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namelists for 4 test cases + calc diss for benthos
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ogurses committed Jul 13, 2023
1 parent ba0c03d commit 39660ed
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63 changes: 63 additions & 0 deletions config/case_2p1z1d/job_albedo
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#!/bin/bash
#SBATCH --job-name=test_3zoo_ballast
#SBATCH --account=nwg_hauck.maresys
#SBATCH --partition=mpp
#SBATCH -N 9
#SBATCH --cpus-per-task=1
#SBATCH --time=08:00:00
#SBATCH --qos=12h
#SBATCH --tasks-per-node 96 # using all 128CPus we exceed the maxload limit (>130) of many used nodes when us parallel I/O

#SBATCH -o slurm-out.out
#SBATCH -e slurm-err.out
#SBATCH [email protected]
#SBATCH --mail-type=END

# disable hyperthreading
#SBATCH --hint=nomultithread

module purge
source ../env/albedo/shell
export OMP_NUM_THREADS=1
ulimit -s unlimited


# determine JOBID
JOBID=`echo $SLURM_JOB_ID |cut -d"." -f1`

ln -s ../bin/fesom.x . # cp -n ../bin/fesom.x
#cp -n ../../config/namelist.config .
#cp -n ../../config/namelist.forcing .
#cp -n ../../config/namelist.oce .
#cp -n ../../config/namelist.ice .
#cp -n ../../config/namelist.io .
#cp -n ../../config/namelist.icepack .

#___DETERMINE SLURM JOBID+OUTPUTFILE____________________________________________
jobid=$(echo $SLURM_JOB_ID | cut -d"." -f1)
fname="fesom2.0.out"

date
srun --mpi=pmi2 ./fesom.x > fesom2.0.out #${fname}
date

#qstat -f $PBS_JOBID
#export EXITSTATUS=$?
#if [ ${EXITSTATUS} -eq 0 ] || [ ${EXITSTATUS} -eq 127 ] ; then
#sbatch job_albedo
#fi

Resultpath='/albedo/scratch/user/ogurses/test_14.06.2023/'
test -e $Resultpath/fesom.1970.oce.restart.nc && exit

IsInFile=$( tail -1 fesom2.0.out | grep -c should)
if (( IsInFile > 0 )); then
# submit next #job \
echo "submitting next job"
cp fesom2.0.out fesom.out.done
sbatch job_albedo
else
echo "something is wrong, last line of fesom.out reads"
echo $( tail -1 fesom2.0.out)
echo "abnormal termination of job script"
fi
63 changes: 63 additions & 0 deletions config/case_2p1z1d/namelist.config
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! This is the namelist file for model general configuration

&modelname
runid='fesom'
/

&timestep
step_per_day=32 !96 !96 !72 !72 !45 !72 !96
run_length= 1 !62 !62 !62 !28
run_length_unit='y' ! y, m, d, s
/

&clockinit ! the model starts at
timenew=0.0
daynew=1
yearnew=1958
/

&paths
MeshPath='/albedo/work/projects/p_recompdaf/frbunsen/FESOM2/meshes/core2/'
ClimateDataPath='/albedo/work/projects/MarESys/ogurses/input/corrected_input/'
ResultPath='/albedo/scratch/user/ogurses/test_14.06.2023/'
/

&restart_log
restart_length=1 !only required for d,h,s cases, y, m take 1
restart_length_unit='y' !output period: y, d, h, s
logfile_outfreq=960 !in logfile info. output frequency, # steps
/

&ale_def
which_ALE='zstar' ! 'linfs','zlevel', 'zstar'
use_partial_cell=.true.
/

&geometry
cartesian=.false.
fplane=.false.
cyclic_length=360 ![degree]
rotated_grid=.true. !option only valid for coupled model case now
force_rotation=.true.
alphaEuler=50. ![degree] Euler angles, convention:
betaEuler=15. ![degree] first around z, then around new x,
gammaEuler=-90. ![degree] then around new z.
/

&calendar
include_fleapyear=.false.
/

&run_config
use_ice=.true. ! ocean+ice
use_cavity=.false. !
use_cavity_partial_cell=.false.
use_floatice = .false.
use_sw_pene=.true.
num_fesom_groups = 1
/

&machine
n_levels=2
n_part= 12, 36 ! 432 number of partitions on each hierarchy level
/
63 changes: 63 additions & 0 deletions config/case_2p1z1d/namelist.forcing
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! This is the namelist file for forcing

&forcing_exchange_coeff
Ce_atm_oce=0.00175 ! exchange coeff. of latent heat over open water
Ch_atm_oce=0.00175 ! exchange coeff. of sensible heat over open water
Cd_atm_oce=0.001 ! drag coefficient between atmosphere and water
Ce_atm_ice=0.00175 ! exchange coeff. of latent heat over ice
Ch_atm_ice=0.00175 ! exchange coeff. of sensible heat over ice
Cd_atm_ice=0.0012 ! drag coefficient between atmosphere and ice
Swind =0.0 ! parameterization for coupled current feedback
/

&forcing_bulk
AOMIP_drag_coeff=.false.
ncar_bulk_formulae=.true.
ncar_bulk_z_wind=10.0 ! height at which wind forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m)
ncar_bulk_z_tair=10.0 ! height at which temp forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m)
ncar_bulk_z_shum=10.0 ! height at which humi forcing is located (CORE, JRA-do: 10m, JRA, NCEP:2m)

/

&land_ice
use_landice_water=.false.
landice_start_mon=5
landice_end_mon=10
/

&nam_sbc
nm_xwind_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/uas.clim61' ! name of file with winds, if nm_sbc=2
nm_ywind_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/vas.clim61' ! name of file with winds, if nm_sbc=2
nm_humi_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/huss.clim61' ! name of file with humidity
nm_qsr_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/rsds.clim61' ! name of file with solar heat
nm_qlw_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/rlds.clim61' ! name of file with Long wave
nm_tair_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/tas.clim61' ! name of file with 2m air temperature
nm_prec_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/prra.clim61' ! name of file with total precipitation
nm_snow_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/prsn.clim61' ! name of file with snow precipitation
nm_mslp_file = '/albedo/work/projects/MarESys/FROM-OLLIE/forcing_JRA55-do-v1.4.0_clim61/psl.clim61' ! air_pressure_at_sea_level
nm_xwind_var = 'uas' ! name of variable in file with wind
nm_ywind_var = 'vas' ! name of variable in file with wind
nm_humi_var = 'huss' ! name of variable in file with humidity
nm_qsr_var = 'rsds' ! name of variable in file with solar heat
nm_qlw_var = 'rlds' ! name of variable in file with Long wave
nm_tair_var = 'tas' ! name of variable in file with 2m air temperature
nm_prec_var = 'prra' ! name of variable in file with total precipitation
nm_snow_var = 'prsn' ! name of variable in file with total precipitation
nm_mslp_var = 'psl' ! name of variable in file with air_pressure_at_sea_level
nm_nc_iyear = 1900
nm_nc_imm = 1 ! initial month of time axis in netCDF
nm_nc_idd = 1 ! initial day of time axis in netCDF
nm_nc_freq = 1 ! data points per day (i.e. 86400 if the time axis is in seconds)
nm_nc_tmid = 0 ! 1 if the time stamps are given at the mid points of the netcdf file, 0 otherwise (i.e. 1 in CORE1, CORE2; 0 in JRA55)
y_perpetual=.true.
l_xwind=.true. l_ywind=.true. l_humi=.true. l_qsr=.true. l_qlw=.true. l_tair=.true. l_prec=.true. l_mslp=.true. l_cloud=.false. l_snow=.true.
!nm_runoff_file ='/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/CORE2_runoff.nc'
nm_runoff_file ='/albedo/pool/FESOM/forcing/CORE2/runoff.nc'
runoff_data_source ='CORE2' !Dai09, CORE2
!nm_runoff_file ='/work/ollie/qwang/FESOM2_input/mesh/CORE2_finaltopo_mean/forcing_data_on_grid/runoff_clim.nc'
!runoff_data_source ='Dai09' !Dai09, CORE2, JRA55
!runoff_climatology =.true.
!nm_sss_data_file ='/work/ollie/clidyn/forcing/JRA55-do-v1.4.0/PHC2_salx.nc'
nm_sss_data_file ='/albedo/pool/FESOM/forcing/CORE2/PHC2_salx.nc'
sss_data_source ='CORE2'
/
31 changes: 31 additions & 0 deletions config/case_2p1z1d/namelist.ice
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! Ice namelist
&ice_dyn
whichEVP=0 ! 0=standart; 1=mEVP; 2=aEVP
Pstar=30000.0 ! [N/m^2]
ellipse=2.0
c_pressure=20.0 ! ice concentration parameter used in ice strength computation
delta_min=1.0e-11 ! [s^(-1)]
evp_rheol_steps=120 ! number of EVP subcycles
alpha_evp=250 ! constant that control numerical stability of mEVP. Adjust with resolution.
beta_evp=250 ! constant that control numerical stability of mEVP. Adjust with resolution.
c_aevp=0.15 ! a tuning constant in aEVP. Adjust with resolution.
Cd_oce_ice=0.0055 ! drag coef. oce - ice
ice_gamma_fct=0.5 ! smoothing parameter
ice_diff=0.0 ! diffusion to stabilize
theta_io=0.0 ! rotation angle
ice_ave_steps=1 ! ice step=ice_ave_steps*oce_step
/

&ice_therm
Sice=4.0 ! Ice salinity 3.2--5.0 ppt.
h0=.5 ! Lead closing parameter [m]
emiss_ice=0.97 ! Emissivity of Snow/Ice,
emiss_wat=0.97 ! Emissivity of open water
albsn=0.81 ! Albedo: frozen snow
albsnm=0.77 ! melting snow
albi=0.7 ! frozen ice
albim=0.68 ! melting ice
albw=0.1 ! open water
con=2.1656 ! Thermal conductivities: ice; W/m/K
consn=0.31 ! snow
/
146 changes: 146 additions & 0 deletions config/case_2p1z1d/namelist.icepack
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&env_nml ! In the original release these variables are defined in the icepack.settings
nicecat = 5 ! number of ice thickness categories
nfsdcat = 1 ! number of floe size categories
nicelyr = 4 ! number of vertical layers in the ice
nsnwlyr = 4 ! number of vertical layers in the snow
ntraero = 0 ! number of aerosol tracers (up to max_aero in ice_domain_size.F90)
trzaero = 0 ! number of z aerosol tracers (up to max_aero = 6)
tralg = 0 ! number of algal tracers (up to max_algae = 3)
trdoc = 0 ! number of dissolve organic carbon (up to max_doc = 3)
trdic = 0 ! number of dissolve inorganic carbon (up to max_dic = 1)
trdon = 0 ! number of dissolve organic nitrogen (up to max_don = 1)
trfed = 0 ! number of dissolved iron tracers (up to max_fe = 2)
trfep = 0 ! number of particulate iron tracers (up to max_fe = 2)
nbgclyr = 0 ! number of zbgc layers
trbgcz = 0 ! set to 1 for zbgc tracers (needs TRBGCS = 0 and TRBRI = 1)
trzs = 0 ! set to 1 for zsalinity tracer (needs TRBRI = 1)
trbri = 0 ! set to 1 for brine height tracer
trage = 0 ! set to 1 for ice age tracer
trfy = 0 ! set to 1 for first-year ice area tracer
trlvl = 0 ! set to 1 for level and deformed ice tracers
trpnd = 0 ! set to 1 for melt pond tracers
trbgcs = 0 ! set to 1 for skeletal layer tracers (needs TRBGCZ = 0)
ndtd = 1 ! dynamic time steps per thermodynamic time step
/

&grid_nml
kcatbound = 1
/

&tracer_nml
tr_iage = .false.
tr_FY = .false.
tr_lvl = .false.
tr_pond_cesm = .false.
tr_pond_topo = .false.
tr_pond_lvl = .false.
tr_aero = .false.
tr_fsd = .false.
/

&thermo_nml
kitd = 1
ktherm = 1
conduct = 'bubbly'
a_rapid_mode = 0.5e-3
Rac_rapid_mode = 10.0
aspect_rapid_mode = 1.0
dSdt_slow_mode = -5.0e-8
phi_c_slow_mode = 0.05
phi_i_mushy = 0.85
ksno = 0.3
/

&shortwave_nml
shortwave = 'ccsm3'
albedo_type = 'ccsm3'
albicev = 0.78
albicei = 0.36
albsnowv = 0.98
albsnowi = 0.70
albocn = 0.1
ahmax = 0.3
R_ice = 0.
R_pnd = 0.
R_snw = 1.5
dT_mlt = 1.5
rsnw_mlt = 1500.
kalg = 0.6
/

&ponds_nml
hp1 = 0.01
hs0 = 0.
hs1 = 0.03
dpscale = 1.e-3
frzpnd = 'hlid'
rfracmin = 0.15
rfracmax = 1.
pndaspect = 0.8
/

&forcing_nml
formdrag = .false.
atmbndy = 'default'
calc_strair = .true.
calc_Tsfc = .true.
highfreq = .false.
natmiter = 5
ustar_min = 0.0005
emissivity = 0.95
fbot_xfer_type = 'constant'
update_ocn_f = .false.
l_mpond_fresh = .false.
tfrz_option = 'linear_salt'
oceanmixed_ice = .true.
wave_spec_type = 'none'
/

&dynamics_nml
kstrength = 1
krdg_partic = 1
krdg_redist = 1
mu_rdg = 3
Cf = 17.
P_star = 27000.
C_star = 20.
/

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!! Icepack output namelist !!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

&nml_list_icepack
io_list_icepack = 'aicen ',1, 'm', 4, ! Sea ice concentration
'vicen ',1, 'm', 4, ! Volume per unit area of ice
'vsnon ',1, 'm', 4, ! Volume per unit area of snow
!'Tsfcn ',1, 'm', 4, ! Sea ice surf. temperature
!'iagen ',1, 'm', 4, ! Sea ice age
!'FYn ',1, 'm', 4, ! First year ice
!'lvln ',1, 'm', 4, ! Ridged sea ice area and volume
!'pond_cesmn',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness
!'pond_topon',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness
!'pond_lvln ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness
!'brinen ',1, 'm', 4, ! Volume fraction of ice with dynamic salt
!'qicen ',1, 'm', 4, ! Sea ice enthalpy
!'sicen ',1, 'm', 4, ! Sea ice salinity
!'qsnon ',1, 'm', 4, ! Snow enthalpy
! Average over thicknes classes
!'aice ',1, 'm', 4, ! Sea ice concentration
!'vice ',1, 'm', 4, ! Volume per unit area of ice
!'vsno ',1, 'm', 4, ! Volume per unit area of snow
!'Tsfc ',1, 'm', 4, ! Sea ice surf. temperature
!'iage ',1, 'm', 4, ! Sea ice age
!'FY ',1, 'm', 4, ! First year ice
!'lvl ',1, 'm', 4, ! Ridged sea ice area and volume
!'pond_cesm ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness
!'pond_topo ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness
!'pond_lvl ',1, 'm', 4, ! Melt ponds area, volume and refrozen lid thickness
!'brine ',1, 'm', 4, ! Volume fraction of ice with dynamic salt
!'qice ',1, 'm', 4, ! Sea ice enthalpy
!'sice ',1, 'm', 4, ! Sea ice salinity
!'qsno ',1, 'm', 4, ! Snow enthalpy
! Other variables
!'uvel ',1, 'm', 4, ! x-component of sea ice velocity
!'vvel ',1, 'm', 4, ! y-component of sea ice velocity
/
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