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NEMO ocean engine

Gurvan Madec, and the NEMO team
gurvan.madec@locean-ipsl.umpc.fr
nemo_st@locean-ipsl.umpc.fr

Date: January 2016
- version 3.6 stable -

Note du Pôle de modélisation de l'Institut Pierre-Simon Laplace No 27

ISSN No 1288-1619.

Contents
Abstract / Résumé
Disclaimer
Introduction
Model basics
- Primitive Equations
- The Horizontal Pressure Gradient
- Curvilinear z-coordinate System
- Curvilinear generalised vertical coordinate System
- Subgrid Scale Physics
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
- Domain: Horizontal Grid (mesh) (domhgr)
- Domain: Vertical Grid (domzgr)
- Domain: Initial State (istate and dtatsd)
Ocean Tracers (TRA)
- Tracer Advection (traadv)
- Tracer Lateral Diffusion (traldf)
- Tracer Vertical Diffusion (trazdf)
- External Forcing
- Bottom Boundary Layer (trabbl.F90)
- Tracer damping (tradmp)
- Tracer time evolution (tranxt)
- Equation of State (eosbn2)
- Horizontal Derivative in zps-coordinate (zpshde)
Ocean Dynamics (DYN)
- Sea surface height and diagnostic variables ( $\eta$ , $\zeta$ , $\chi$ , )
- Coriolis and Advection: vector invariant form
- Coriolis and Advection: flux form
- Hydrostatic pressure gradient (dynhpg)
- Surface pressure gradient (dynspg)
- Lateral diffusion term (dynldf)
- Vertical diffusion term (dynzdf.F90)
- External Forcings
- Time evolution term (dynnxt)
- Neptune effect (dynnept)
Surface Boundary Condition (SBC, ISF, ICB)
- Surface boundary condition for the ocean
- Input Data generic interface
- Analytical formulation (sbcana)
- Flux formulation (sbcflx)
- Bulk formulation (sbcblk_core, sbcblk_clio or sbcblk_mfs)
- Coupled formulation (sbccpl)
- Atmospheric pressure (sbcapr)
- Tidal Potential (sbctide)
- River runoffs (sbcrnf)
- Ice shelf melting (sbcisf)
- Handling of icebergs (ICB)
- Miscellaneous options
Lateral Boundary Condition (LBC)
- Boundary Condition at the Coast (rn_shlat)
- Model Domain Boundary Condition (jperio)
- Exchange with neighbouring processors (lbclnk, lib_mpp)
- Unstructured Open Boundary Conditions (key_ bdy) (BDY)
Lateral Ocean Physics (LDF)
- Lateral Mixing Coefficient (ldftra, ldfdyn)
- Direction of Lateral Mixing (ldfslp)
- Eddy Induced Velocity (traadv_eiv, ldfeiv)
Vertical Ocean Physics (ZDF)
- Vertical Mixing
- Convection
- Double Diffusion Mixing (key_ zdfddm)
- Bottom and Top Friction (zdfbfr)
- Tidal Mixing (key_ zdftmx)
- 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)
- NetCDF4 Support (key_ netcdf4)
- Tracer/Dynamics Trends (TRD)
- 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
- Theoretical details
- Offline observation operator
- Observation Utilities
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
- Closed seas (closea.F90)
- Sub-Domain Functionality (jpizoom, jpjzoom)
- Accelerating the Convergence (nn_acc = 1)
- Accuracy and Reproducibility (lib_fortran.F90)
- Model Optimisation, Control Print and Benchmark
- Elliptic solvers (SOL)
Configurations
- Introduction
- Water column model: 1D model (C1D) (key_ c1d)
- ORCA family: global ocean with tripolar grid
- GYRE family: double gyre basin
- EEL family: periodic channel
- AMM: atlantic margin configuration
Curvilinear Coordinate Equations
- The chain rule for coordinates
- Continuity Equation in coordinates
- Momentum Equation in 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
- Discrete total energy conservation : flux form
- Discrete enstrophy conservation
- Conservation Properties on Tracers
- Conservation Properties on Lateral Momentum Physics
- Conservation Properties on Vertical Momentum Physics
- Conservation Properties on Tracer Physics
Iso-neutral diffusion and eddy advection using triads
- Choice of namtra_ldf namelist parameters
- Triad formulation of iso-neutral diffusion
- Eddy induced advection formulated as a skew flux
Coding Rules
- The program structure
- Coding conventions
- Naming Conventions
- The program structure
Index
Bibliography
About this document ...

Gurvan Madec and the NEMO Team
NEMO European Consortium2017-02-17