Branch of fesom2.6 including recom and tracer parallelisation

CMakeLists.txt

@@ -18,7 +18,7 @@ set(USE_YAC             OFF CACHE BOOL "compile fesom with yac")
 set(CRAY                OFF CACHE BOOL "compile with cray ftn")
 set(USE_ICEPACK         OFF CACHE BOOL "compile fesom with the Iceapck modules for sea ice column physics.")
 set(OPENMP_REPRODUCIBLE OFF CACHE BOOL "serialize OpenMP loops that are critical for reproducible results")
-set(RECOM_COUPLED       OFF CACHE BOOL "compile fesom including biogeochemistry, REcoM3")
+set(RECOM_COUPLED       ON  CACHE BOOL "compile fesom including biogeochemistry, REcoM3")
 set(CISO_COUPLED        OFF CACHE BOOL "compile ciso coupled to REcoM3. RECOM_COUPLED has to be active")
 set(USE_MULTIO          OFF CACHE BOOL "Use MULTIO for IO, either grib or binary for now. This also means path to MULTIO installation has to provided using env MULTIO_INSTALL_PATH='..' and multio configuration yamls must be present to run the model with MULTIO")
 set(OASIS_WITH_YAC      OFF CACHE BOOL "Useing a version of OASIS compiled with YAC instead of SCRIP for interpolation?")

config/bin_2p1z1d_tp/namelist.config

@@ -0,0 +1,134 @@
+! ============================================================================
+! ============ 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      = 48         ! 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 = 2000                 ! initial year
+/
+
+! ============================================================================
+! MESH, INITIALIZATION & OUTPUT PATHS
+! ============================================================================
+&paths
+MeshPath         = '/albedo/work/projects/p_recompdaf/frbunsen/FESOM2/meshes/core2/'   ! path to mesh files (nod2d.out, elem2d.out, etc.)
+ClimateDataPath  = '/albedo/work/user/yye/fesom2/initial_files/pi_init/'          ! path to initial conditions (temperature, salinity)
+ResultPath       = './'               ! 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 = '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'     ! 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.)
+num_fesom_groups         = 1
+/
+
+! ============================================================================
+! 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)
+/

config/bin_2p1z1d_tp/namelist.cvmix

@@ -0,0 +1,211 @@
+! ============================================================================
+! ========== 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'
+/
+