Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fesom2 4phy #607

Open
wants to merge 3 commits into
base: fesom2_3zoo_ballast
Choose a base branch
from
Open

Fesom2 4phy #607

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
1e40a83
phaeocystis added
mueller79 Jun 25, 2024
08c596a
merge: phaeocystis and updated photodamage fxn
mueller79 Jun 26, 2024
bbdb828
Phaeocystis merged with özgürs model version (most recent)
mueller79 Jun 28, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
63 changes: 63 additions & 0 deletions bin_run1_20240618/job_albedo
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,63 @@
#!/bin/bash
#SBATCH --job-name=test_3zoo_ballast_phaeo_özgür
#SBATCH --account=nwg_hauck.maresys
#SBATCH --partition=mpp
#SBATCH -N 9
#SBATCH --cpus-per-task=1
#SBATCH --time=00:30:00
#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/work/user/simuel001/PHAEO_TEST/'
test -e $Resultpath/fesom.1959.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 bin_run1_20240618/namelist.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,63 @@
! 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/work/user/simuel001/PHAEO_TEST/'
/

&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 bin_run1_20240618/namelist.forcing
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,63 @@
! 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 bin_run1_20240618/namelist.ice
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
! 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 bin_run1_20240618/namelist.icepack
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,146 @@
&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
/
Loading