AWI-ESM3 CO2 coupling

config/bin_2p3z2d/namelist.config

@@ -1,76 +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/work/user/...'
+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            ! --> 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 = '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'       ! '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 = .true.       ! 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_transit=.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.
-ib_num=1
-use_icebergs=.false.
-steps_per_ib_step=8
-ib_async_mode=0
+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_2p3z2d/namelist.dyn

@@ -1,24 +1,79 @@
+! ============================================================================
+! ========== Namelist file for FESOM2 momentum dynamics ======================
+! ============================================================================
+! This file contains configuration for momentum equations and dynamics:
+! - Horizontal viscosity schemes and parameters
+! - Momentum advection options
+! - Free-slip vs no-slip boundary conditions
+! - Vertical velocity splitting
+! - Split-explicit barotropic subcycling
+! - Energy diagnostics
+! ============================================================================
+
+! ============================================================================
+! HORIZONTAL VISCOSITY
+! ============================================================================
 &dynamics_visc
-visc_gamma0  = 0.003 ! [m/s],   backgroung viscosity= gamma0*len, it should be as small a s possible (keep it < 0.01 m/s).
-visc_gamma1  = 0.1   ! [nodim], for computation of the flow aware viscosity
-visc_gamma2  = 0.285 ! [s/m],   is only used in easy backscatter option
-visc_easybsreturn= 1.5
-
-opt_visc     = 5          
-! 5=Kinematic (easy) Backscatter
-! 6=Biharmonic flow aware (viscosity depends on velocity Laplacian)
-! 7=Biharmonic flow aware (viscosity depends on velocity differences)
-! 8=Dynamic Backscatter
-
-use_ivertvisc= .true.  
+! --- Biharmonic Viscosity Coefficients ---
+visc_gamma0        = 0.003       ! background viscosity coefficient [m/s]
+                                 ! viscosity = gamma0 × element_length
+                                 ! keep < 0.01 m/s for numerical stability
+visc_gamma1        = 0.1         ! flow-aware viscosity coefficient [dimensionless]
+visc_gamma2        = 0.285       ! additional viscosity coefficient [s/m]
+                                 ! only used for easy backscatter (opt_visc=5) and dynamic backscatter (opt_visc=8)
+visc_easybsreturn  = 1.5         ! energy return parameter for easy backscatter [dimensionless]
+
+! --- Harmonic (Laplacian) Viscosity Coefficients (for opt_visc=7) ---
+! When both are 0, opt_visc=7 is pure biharmonic viscosity.
+! When > 0, harmonic viscosity is added to biharmonic (combined mode).
+visc_gamma0_h      = 0.0         ! < 0.003 background harmonic viscosity coefficient [m/s]
+visc_gamma1_h      = 0.0         ! < 0.05  flow-aware harmonic viscosity coefficient [dimensionless]
+
+! --- Viscosity Scheme Selection ---
+opt_visc           = 5           ! horizontal viscosity scheme:
+                                 !   5 = Kinematic (easy) Backscatter
+                                 !   6 = Biharmonic flow-aware (depends on velocity Laplacian)
+                                 !   7 = Biharmonic flow-aware (depends on velocity differences)
+                                 !       + optional Laplacian when visc_gamma0_h or visc_gamma1_h > 0
+                                 !   8 = Dynamic Backscatter
+check_opt_visc     = .true.      ! check if opt_visc=5 is valid based on resolution/Rossby radius ratio
+
+! --- Vertical Viscosity ---
+use_ivertvisc      = .true.      ! use implicit vertical viscosity (recommended for stability)
 /
 
+! ============================================================================
+! GENERAL DYNAMICS SETTINGS
+! ============================================================================
 &dynamics_general
-momadv_opt   = 2       ! option for momentum advection in moment only =2
-use_freeslip = .false. ! Switch on free slip
-use_wsplit   = .false. ! Switch for implicite/explicte splitting of vert. velocity
-wsplit_maxcfl= 1.0     ! maximum allowed CFL criteria in vertical (0.5 < w_max_cfl < 1.) 
-                       ! in older FESOM it used to be w_exp_max=1.e-3
-ldiag_KE=.false.       ! activates energy diagnostics
+! --- Momentum Advection ---
+momadv_opt         = 2           ! momentum advection option (only 2 is currently supported)
+
+! --- Boundary Conditions ---
+use_freeslip       = .false.     ! enable free-slip lateral boundary conditions (false = no-slip)
+
+! --- Vertical Velocity Splitting ---
+use_wsplit         = .false.     ! enable implicit/explicit splitting of vertical velocity
+wsplit_maxcfl      = 1.0         ! maximum allowed vertical CFL criterion (range: 0.5-1.0)
+                                 ! in older FESOM versions this was w_exp_max=1.e-3
+
+! --- Energy Diagnostics ---
+ldiag_KE           = .false.     ! enable kinetic energy diagnostics (requires additional computation)
+
+! --- Time Stepping ---
+AB_order           = 2           ! Adams-Bashforth time stepping order (2 or 3)
+
+! --- Split-Explicit Barotropic Subcycling ---
+use_ssh_se_subcycl = .false.     ! enable split-explicit subcycling for barotropic mode
+                                 ! (faster time stepping for sea surface height)
+se_BTsteps         = 50          ! number of barotropic subcycles per baroclinic time step
+se_BTtheta         = 0.14        ! implicitness parameter for barotropic solver (0-1, default: 0.14)
+se_bottdrag        = .true.      ! include bottom drag in barotropic subcycling
+se_bdrag_si        = .true.      ! use semi-implicit bottom drag (true) or explicit (false)
+se_visc            = .true.      ! include viscosity in barotropic subcycling
+se_visc_gamma0     = 10          ! background viscosity for barotropic mode [dimensionless]
+se_visc_gamma1     = 19500       ! flow-aware viscosity for barotropic mode [dimensionless]
+                                 ! typical values: 19500 (CORE2@32spd), 2750 (CORE2@72spd)
+se_visc_gamma2     = 0           ! additional viscosity for barotropic mode [dimensionless]
 /