The Nucleus for European Modelling of the Ocean (NEMO) is a framework of ocean related engines, namely OPA1.1 for the ocean dynamics and thermodynamics, LIM1.2 for the sea-ice dynamics and thermodynamics, TOP1.3 for the biogeochemistry (both transport (TRP) and sources minus sinks (LOBSTER, PISCES)1.4. It is intended to be a flexible tool for studying the ocean and its interactions with the other components of the earth climate system (atmosphere, sea-ice, biogeochemical tracers, ...) over a wide range of space and time scales. This documentation provides information about the physics represented by the ocean component of NEMO and the rationale for the choice of numerical schemes and the model design. More specific information about running the model on different computers, or how to set up a configuration, are found on the NEMO web site (www.nemo-ocean.eu).
The ocean component of NEMO has been developed from the OPA model, release 8.2, described in Madec et al. . This model has been used for a wide range of applications, both regional or global, as a forced ocean model and as a model coupled with the sea-ice and/or the atmosphere.
This manual is organised in as follows. Chapter 2 presents the model basics, the equations and their assumptions, the vertical coordinates used, and the subgrid scale physics. This part deals with the continuous equations of the model (primitive equations, with temperature, salinity and an equation of seawater). The equations are written in a curvilinear coordinate system, with a choice of vertical coordinates ( or , with the rescaled height coordinate formulation z*, or s*). Momentum equations are formulated in the vector invariant form or in the flux form. Dimensional units in the meter, kilogram, second (MKS) international system are used throughout.
The following chapters deal with the discrete equations. Chapter 3 presents the time domain. The model time stepping environment is a three level scheme in which the tendency terms of the equations are evaluated either centered in time, or forward, or backward depending of the nature of the term. Chapter 4 presents the space domain. The model is discretised on a staggered grid (Arakawa C grid) with masking of land areas. Vertical discretisation used depends on both how the bottom topography is represented and whether the free surface is linear or not. Full step or partial step -coordinate or - (terrain-following) coordinate is used with linear free surface (level position are then fixed in time). In non-linear free surface, the corresponding rescaled height coordinate formulation (z* or s*) is used (the level position then vary in time as a function of the sea surface heigh). The following two chapters (5 and 6) describe the discretisation of the prognostic equations for the active tracers and the momentum. Explicit, split-explicit and filtered free surface formulations are implemented. A number of numerical schemes are available for momentum advection, for the computation of the pressure gradients, as well as for the advection of tracers (second or higher order advection schemes, including positive ones).
Surface boundary conditions (chapter 7) can be implemented as prescribed fluxes, or bulk formulations for the surface fluxes (wind stress, heat, freshwater). The model allows penetration of solar radiation There is an optional geothermal heating at the ocean bottom. Within the NEMO system the ocean model is interactively coupled with a sea ice model (LIM) and with biogeochemistry models (PISCES, LOBSTER). Interactive coupling to Atmospheric models is possible via the OASIS coupler [Valcke, 2006]. Two-way nesting is also available through an interface to the AGRIF package (Adaptative Grid Refinement in FORTRAN) [Debreu et al., 2008]. The interface code for coupling to an alternative sea ice model (CICE, Hunke and Lipscomb ) has now been upgraded so that it works for both global and regional domains, although AGRIF is still not available.
Other model characteristics are the lateral boundary conditions (chapter 8). Global configurations of the model make use of the ORCA tripolar grid, with special north fold boundary condition. Free-slip or no-slip boundary conditions are allowed at land boundaries. Closed basin geometries as well as periodic domains and open boundary conditions are possible.
Physical parameterisations are described in chapters 9 and 10. The
model includes an implicit treatment of vertical viscosity and diffusivity. The lateral
Laplacian and biharmonic viscosity and diffusion can be rotated following a geopotential
or neutral direction. There is an optional eddy induced velocity [Gent and Mcwilliams, 1990] with a
space and time variable coefficient Tréguier et al. . The model has vertical harmonic
viscosity and diffusion with a space and time variable coefficient, with options to compute
the coefficients with Blanke and Delecluse , Pacanowski and Philander ,
or Umlauf and Burchard  mixing schemes.
CPP keys and namelists are used for inputs to the code.
Some CPP keys are implemented in the FORTRAN code to allow code selection at compiling step. This selection of code at compilation time reduces the reliability of the whole platform since it changes the code from one set of CPP keys to the other. It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time. Usual coding looks like :
#if defined key_option1
This part of the FORTRAN code will be active
only if key_option1 is activated at compiling step
The namelist allows to input variables (character, logical, real and integer) into the code. There is one namelist file for each component of NEMO (dynamics, sea-ice, biogeochemistry...) containing all the FOTRAN namelists needed. The implementation in NEMO uses a two step process. For each FORTRAN namelist, two files are read:
Model outputs management and specific online diagnostics are described in chapters 11. The diagnostics includes the output of all the tendencies of the momentum and tracers equations, the output of tracers tendencies averaged over the time evolving mixed layer, the output of the tendencies of the barotropic vorticity equation, the computation of on-line floats trajectories... Chapter 12 describes a tool which reads in observation files (profile temperature and salinity, sea surface temperature, sea level anomaly and sea ice concentration) and calculates an interpolated model equivalent value at the observation location and nearest model timestep. Originally developed of data assimilation, it is a fantastic tool for model and data comparison. Chapter 13 describes how increments produced by data assimilation may be applied to the model equations. Finally, Chapter 16 provides a brief introduction to the pre-defined model configurations (water column model, ORCA and GYRE families of configurations).
The model is implemented in FORTRAN 90, with preprocessing (C-pre-processor). It runs under UNIX. It is optimized for vector computers and parallelised by domain decomposition with MPI. All input and output is done in NetCDF (Network Common Data Format) with a optional direct access format for output. To ensure the clarity and readability of the code it is necessary to follow coding rules. The coding rules for OPA include conventions for naming variables, with different starting letters for different types of variables (real, integer, parameter...). Those rules are briefly presented in Appendix E and a more complete document is available on the NEMO web site.
The model is organized with a high internal modularity based on physics. For example, each trend (, a term in the RHS of the prognostic equation) for momentum and tracers is computed in a dedicated module. To make it easier for the user to find his way around the code, the module names follow a three-letter rule. For example, traldf.F90 is a module related to the TRAcers equation, computing the Lateral DiFfussion. Furthermore, modules are organized in a few directories that correspond to their category, as indicated by the first three letters of their name (Tab. 1.1).
The manual mirrors the organization of the model. After the presentation of the continuous equations (Chapter 2), the following chapters refer to specific terms of the equations each associated with a group of modules (Tab. 1.1).
|Chapter 3||-||model time STePping environment|
|Chapter 4||DOM||model DOMain|
|Chapter 5||TRA||TRAcer equations (potential temperature and salinity)|
|Chapter 6||DYN||DYNamic equations (momentum)|
|Chapter 7||SBC||Surface Boundary Conditions|
|Chapter 8||LBC||Lateral Boundary Conditions (also OBC and BDY)|
|Chapter 9||LDF||Lateral DiFfusion (parameterisations)|
|Chapter 10||ZDF||vertical (Z) DiFfusion (parameterisations)|
|Chapter 11||DIA||I/O and DIAgnostics (also IOM, FLO and TRD)|
|Chapter 12||OBS||OBServation and model comparison|
|Chapter 13||ASM||ASsiMilation increment|
|Chapter 15||SOL||Miscellaneous topics (including solvers)|
|Chapter 16||-||predefined configurations (including C1D)|
The main modifications from OPA v8 and NEMO/OPA v3.2 are :
The main modifications from NEMO/OPA v3.2 and v3.3 are :
The main modifications from NEMO/OPA v3.3 and v3.4 are :
The main modifications from NEMO/OPA v3.4 and v3.6 are :
Features becoming obsolete: LIM2 (replaced by LIM3 monocategory) ; IOIPSL (replaced by XIOS) ;
Features that has been removed : LOBSTER (now included in PISCES) ; OBC, replaced by BDY ;
Gurvan Madec and the NEMO Team
NEMO European Consortium2017-02-17