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Fesom 2.7.0 standalone #1399

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83de836
working 2.7.0 on levante
JanStreffing Nov 17, 2025
fa48a80
fix(fesom2.7): minor syntax error in comp_command
pgierz Mar 10, 2026
4286a98
chore: adds comment about pool cleanup for @christian-stepanek
pgierz Mar 10, 2026
0370773
fix: corrects pool directory for cavity72k on albedo, adds note for @…
pgierz Mar 10, 2026
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704 changes: 704 additions & 0 deletions configs/components/fesom/fesom-2.7.yaml
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133 changes: 133 additions & 0 deletions namelists/fesom2/2.7.0/namelist.config
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! ============================================================================
! ============ 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' ! run identifier (used in output filenames)
/

! ============================================================================
! TIME STEPPING AND RUN LENGTH
! ============================================================================
&timestep
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)
/

! ============================================================================
! 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 = '/pool/data/AWICM/FESOM2/MESHES_FESOM2.1/core2/' ! path to mesh files (nod2d.out, elem2d.out, etc.)
ClimateDataPath = '/pool/data/AWICM/FESOM2/INITIAL/phc3.0/' ! path to initial conditions (temperature, salinity)
ResultPath = '/work/ab0246/$USER/runtime/fesom2/' ! path for output files and fesom.clock file
/

! ============================================================================
! RESTART AND LOGGING CONFIGURATION
! ============================================================================
&restart_log
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 = 'y' ! unit: 'y', 'm', 'd', 'h', 's', 'off'
bin_restart_length = 1 ! frequency for binary derived type restart files
bin_restart_length_unit = 'y' ! 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' ! 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. ! 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 = .true. ! include leap years in calendar (false = 365-day year, true = 365/366-day year)
/

! ============================================================================
! MODEL COMPONENTS AND FEATURES
! ============================================================================
&run_config
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 ! 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)
/
211 changes: 211 additions & 0 deletions namelists/fesom2/2.7.0/namelist.cvmix
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! ============================================================================
! ========== Namelist file for FESOM2 CVMix parameterizations ===============
! ============================================================================
! This file contains configuration for CVMix (Community Vertical Mixing)
! parameterizations:
! - TKE (Turbulent Kinetic Energy) scheme
! - IDEMIX (Internal Wave Dissipation, Energy, and Mixing)
! - PP (Pacanowski-Philander) scheme
! - KPP (K-Profile Parameterization)
! - TIDAL mixing parameterization
!
! Select the active scheme in namelist.oce (mix_scheme parameter)
! ============================================================================

! ============================================================================
! TKE (TURBULENT KINETIC ENERGY) SCHEME
! ============================================================================
&param_tke
! --- TKE Model Parameters ---
tke_c_k = 0.1 ! TKE parameter c_k [dimensionless]
tke_c_eps = 0.7 ! TKE dissipation parameter c_eps [dimensionless]
tke_alpha = 30.0 ! TKE stability function parameter [dimensionless]

! --- Mixing Length ---
tke_mxl_min = 1.0e-8 ! minimum mixing length [m]
tke_mxl_choice = 2 ! mixing length calculation method:
! 1 = not implemented
! 2 = Blanke & Delecluse option (currently only option)

! --- Viscosity/Diffusivity Limits ---
tke_kappaM_min = 0.0 ! minimum momentum diffusivity [m²/s]
tke_kappaM_max = 100.0 ! maximum momentum diffusivity [m²/s]

! --- Boundary Conditions ---
tke_cd = 3.75 ! surface boundary condition parameter
! 3.75 for Dirichlet BC, 1.0 for Neumann BC

! --- TKE Minimum Values ---
tke_surf_min = 1.0e-4 ! minimum surface TKE [m²/s²]
tke_min = 1.0e-6 ! minimum interior TKE [m²/s²]

! --- Langmuir Turbulence ---
tke_dolangmuir = .false. ! include Langmuir turbulence parameterization
/

! ============================================================================
! IDEMIX (INTERNAL WAVE ENERGY PARAMETERIZATION)
! ============================================================================
! Based on Olbers & Eden (2013) and von Pollmann et al. (2017)
! ============================================================================
&param_idemix
! --- Time Scales ---
idemix_tau_v = 172800.0 ! vertical symmetrization time scale [s] (2 days)
idemix_tau_h = 1296000.0 ! horizontal symmetrization time scale [s] (15 days)

! --- Spectral Parameters ---
idemix_gamma = 1.570 ! spectral shape constant [dimensionless] (order 1)
idemix_jstar = 5.0 ! spectral bandwidth in vertical modes [dimensionless]
idemix_mu0 = 0.33333333 ! dissipation parameter [dimensionless]

! --- Energy Forcing ---
idemix_sforcusage = 0.2 ! fraction of surface forcing used [dimensionless]
idemix_n_hor_iwe_prop_iter = 5 ! iterations for horizontal wave propagation

! --- Surface Forcing (Wind-Generated Internal Waves) ---
idemix_surforc_file = '/pool/data/AWICM/FESOM2/FORCING/IDEMIX/fourier_smooth_2005_cfsr_inert_rgrid.nc' ! path to surface forcing file
idemix_surforc_vname = 'var706' ! variable name in surface forcing file

! --- Bottom Forcing (Tidal Internal Waves) ---
!idemix_botforc_file = '/albedo/pool/FESOM/fesom2.0/forcing/idemix/forcing_idemix_final_bin/FIN_tidal_energy_gx1v6_20090205_CESMJayne_remapnn_0.40deg.nc' ! path to bottom forcing !file
!idemix_botforc_vname = 'wave_dissipation' ! variable name in bottom forcing file
idemix_botforc_file = '/albedo/pool/FESOM/fesom2.0/forcing/idemix/forcing_idemix_final_bin/FIN_STORMTIDE2_M2_plus_NYCANDER_CnoM2_bin_0.40deg.nc' ! path to bottom forcing file,
idemix_botforc_vname = 'stormt_M2_plus_nycand_CnoM2' ! variable name in bottom forcing file

/

! ============================================================================
! PP (PACANOWSKI-PHILANDER) SCHEME
! ============================================================================
! Based on Pacanowski & Philander (1981)
! ============================================================================
&param_pp
! --- PP Variant ---
pp_use_fesompp = .true. ! use FESOM flavor of PP (true) or original PP (false)

! --- Mixing Coefficients ---
pp_Av0 = 0.01 ! reference mixing coefficient [m²/s]
pp_alpha = 5.0 ! Richardson number dependency parameter [dimensionless]
! (alpha in eq. 1 of Pacanowski & Philander 1981)
pp_exp = 2.0 ! Richardson number exponent [dimensionless]
! (n in eq. 1 of Pacanowski & Philander 1981)

! --- Background Mixing ---
pp_Avbckg = 1.0e-4 ! constant background viscosity [m²/s]
pp_Kvbckg = 1.0e-5 ! constant background diffusivity [m²/s]
pp_use_nonconstKvb = .true. ! use latitude and depth dependent background diffusivity
/

! ============================================================================
! KPP (K-PROFILE PARAMETERIZATION)
! ============================================================================
! Based on Large et al. (1994) with CVMix implementation options
! ============================================================================
&param_kpp
! --- KPP Implementation ---
kpp_use_fesomkpp = .false. ! use CVMix MOM5-like KPP (true) or MOM6-like KPP (false)

! --- Ocean Boundary Layer (OBL) Depth Calculation ---
kpp_use_enhanceKv = .true. ! add enhanced diffusivity at base of boundary layer
kpp_use_compEkman = .true. ! compute Ekman depth limit for OBL depth
kpp_use_monob = .true. ! compute Monin-Obukhov limit for OBL depth

! --- Interpolation Methods ---
kpp_interptype_ri = "linear" ! interpolation type for OBL depth determination:
! 'linear', 'quadratic', 'cubic'
kpp_interptype_atobl = "LMD94" ! interpolation of viscosity/diffusivity at OBL depth:
! 'linear', 'quadratic', 'cubic', 'LMD94'
kpp_matchtechc = "ParabolicNonLocal" ! diffusivity and non-local transport profile:
! 'SimpleShapes', 'MatchGradient', 'MatchBoth', 'ParabolicNonLocal'

! --- Mixing Below OBL ---
kpp_internalmix = "KPP" ! Richardson number dependent mixing below OBL:
! 'KPP' or 'PP'
kpp_pp_Av0 = 0.01 ! mixing coefficient for PP scheme below OBL [m²/s]

! --- Shear Mixing Parameters ---
kpp_Av0 = 5.0e-3 ! leading coefficient of shear mixing [m²/s] (default: 5e-3)
kpp_Kv0 = 5.0e-3 ! leading coefficient of shear diffusion [m²/s]
kpp_Ri0 = 0.7 ! critical Richardson number [dimensionless] (0.7 in LMD94)

! --- Background Mixing ---
kpp_use_nonconstKvb = .true. ! use non-constant background diffusivity (FESOM1.4 formulation)
kpp_Avbckg = 1.0e-4 ! constant background viscosity [m²/s]
kpp_Kvbckg = 1.0e-5 ! constant background diffusivity [m²/s]

! --- Sea Ice Effects ---
kpp_reduce_tauuice = .false. ! reduce wind stress (u*) under sea ice

! --- Langmuir Options in cvmix KPP ---

! Stokes Similarty package
! If true, use Stokes Similarty package (i.e. include wave‐related / Stokes drift
! effects in the surface layer). Triggers usage of additional routines
! that alter the shape functions, or mixing formulations, incorporating wave /
! Stokes drift effects consistent with Monin–Obukhov similarity theory
! (MOST). The code logic probably augments or replaces parts of the standard boundary
! (layer similarity (or nonlocal mixing) using a Stokes‐drift‐aware correction.
kpp_use_StokesMOST= .false. !.true.

! approximate proportionality between surface wind velocity and stokes velocity
! U_stokes ~ kpp_A_stokes * U_wind
kpp_A_stokes = 0.005 ! a

! Langmuir option
! Option of Langmuir enhanced mixing apply an enhancement factor to the
! turbulent velocity scale
! LWF16 - MixingCoefEnhancement = Langmuir_EFactor
! RWHGK16 - MixingCoefEnhancement = cvmix_one + ShapeNoMatchAtS/NMshapeMax * &
! (Langmuir_EFactor - cvmix_one)
! NONE - Langmuir switched off, MixingCoefEnhancement=1
kpp_langmuir_mixing= "NONE" !"LWF16"

! Option of Langmuir turbulence enhanced entrainment - modify the unresolved shear
! LWF16 - Li Q., Webb A., Fox-Kemper B., Craig A., Danabasoglu G.,
! Large W., Vertenstein M., 2016, Langmuir mixing effects on
! global climate: WAVEWATCH III in CESM, Ocean Modelling 103 (2016) 145–160
!
! LF17 - Li Q., Fox-Kemper B., Breivik O., Webb A., 2017, Statistical
! models of global Langmuir mixing, Ocean Modelling 113 (2017) 95–114
!
! RWHGK16 - Reichl B., Wang D., Hara T., Ginis I. and Kukulka T, 2016, Impact
! of Sea-State-Dependent Langmuir Turbulence on the Ocean
! Response to a Tropical Cyclone, Mon. Wea. Rev., 144
!
! NONE -
kpp_langmuir_entrainment= "NONE" !"LF17"
/


! ============================================================================
! TIDAL MIXING PARAMETERIZATION
! ============================================================================
! Based on Simmons et al. (2004)
! ============================================================================
&param_tidal
! --- Tidal Mixing Scheme ---
tidal_mixscheme = "Simmons" ! tidal mixing scheme (currently only 'Simmons' implemented)

! --- Energy Dissipation Parameters ---
tidal_efficiency = 0.2 ! mixing efficiency [dimensionless, 0-1]
! (Gamma in Simmons et al. 2004)
tidal_lcl_mixfrac = 0.33 ! local dissipation fraction [dimensionless]
! (q in Simmons et al. 2004)
! fraction of tidal energy dissipated locally vs radiated away

! --- Vertical Structure ---
tidal_vert_decayscale = 500.0 ! vertical decay scale [m]
! (zeta in Simmons et al. 2004)
! controls vertical distribution of tidal mixing

! --- Diffusivity Limits ---
tidal_max_coeff = 50e-4 ! maximum tidal diffusivity [m²/s]

! --- Spatial Limits ---
tidal_depth_cutoff = 0.0 ! minimum depth for tidal mixing [m, positive downward]
! (0.0 = compute everywhere)

! --- Bottom Forcing (Tidal Energy Input) ---
tidal_botforc_file = '/pool/data/AWICM/FESOM2/FORCING/IDEMIX/tidal_energy_gx1v6_20090205_rgrid.nc'
/

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