Fesom2.7 recom3.1

.gitignore

@@ -16,3 +16,4 @@ Makefile.in
 mesh_part/build
 test/output_pi 
 src/cvmix_driver/CVMix-*
+finished_config.yaml

config/bin_2p1z1d/job_albedo

@@ -1,16 +1,15 @@
 #!/bin/bash
-#SBATCH --account=nwg_hauck.maresys # edit your account
+#SBATCH --account=biogeo_model.biogeo_model # edit your account
 #SBATCH --job-name=recom
 #SBATCH --partition=mpp
 #SBATCH --time=01:30:00
-####SBATCH --constraint="[rack1|rack3]"
 #SBATCH --qos=12h
 #SBATCH --nodes=9            # Number of tasks (MPI) tasks to be launched
 #SBATCH --tasks-per-node 96 #8 #4  # using all 128CPus we exceed the maxload limit (>130) of many used nodes when us parallel I/O
 #SBATCH --cpus-per-task 1
 
-#SBATCH -o fesom2o.out
-#SBATCH -e fesom2e.out
+#SBATCH -o slurm-out.out
+#SBATCH -e slurm-err.out
 
 # disable hyperthreading
 #SBATCH --hint=nomultithread
@@ -35,23 +34,22 @@ cp -n ../config/namelist.icepack .
 
 #___DETERMINE SLURM JOBID+OUTPUTFILE____________________________________________
 jobid=$(echo $SLURM_JOB_ID | cut -d"." -f1)
-fname="fesom2_${SLURM_JOB_NAME}_${jobid}.out"
+fname="fesom2.0.out"
 
 #___PUT JOB IN QUEUE____________________________________________________________
 date
-####srun --mpi=pmi2 ./fesom.x >> ${fname}
 srun --mpi=pmi2 ./fesom.x > fesom2.0.out
 date
 
 #qstat -f $PBS_JOBID
 #export EXITSTATUS=$?
 #if [ ${EXITSTATUS} -eq 0 ] || [ ${EXITSTATUS} -eq 127 ] ; then
-#sbatch job_ollie
+#sbatch job_albedo
 #fi
 
-#Resultpath='/albedo/scratch/user/ogurses/ocean_only/'
-Resultpath='/albedo/scratch/user/ogurses/fesom2.5_recom_st1_vsink_vben_diags/'
-test -d $Resultpath/fesom.2019.oce.restart && exit
+
+Resultpath='/albedo/scratch/user/XXXX/'
+test -e $Resultpath/fesom.XXXX.oce.restart && exit
 
 IsInFile=$( tail -3 fesom2.0.out | grep -c timesteps)
 if (( IsInFile > 0 )); then

config/bin_2p1z1d/namelist.config

@@ -1,67 +1,133 @@
-! This is the namelist file for model general configuration
+! ============================================================================
+! ============ Namelist file for FESOM2 general configuration ================
+! ============================================================================
+! This file contains the main configuration parameters for FESOM2, including:
+! - Model identification and run settings
+! - Time stepping and simulation duration
+! - Initial time/date settings
+! - File paths for mesh, forcing, and output
+! - Restart and logging configuration
+! - Vertical coordinate system (ALE)
+! - Grid geometry and rotation
+! - Calendar settings
+! - Model components (ice, cavities, etc.)
+! - Parallel decomposition
+! - Iceberg settings
+! ============================================================================
 
+! ============================================================================
+! RUN IDENTIFICATION
+! ============================================================================
 &modelname
-runid='fesom'
+runid = 'fesom'        ! run identifier (used in output filenames)
 /
 
+! ============================================================================
+! TIME STEPPING AND RUN LENGTH
+! ============================================================================
 &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
+step_per_day      = 36         ! number of time steps per day (determines dt = 86400/step_per_day seconds)
+                                ! common values: 32 (45min), 48 (30min), 72 (20min), 96 (15min), 192 (7min 30sec), 
+                                ! 216 (6min 40sec), 240 (6min), 288 (5min), 360 (4min), 720 (2min), 1440 (1min), 2880 (30sec)
+run_length        = 1          ! total length of simulation run
+run_length_unit   = 'y'        ! unit for run_length: 'y' (years), 'm' (months), 'd' (days), 's' (steps)
 /
 
-&clockinit              ! the model starts at
-timenew=0.0
-daynew=1
-yearnew=1958
+! ============================================================================
+! INITIAL TIME/DATE SETTINGS
+! ============================================================================
+&clockinit
+timenew = 0.0                  ! initial time within the day [seconds] (0.0 = midnight)
+daynew  = 1                    ! initial day of the month (1-31)
+yearnew = 1958                 ! initial year
 /
 
+! ============================================================================
+! MESH, INITIALIZATION & OUTPUT PATHS
+! ============================================================================
 &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/fesom2.5_recom_st1_vsink_vben_diags/'
+MeshPath         = '/albedo/work/projects/p_recompdaf/frbunsen/FESOM2/meshes/core2/'   ! path to mesh files (nod2d.out, elem2d.out, etc.)
+ClimateDataPath  = '/albedo/work/projects/MarESys/ogurses/input/corrected_input/'      ! path to initial conditions (temperature, salinity)
+ResultPath       = '/albedo/scratch/user/XXXX'
 /
 
+! ============================================================================
+! RESTART AND LOGGING CONFIGURATION
+! ============================================================================
 &restart_log
-restart_length=1            ! --> do netcdf restart ( only required for d,h,s cases, y, m take 1)
-restart_length_unit='y'     !output period: y, d, h, s, off
-raw_restart_length=1        ! --> do core dump restart
-raw_restart_length_unit='off' ! e.g. y, d, h, s, off
-bin_restart_length=1        ! --> do derived type binary restart 
-bin_restart_length_unit='off' ! e.g. y, d, h, s, off
-logfile_outfreq=960     !in logfile info. output frequency, # steps
+restart_length          = 1        ! frequency for netCDF restart files (required for d,h,s; y,m use 1)
+restart_length_unit     = 'y'      ! unit: 'y' (years), 'm' (months), 'd' (days), 'h' (hours), 's' (steps), 'off' (disabled)
+raw_restart_length      = 1        ! frequency for raw core dump restart files
+raw_restart_length_unit = 'off'      ! unit: 'y', 'm', 'd', 'h', 's', 'off'
+bin_restart_length      = 1        ! frequency for binary derived type restart files
+bin_restart_length_unit = 'off'      ! unit: 'y', 'm', 'd', 'h', 's', 'off'
+logfile_outfreq         = 960      ! log file output frequency [number of time steps]
 /
 
+! ============================================================================
+! VERTICAL COORDINATE SYSTEM (ALE - Arbitrary Lagrangian-Eulerian)
+! ============================================================================
 &ale_def
-which_ALE='zstar'       ! 'linfs','zlevel', 'zstar'
-use_partial_cell=.true.
+which_ALE          = 'zstar'     ! vertical coordinate type:
+                                  !   'linfs'  = linear free surface
+                                  !   'zlevel' = z-level (fixed depth levels)
+                                  !   'zstar'  = z-star (terrain-following with SSH scaling)
+use_partial_cell   = .false.     ! use partial bottom cells for better topography representation (not recommended)
 /
 
+! ============================================================================
+! GRID GEOMETRY AND ROTATION
+! ============================================================================
 &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.
+cartesian       = .false.        ! use Cartesian coordinates (false = spherical Earth)
+fplane          = .false.        ! use f-plane approximation (constant Coriolis parameter)
+cyclic_length   = 360            ! length of cyclic domain [degrees] (360 = global)
+rotated_grid    = .true.         ! use rotated grid (typically for coupled models to avoid pole singularity)
+force_rotation  = .true.         ! force grid rotation even if not coupled
+alphaEuler      = 50.            ! first Euler angle (rotation around z-axis) [degrees]
+betaEuler       = 15.            ! second Euler angle (rotation around new x-axis) [degrees]
+gammaEuler      = -90.           ! third Euler angle (rotation around new z-axis) [degrees]
+                                  ! Euler angle convention: rotate first around z, then around new x, then around new z
 /
 
+! ============================================================================
+! CALENDAR SETTINGS
+! ============================================================================
 &calendar
-include_fleapyear=.false.
+include_fleapyear = .false.       ! include leap years in calendar (false = 365-day year, true = 365/366-day year)
 /
 
+! ============================================================================
+! MODEL COMPONENTS AND FEATURES
+! ============================================================================
 &run_config
-use_ice=.true.                  ! ocean+ice
-use_cavity=.false.              !
-use_cavity_partial_cell=.false. 
-use_floatice = .false.
-use_sw_pene=.true.
-flag_debug=.false.
+use_ice                  = .true.        ! enable sea ice model
+use_cavity               = .false.       ! enable ice shelf cavities
+use_cavity_partial_cell  = .false.       ! use partial cells in ice shelf cavities (not recommended)
+use_floatice             = .false.       ! enable floating ice (icebergs)
+use_sw_pene              = .true.        ! enable shortwave radiation penetration into ocean
+flag_debug               = .false.       ! enable debug output (verbose logging)
+use_transit              = .false.       ! enable transient tracer module (CFCs, SF6, etc.)
 /
 
+! ============================================================================
+! PARALLEL DECOMPOSITION (DOMAIN PARTITIONING)
+! ============================================================================
 &machine
-n_levels=2
-n_part= 12, 36          ! 432 number of partitions on each hierarchy level
+n_levels = 2             ! number of hierarchy levels for domain decomposition
+n_part   = 2, 128        ! number of partitions at each level (total CPUs = product of n_part)
+                         ! example: 2 x 128 = 256 MPI tasks
+                         ! adjust based on mesh size and available compute resources
+                         ! maximum scaling reached at ~300 FESOM2 2D nodes per CPU (see first line in nod2d.out for number of 2D nodes)
+/
+
+! ============================================================================
+! ICEBERG SETTINGS
+! ============================================================================
+&icebergs
+use_icesheet_coupling = .false.  ! enable ice sheet model
+ib_num                = 1        ! number of iceberg classes
+use_icebergs          = .false.  ! enable iceberg module
+steps_per_ib_step     = 8        ! ocean time steps per iceberg time step (iceberg subcycling)
+ib_async_mode         = 0        ! iceberg asynchronous mode (0=synchronous, 1=asynchronous)
 /

config/bin_2p1z1d/namelist.forcing

@@ -23,11 +23,23 @@ ncar_bulk_z_shum=10.0 ! height at which humi forcing is located (CORE, JRA-do: 1
 use_landice_water=.false.
 landice_start_mon=5
 landice_end_mon=10
+fwf_path='./mesh/'
+
+/
+
+&age_tracer
+use_age_tracer=.false.
+use_age_mask=.false.
+age_tracer_path='./mesh/'
+age_start_year=2000
+
 /
 
 &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_xstre_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_ystre_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
@@ -37,24 +49,32 @@ landice_end_mon=10
    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_xstre_var  = 'uas'   ! name of variable in file with wind
+   nm_ystre_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_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.
+   l_xwind=.true. l_ywind=.true. l_xstre=.false. l_ystre=.false. 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      ='/albedo/pool/FESOM/forcing/CORE2/runoff.nc'
    runoff_data_source ='CORE2'	!Dai09, CORE2
    !runoff_data_source ='Dai09'  !Dai09, CORE2, JRA55
    !runoff_climatology =.true.
-   nm_sss_data_file    ='/albedo/pool/FESOM/forcing/CORE2/PHC2_salx.nc'
    sss_data_source    ='CORE2'
+   nm_sss_data_file   ='/albedo/pool/FESOM/forcing/CORE2/PHC2_salx.nc'
+   chl_data_source    ='None' !'Sweeney' monthly chlorophyll climatology or 'NONE' for constant chl_const (below). Make use_sw_pene=.TRUE. in namelist.config!
+   nm_chl_data_file   ='/pool/data/AWICM/FESOM2/FORCING/JRA55-do-v1.4.0/Sweeney/Sweeney_2005.nc'
+   chl_const          = 0.1
+   use_runoff_mapper  = .FALSE.
+   runoff_basins_file = 'runoff_maps_regular.nc'
+   runoff_radius      = 500000.
 /

config/bin_2p1z1d/namelist.io

@@ -55,7 +55,6 @@ io_list =  'sst       ',1, 'm', 4,
            'Hp        ',1, 'm', 4,
            'aFe       ',1, 'm', 4,
            'aN        ',1, 'm', 4,
-           'denb      ',1, 'm', 4,
            'benN      ',1, 'm', 4,
            'benC      ',1, 'm', 4,
            'benSi     ',1, 'm', 4,