EOF
&ocean_initialConditions_nml
initial_salinity_type = 0 ! 0: none, 1: read S from initial_state.nc
initial_temperature_type = 0 ! 0: none, 1: read T from initial_state.nc
initialize_fromRestart = .TRUE.
/
EOF
#
else
#
if [[ "$initialiseOcean" == "fromClimatology" ]]; then
cat >> ${oce_namelist} << EOF
&ocean_initialConditions_nml
initial_salinity_type = 1 ! 0: none, 1: read S from initial_state.nc
initial_temperature_type = 1 ! 0: none, 1: read T from initial_state.nc
initialize_fromRestart = .FALSE.
/
EOF
else
cat >> ${oce_namelist} << EOF
&ocean_initialConditions_nml
initial_salinity_type = 0 ! 0: none, 1: read S from initial_state.nc
initial_temperature_type = 0 ! 0: none, 1: read T from initial_state.nc
initialize_fromRestart = .FALSE.
/
EOF
fi
fi
#
cat >> ${oce_namelist} << EOF
&ocean_diagnostics_nml
diagnostics_level = 1
diagnose_for_horizontalVelocity = .FALSE.
diagnose_for_heat_content = .TRUE. ! T: add heat content to monitoring
/
&io_nml
restart_file_type = 5
write_last_restart = .TRUE.
! restart_write_mode = "joint procs multifile" ! not yet available in ocean model
! lnetcdf_flt64_output = .TRUE. ! 64 bit output in all files
lkeep_in_sync = .TRUE. ! sync after each timestep
/
EOF
add_required_file ${basedir}/run/${oce_namelist} ./
#-----------------------------------------------------------------------------
#
# Ocean initialisation input
#
if [[ "$initialiseOcean" == "fromRestart" ]]; then
# initialise atmosphere and use link to ocean restart:
# link to OMIP-spinup 19346-PCA by Helmuth used for ocean restart-file - second OMIP
#add_link_file /pool/data/ICON/grids/private/Stephan/mpim/${ocean_gridID}/ocean/restart/ocean_omip_long_tke_r2b6_19346-PCA_restart_oce_21010101T000000Z.nc init-restart-oce.nc
# here: jkr0042-1500y
#add_link_file /work/mh0287/users/juergen/icon-oes/experiments/jkr0042/jkr0042_restart_oce_15000101T000000Z.nc init-restart-oce.nc
# general restart file
add_link_file ${restart_dir}/${restart_exp}/${restart_exp}_restart_oce_${restart_yea}0101T000000Z.nc init-restart-oce.nc
#OMIPrestartfile=restart-omipCIQ_2200y.nc
#add_link_file $Setupdir/$OMIPrestartfile init-restart-oce.nc
#add_link_file init-restart-oce.nc restart_ocean_DOM01.nc
fi
#
if [[ "$initialiseOcean" == "fromClimatology" ]]; then
add_link_file ${ocean_data_InputFolder}/initial_condition/r0001/ts_phc3.0_annual_icon_grid_0014_R02B04_O_L40.nc initial_state.nc
fi
# Ocean grid
#
#add_required_file ${ocean_grid_folder}/${ocean_grid} ./
add_link_file ${ocean_grid_folder}/${ocean_grid} $ocean_grid
#
#-----------------------------------------------------------------------------
if [ $mpi_total_procs -lt `expr $mpi_oce_procs + 1` ] ; then
echo "Too few mpi_total_procs for requested mpi_oce_procs."
echo "-> check mpi_total_procs and mpi_oce_procs. Exiting."
check_error 0
exit
fi
#-----------------------------------------------------------------------------
#!/bin/ksh
#=============================================================================
#
# This section of the run script prepares and starts the model integration.
#
# MODEL and START must be defined as environment variables or
# they must be substituted with appropriate values.
#
# Marco Giorgetta, MPI-M, 2010-04-21
#
#-----------------------------------------------------------------------------
final_status_file=${basedir}/run/${job_name}.final_status
rm -f ${final_status_file}
#-----------------------------------------------------------------------------
#
# directories definition
#
RUNSCRIPTDIR=${basedir}/run
if [ x$grids_folder = x ] ; then
HGRIDDIR=${basedir}/grids
else
HGRIDDIR=$grids_folder
fi
# experiment directory, with plenty of space, create if new
EXPDIR=${basedir}/experiments/${EXPNAME}
if [ ! -d ${EXPDIR} ] ; then
mkdir -p ${EXPDIR}
fi
#
ls -ld ${EXPDIR}
if [ ! -d ${EXPDIR} ] ; then
mkdir ${EXPDIR}
#else
# rm -rf ${EXPDIR}
# mkdir ${EXPDIR}
fi
ls -ld ${EXPDIR}
check_error $? "${EXPDIR} does not exist?"
cd ${EXPDIR}
#-----------------------------------------------------------------------------
final_status_file=${RUNSCRIPTDIR}/${job_name}.final_status
rm -f ${final_status_file}
#-----------------------------------------------------------------------------
# set up the model lists if they do not exist
# this works for single model runs
# for coupled runs the lists should be declared explicilty
if [ x$namelist_list = x ]; then
# minrank_list=( 0 )
# maxrank_list=( 65535 )
# incrank_list=( 1 )
minrank_list[0]=0
maxrank_list[0]=65535
incrank_list[0]=1
if [ x$atmo_namelist != x ]; then
# this is the atmo model
namelist_list[0]="$atmo_namelist"
modelname_list[0]="atmo"
modeltype_list[0]=1
run_atmo="true"
elif [ x$ocean_namelist != x ]; then
# this is the ocean model
namelist_list[0]="$ocean_namelist"
modelname_list[0]="oce"
modeltype_list[0]=2
elif [ x$psrad_namelist != x ]; then
# this is the psrad model
namelist_list[0]="$psrad_namelist"
modelname_list[0]="psrad"
modeltype_list[0]=3
elif [ x$hamocc_namelist != x ]; then
# this is the hamocc model
namelist_list[0]="$hamocc_namelist"
modelname_list[0]="hamocc"
modeltype_list[0]=4
elif [ x$testbed_namelist != x ]; then
# this is the testbed model
namelist_list[0]="$testbed_namelist"
modelname_list[0]="testbed"
modeltype_list[0]=99
else
check_error 1 "No namelist is defined"
fi
fi
#-----------------------------------------------------------------------------
#-----------------------------------------------------------------------------
# set some default values and derive some run parameteres
restart=${restart:=".false."}
restartSemaphoreFilename='isRestartRun.sem'
#AUTOMATIC_RESTART_SETUP:
if [ -f ${restartSemaphoreFilename} ]; then
restart=.true.
# do not delete switch-file, to enable restart after unintended abort
#[[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename}
else
if [[ "$initialiseOcean" == "FALSE" ]]; then
#echo "nothing to do?"
#restart_dir=/work/mh0033/m300466/icon-ruby/icon-ruby0/experiments
#restart_dir=/work/mh0287/users/stephan/Icon/Git_repos/icon.oes.20191216/experiments
#restart_dir=/work/mh0469/m211032/Icon/Git_Icon/icon.oes.20200506/experiments
#restart_dir=/work/mh0287/m211032/Icon/Git_Icon/icon.oes.20200506/experiments
#restart_dir=".."
add_link_file ${restart_dir}/${restart_exp}/${restart_exp}_restart_atm_${restart_yea}0101T000000Z.nc init-restart-atm.nc
add_link_file ${restart_dir}/${restart_exp}/${restart_exp}_restart_oce_${restart_yea}0101T000000Z.nc init-restart-oce.nc
add_link_file init-restart-atm.nc restart_atm_DOM01.nc
add_link_file init-restart-oce.nc restart_ocean_DOM01.nc
fi
fi
#END AUTOMATIC_RESTART_SETUP
#
# wait 5min to let GPFS finish the write operations
if [ "x$restart" != 'x.false.' -a "x$submit" != 'x' ]; then
if [ x$(df -T ${EXPDIR} | cut -d ' ' -f 2) = gpfs ]; then
sleep 10;
fi
fi
# fill some checks
run_atmo=${run_atmo="false"}
if [ x$atmo_namelist != x ]; then
run_atmo="true"
fi
run_jsbach=${run_jsbach="false"}
run_ocean=${run_ocean="false"}
if [ x$ocean_namelist != x ]; then
run_ocean="true"
fi
run_psrad=${run_psrad="false"}
if [ x$psrad_namelist != x ]; then
run_psrad="true"
fi
run_hamocc=${run_hamocc="false"}
if [ x$hamocc_namelist != x ]; then
run_hamocc="true"
fi
#-----------------------------------------------------------------------------
# add grids to required files
all_grids="${atmo_dyn_grids} ${atmo_rad_grids} ${ocean_grids}"
for gridfile in ${all_grids}; do
#
gridfile=${gridfile//\'/} # strip all ' in case ' is used to delimit the grid names
gridfile=${gridfile//\"/} # strip all " in case " is used to delimit the grid names
gridfile=${gridfile//\,/} # strip all , in case , is used to separate the grid names
#
grfinfofile=${gridfile%.nc}-grfinfo.nc
#
ls -l ${HGRIDDIR}/$gridfile
check_error $? "${HGRIDDIR}/$gridfile does not exist."
add_link_file ${HGRIDDIR}/${gridfile} ./
if [ -f ${HGRIDDIR}/${grfinfofile} ]; then
add_link_file ${HGRIDDIR}/${grfinfofile} ./
fi
done
#-----------------------------------------------------------------------------
# print_required_files
copy_required_files
link_required_files
#-----------------------------------------------------------------------------
# get restart files
if [ x$restart_atmo_from != "x" ] ; then
rm -f restart_atm_DOM01.nc
# ln -s ${basedir}/experiments/${restart_from_folder}/${restart_atmo_from} ${EXPDIR}/restart_atm_DOM01.nc
cp ${basedir}/experiments/${restart_from_folder}/${restart_atmo_from} cp_restart_atm.nc
ln -s cp_restart_atm.nc restart_atm_DOM01.nc
restart=".true."
fi
if [ x$restart_ocean_from != "x" ] ; then
rm -f restart_oce.nc
# ln -s ${basedir}/experiments/${restart_from_folder}/${restart_ocean_from} ${EXPDIR}/restart_oce.nc
cp ${basedir}/experiments/${restart_from_folder}/${restart_ocean_from} cp_restart_oce_DOM01.nc
ln -s cp_restart_oce_DOM01.nc restart_oce_DOM01.nc
restart=".true."
fi
#-----------------------------------------------------------------------------
read_restart_namelists=${read_restart_namelists:=".true."}
#-----------------------------------------------------------------------------
#
# create ICON master namelist
# ------------------------
# For a complete list see Namelist_overview and Namelist_overview.pdf
#-----------------------------------------------------------------------------
# create master_namelist
master_namelist=icon_master.namelist
if [ x$end_date = x ]; then
cat > $master_namelist << EOF
&master_nml
lrestart = $restart
/
&master_time_control_nml
experimentStartDate = "$start_date"
restartTimeIntval = "$restart_interval"
checkpointTimeIntval = "$checkpoint_interval"
/
&time_nml
is_relative_time = .false.
/
EOF
else
if [ x$calendar = x ]; then
calendar='proleptic gregorian'
calendar_type=1
else
calendar=$calendar
calendar_type=$calendar_type
fi
cat > $master_namelist << EOF
&master_nml
lrestart = $restart
read_restart_namelists = $read_restart_namelists
/
&master_time_control_nml
calendar = "$calendar"
checkpointTimeIntval = "$checkpoint_interval"
restartTimeIntval = "$restart_interval"
experimentStartDate = "$start_date"
experimentStopDate = "$end_date"
/
&time_nml
is_relative_time = .false.
/
EOF
fi
#-----------------------------------------------------------------------------
#-----------------------------------------------------------------------------
# add model component to master_namelist
add_component_to_master_namelist()
{
model_namelist_filename="$1"
model_name=$2
model_type=$3
model_min_rank=$4
model_max_rank=$5
model_inc_rank=$6
cat >> $master_namelist << EOF
&master_model_nml
model_name="$model_name"
model_namelist_filename="$model_namelist_filename"
model_type=$model_type
model_min_rank=$model_min_rank
model_max_rank=$model_max_rank
model_inc_rank=$model_inc_rank
/
EOF
#-----------
#get namelist
if [ -f ${RUNSCRIPTDIR}/$model_namelist_filename ] ; then
mv -f ${RUNSCRIPTDIR}/$model_namelist_filename ${EXPDIR}
check_error $? "mv -f ${RUNSCRIPTDIR}/$model_namelist_filename"
else
check_error 1 "${RUNSCRIPTDIR}/$model_namelist_filename does not exist"
fi
}
#-----------------------------------------------------------------------------
no_of_models=${#namelist_list[*]}
echo "no_of_models=$no_of_models"
j=0
while [ $j -lt ${no_of_models} ]
do
add_component_to_master_namelist "${namelist_list[$j]}" "${modelname_list[$j]}" ${modeltype_list[$j]} ${minrank_list[$j]} ${maxrank_list[$j]} ${incrank_list[$j]}
j=`expr ${j} + 1`
done
#-----------------------------------------------------------------------------
# Add JSBACH part to master_namelist
if [[ $run_jsbach == @(yes|true) ]]; then
cat >> $master_namelist << EOF
&jsb_control_nml
is_standalone = .false.
restart_jsbach = .false.
debug_level = 0
timer_level = 0
/
EOF
#
if [[ -n ${atmo_dyn_grids} ]]; then
set -A gridfiles $atmo_dyn_grids
no_of_domains=${#gridfiles[*]}
else
no_of_domains=1
fi
echo "no_of_domains=$no_of_domains"
domain=""
domain_suffix=""
j=1
while [ $j -le ${no_of_domains} ]
do
if [[ $no_of_domains -gt 1 ]]; then
# no_of_domains < 10 !
domain=" DOM0${j}"
domain_suffix="_d${j}"
fi
cat >> $master_namelist << EOF
&jsb_model_nml
model_id = $j
model_name = "JSBACH${domain}"
model_shortname = "jsb${domain_suffix}"
model_description = 'JSBACH land surface model'
model_namelist_filename = "${lnd_namelist}${domain_suffix}"
/
EOF
if [[ -f ${RUNSCRIPTDIR}/NAMELIST_${EXPNAME}_lnd${domain_suffix} && -f ${EXPDIR}/NAMELIST_${EXPNAME}_lnd${domain_suffix} ]] ; then
# namelist file has already been copied to expdir by copy_required_files above
rm ${RUNSCRIPTDIR}/NAMELIST_${EXPNAME}_lnd${domain_suffix}
check_error $? "rm ${RUNSCRIPTDIR}/NAMELIST_${EXPNAME}_lnd${domain_suffix}"
else
check_error 1 "${RUNSCRIPTDIR}/NAMELIST_${EXPNAME}_lnd${domain_suffix} does not exist"
fi
j=`expr ${j} + 1`
done
fi
#
# get model
#
ls -l ${MODEL}
check_error $? "${MODEL} does not exist?"
#
ldd -v ${MODEL}
#
#-----------------------------------------------------------------------------
#
# start experiment
#
rm -f finish.status
#
date
${START} ${MODEL} # > out.txt 2>&1
date
#
if [ -r finish.status ] ; then
check_final_status 0 "${START} ${MODEL}"
else
check_final_status -1 "${START} ${MODEL}"
fi
#
#-----------------------------------------------------------------------------
#
finish_status=`cat finish.status`
echo $finish_status
echo "============================"
echo "Script run successfully: $finish_status"
echo "============================"
#-----------------------------------------------------------------------------
# rm output_schedule_steps*
#-----------------------------------------------------------------------------
if [[ "x$use_hamocc" = "xyes" ]]; then
# store HAMOCC log file
strg="$(ls -rt ${EXPNAME}_hamocc_EU*.nc* | tail -1 )"
prefx="${EXPNAME}_hamocc_EU_tendencies"
foo=${strg##${prefx}}
foo=${foo%%.*}
bgcout_file="bgcout_${foo}"
mv bgcout $bgcout_file
fi
#-----------------------------------------------------------------------------
namelist_list=""
#-----------------------------------------------------------------------------
# check if we have to restart, ie resubmit
# Note: this is a different mechanism from checking the restart
if [ $finish_status = "RESTART" ] ; then
echo "restart next experiment..."
this_script="${RUNSCRIPTDIR}/${job_name}"
echo 'this_script: ' "$this_script"
touch ${restartSemaphoreFilename}
cd ${RUNSCRIPTDIR}
${submit} $this_script $run_param_0
else
[[ -f ${restartSemaphoreFilename} ]] && rm ${restartSemaphoreFilename}
fi
#-----------------------------------------------------------------------------
# automatic call/submission of post processing if available
if [ "x${autoPostProcessing}" = "xtrue" ]; then
# check if there is a postprocessing is available
cd ${RUNSCRIPTDIR}
targetPostProcessingScript="./post.${EXPNAME}.run"
[[ -x $targetPostProcessingScript ]] && ${submit} ${targetPostProcessingScript}
cd -
fi
#-----------------------------------------------------------------------------
cd $RUNSCRIPTDIR
#-----------------------------------------------------------------------------
# exit 0
#
# vim:ft=sh
#-----------------------------------------------------------------------------