Contents

• Introduction
• Model basics
  • Primitive Equations
    • Vector Invariant Formulation
    • Boundary Conditions
  • The Horizontal Pressure Gradient
    • Pressure Formulation
    • Free Surface Formulation
  • Curvilinear z-coordinate System
    • Tensorial Formalism
    • Continuous Model Equations
  • Curvilinear generalised vertical coordinate System
    • The s-coordinate Formulation
    • Curvilinear z*-coordinate System
    • Curvilinear Terrain-following s-coordinate
    • Curvilinear $\tilde{z}$-coordinate
  • Subgrid Scale Physics
    • Vertical Subgrid Scale Physics
    • Formulation of the Lateral Diffusive and Viscous Operators
  
  
• Time Domain (STP)
  • Time stepping environment
  • Non-Diffusive Part -- Leapfrog Scheme
  • Diffusive Part -- Forward or Backward Scheme
  • Hydrostatic Pressure Gradient -- semi-implicit scheme
  • The Modified Leapfrog - Asselin Filter scheme
  • Start/Restart strategy
  
  
• Space Domain (DOM)
  • Fundamentals of the Discretisation
    • Arrangement of Variables
    • Discrete Operators
    • Numerical Indexing
  • Domain: Horizontal Grid (mesh) (domhgr.F90 module)
    • Coordinates and scale factors
    • Choice of horizontal grid
    • Output Grid files
  • Domain: Vertical Grid (domzgr.F90 module)
    • Meter Bathymetry
    • $z$-coordinate (ln_zco
    • $z$-coordinate with partial step (ln_zps)
    • $s$-coordinate (ln_sco)
    • $z^*$- or $s^*$-coordinate (add key_ vvl)
    • level bathymetry and mask
  • Domain: Initial State (istate.F90 and dtatsd.F90 modules)
  
  
• Ocean Tracers (TRA)
  • Tracer Advection (traadv.F90)
    • $2^{nd}$ order centred scheme (cen2) (ln_traadv_cen2)
    • Total Variance Dissipation scheme (TVD) (ln_traadv_tvd=true)
    • Monotone Upstream Scheme for Conservative Laws (MUSCL) (ln_traadv_muscl=T)
    • Upstream-Biased Scheme (UBS) (ln_traadv_ubs=true)
    • QUICKEST scheme (QCK) (ln_traadv_qck=true)
  • Tracer Lateral Diffusion (traldf.F90)
    • Iso-level laplacian operator (lap) (ln_traldf_lap=true)
    • Rotated laplacian operator (iso) (ln_traldf_lap=true)
    • Iso-level bilaplacian operator (bilap) (ln_traldf_bilap=true)
    • Rotated bilaplacian operator (bilapg) (ln_traldf_bilap=true)
  • Tracer Vertical Diffusion (trazdf.F90)
  • External Forcing
    • Surface boundary condition (trasbc.F90)
    • Solar Radiation Penetration (traqsr.F90)
    • Bottom Boundary Condition (trabbc.F90)
  • Bottom Boundary Layer (trabbl.F90 - key_ trabbl)
    • Diffusive Bottom Boundary layer (nn_bbl_ldf=1)
    • Advective Bottom Boundary Layer (nn_bbl_adv= 1 or 2)
  • Tracer damping (tradmp.F90)
    • Generating resto.nc using DMP_TOOLS
  • Tracer time evolution (tranxt.F90)
  • Equation of State (eosbn2.F90)
    • Equation Of Seawater (nn_eos = -1, 0, or 1)
    • Brunt-Väisälä Frequency (nn_eos = 0, 1 or 2)
    • Freezing Point of Seawater
  • Horizontal Derivative in zps-coordinate (zpshde.F90)
  
  
• Ocean Dynamics (DYN)
  • Sea surface height and diagnostic variables ($\eta$, $\zeta$, $\chi$, $w$)
    • Horizontal divergence and relative vorticity (divcur.F90)
    • Horizontal divergence and relative vorticity (sshwzv.F90)
  • Coriolis and Advection: vector invariant form
    • Vorticity term (dynvor.F90)
    • Kinetic Energy Gradient term (dynkeg.F90)
    • Vertical advection term (dynzad.F90)
  • Coriolis and Advection: flux form
    • Coriolis plus curvature metric terms (dynvor.F90)
    • Flux form Advection term (dynadv.F90)
  • Hydrostatic pressure gradient (dynhpg.F90)
    • $z$-coordinate with full step (ln_dynhpg_zco)
    • $z$-coordinate with partial step (ln_dynhpg_zps)
    • $s$- and $z$-$s$-coordinates
    • Ice shelf cavity
    • Time-scheme (ln_dynhpg_imp= true/false)
  • Surface pressure gradient (dynspg.F90)
    • Explicit free surface (key_ dynspg_exp)
    • Split-Explicit free surface (key_ dynspg_ts)
    • Filtered free surface (key_ dynspg_flt)
  • Lateral diffusion term (dynldf.F90)
    • Iso-level laplacian operator (ln_dynldf_lap=true)
    • Rotated laplacian operator (ln_dynldf_iso=true)
    • Iso-level bilaplacian operator (ln_dynldf_bilap=true)
  • Vertical diffusion term (dynzdf.F90)
  • External Forcings
  • Time evolution term (dynnxt.F90)
  • Neptune effect (dynnept.F90)
  
  
• Surface Boundary Condition (SBC, ISF, ICB)
  • Surface boundary condition for the ocean
  • Input Data generic interface
    • Input Data specification (fldread.F90)
    • Interpolation on-the-Fly
    • Standalone Surface Boundary Condition Scheme
  • Analytical formulation (sbcana.F90 module)
  • Flux formulation (sbcflx.F90 module)
  • Bulk formulation (sbcblk_core.F90 sbcblk_clio.F90 sbcblk_mfs.F90 modules)
    • CORE Bulk formulea (ln_core=true, sbcblk_core.F90)
    • CLIO Bulk formulea (ln_clio=true, sbcblk_clio.F90)
    • MFS Bulk formulea (ln_mfs=true, sbcblk_mfs.F90)
  • Coupled formulation (sbccpl.F90 module)
  • Atmospheric pressure (sbcapr.F90)
  • Tidal Potential (sbctide.F90)
  • River runoffs (sbcrnf.F90)
  • Ice shelf melting (sbcisf.F90)
  • Handling of icebergs (ICB)
  • Miscellaneous options
    • Diurnal cycle (sbcdcy.F90)
    • Rotation of vector pairs onto the model grid directions
    • Surface restoring to observed SST and/or SSS (sbcssr.F90)
    • Handling of ice-covered area (sbcice_...)
    • Interface to CICE (sbcice_cice.F90)
    • Freshwater budget control (sbcfwb.F90)
    • Neutral drag coefficient from external wave model (sbcwave.F90)
  
  
• Lateral Boundary Condition (LBC)
  • Boundary Condition at the Coast (rn_shlat)
  • Model Domain Boundary Condition (jperio)
    • Closed, cyclic, south symmetric (jperio = 0, 1 or 2)
    • North-fold (jperio = 3 to $6$)
  • Exchange with neighbouring processors (lbclnk.F90, lib_mpp.F90)
  • Unstructured Open Boundary Conditions (key_ bdy) (BDY)
    • The namelists
    • The Flow Relaxation Scheme
    • The Flather radiation scheme
    • Boundary geometry
    • Input boundary data files
    • Volume correction
    • Tidal harmonic forcing
  
  
• Lateral Ocean Physics (LDF)
  • Lateral Mixing Coefficient (ldftra.F90, ldfdyn.F90)
  • Direction of Lateral Mixing (ldfslp.F90)
    • slopes for tracer geopotential mixing in the $s$-coordinate
    • Slopes for tracer iso-neutral mixing
    • slopes for momentum iso-neutral mixing
  • Eddy Induced Velocity (traadv_eiv.F90, ldfeiv.F90)
  
  
• Vertical Ocean Physics (ZDF)
  • Vertical Mixing
    • Constant (key_ zdfcst)
    • Richardson Number Dependent (key_ zdfric)
    • TKE Turbulent Closure Scheme (key_ zdftke)
    • TKE discretization considerations (key_ zdftke)
    • GLS Generic Length Scale (key_ zdfgls)
    • K Profile Parametrisation (KPP) (key_ zdfkpp)
  • Convection
    • Non-Penetrative Convective Adjustment (ln_tranpc=.true.)
    • Enhanced Vertical Diffusion (ln_zdfevd=true)
    • Turbulent Closure Scheme (key_ zdftke or key_ zdfgls)
  • Double Diffusion Mixing (key_ zdfddm)
  • Bottom and Top Friction (zdfbfr.F90 module)
    • Linear Bottom Friction (nn_botfr = 0 or 1)
    • Non-Linear Bottom Friction (nn_botfr = 2)
    • Log-layer Bottom Friction enhancement (nn_botfr = 2, ln_loglayer = .true.)
    • Bottom Friction stability considerations
    • Implicit Bottom Friction (ln_bfrimp$=$T)
    • Bottom Friction with split-explicit time splitting (ln_bfrimp$=$F)
  • Tidal Mixing (key_ zdftmx)
    • Bottom intensified tidal mixing
    • Indonesian area specific treatment (ln_zdftmx_itf)
  • Internal wave-driven mixing (key_ zdftmx_new)
  
  
• Output and Diagnostics (IOM, DIA, TRD, FLO)
  • Old Model Output (default or key_ dimgout)
  • Standard model Output (IOM)
    • XIOS: the IO_SERVER
    • Practical issues
    • XML fundamentals
    • Detailed functionalities
    • XML reference tables
    • CF metadata standard compliance
  • NetCDF4 Support (key_ netcdf4)
  • Tracer/Dynamics Trends (namtrd)
  • On-line Floats trajectories (FLO) (key_ floats)
  • Harmonic analysis of tidal constituents (key_ diaharm)
  • Transports across sections (key_ diadct)
  • Other Diagnostics (key_ diahth, key_ diaar5)
  • Diagnosing the Steric effect in sea surface height
  
  
• Observation and model comparison (OBS)
  • Running the observation operator code example
  • Technical details
    • Profile feedback type observation file header
    • Sea level anomaly feedback type observation file header
    • Sea surface temperature feedback type observation file header
  • Theoretical details
    • Horizontal interpolation methods
    • Grid search
    • Parallel aspects of horizontal interpolation
    • Vertical interpolation operator
  • Offline observation operator
    • Concept
    • Using the offline observation operator
    • Configuring the offline observation operator
    • Advanced usage
  • Observation Utilities
    • Obstools
    • building the obstools
    • Dataplot
  
  
• Apply assimilation increments (ASM)
  • Direct initialization
  • Incremental Analysis Updates
  • Divergence damping initialisation
  • Implementation details
  
  
• Stochastic parametrization of EOS (STO)
  • Stochastic processes
  • Implementation details
  
  
• Miscellaneous Topics
  • Representation of Unresolved Straits
    • Hand made geometry changes
    • Cross Land Advection (tracla.F90)
  • Closed seas (closea.F90)
  • Sub-Domain Functionality (jpizoom, jpjzoom)
    • Simple subsetting of input files via netCDF attributes
  • Accelerating the Convergence (nn_acc = 1)
  • Accuracy and Reproducibility (lib_fortran.F90)
    • Issues with intrinsinc SIGN function (key_ nosignedzero)
    • MPP reproducibility
    • MPP scalability
  • Model Optimisation, Control Print and Benchmark
  • Elliptic solvers (SOL)
    • Successive Over Relaxation (nn_solv=2, solsor.F90)
    • Preconditioned Conjugate Gradient (nn_solv=1, solpcg.F90)
  
  
• Configurations
  • Introduction
  • Water column model: 1D model (C1D) (key_ c1d)
  • ORCA family: global ocean with tripolar grid
    • ORCA tripolar grid
    • ORCA pre-defined resolution
  • GYRE family: double gyre basin
  • EEL family: periodic channel
  • AMM: atlantic margin configuration
  
  
• Curvilinear $s-$Coordinate Equations
  • The chain rule for $s-$coordinates
  • Continuity Equation in $s-$coordinates
  • Momentum Equation in $s-$coordinate
  • Tracer Equation
  
  
• Appendix B : Diffusive Operators
  • Horizontal/Vertical 2nd Order Tracer Diffusive Operators
  • Iso/diapycnal 2nd Order Tracer Diffusive Operators
  • Lateral/Vertical Momentum Diffusive Operators
  
  
• Discrete Invariants of the Equations
  • Introduction / Notations
  • Continuous conservation
  • Discrete total energy conservation : vector invariant form
    • Total energy conservation
    • Vorticity term (coriolis + vorticity part of the advection)
    • Pressure Gradient Term
  • Discrete total energy conservation : flux form
    • Total energy conservation
    • Coriolis and advection terms: flux form
  • Discrete enstrophy conservation
  • Conservation Properties on Tracers
    • Advection Term
  • Conservation Properties on Lateral Momentum Physics
    • Conservation of Potential Vorticity
    • Dissipation of Horizontal Kinetic Energy
    • Dissipation of Enstrophy
    • Conservation of Horizontal Divergence
    • Dissipation of Horizontal Divergence Variance
  • Conservation Properties on Vertical Momentum Physics
  • Conservation Properties on Tracer Physics
    • Conservation of Tracers
    • Dissipation of Tracer Variance
  
  
• Iso-neutral diffusion and eddy advection using triads
  • Choice of namtra_ldf namelist parameters
  • Triad formulation of iso-neutral diffusion
    • The iso-neutral diffusion operator
    • The standard discretization
    • Expression of the skew-flux in terms of triad slopes
    • The full triad fluxes
    • Ensuring the scheme does not increase tracer variance
    • Triad volumes in Griffes's scheme and in NEMO
    • Summary of the scheme
    • Treatment of the triads at the boundaries
    • Limiting of the slopes within the interior
    • Tapering within the surface mixed layer
  • Eddy induced advection formulated as a skew flux
    • The continuous skew flux formulation
    • The discrete skew flux formulation
    • Treatment of the triads at the boundaries
    • Limiting of the slopes within the interior
    • Tapering within the surface mixed layer
    • Streamfunction diagnostics
  
  
• Coding Rules
  • The program structure
  • Coding conventions
  • Naming Conventions
  • The program structure
  
  
• Index
• Bibliography