==============================================================
== HOW TO set up user’s configuration in NEMO version 4.0 : ==
==============================================================
This document describes how a configuration is set up in NEMO.

In NEMO 4.0 two types of configurations can be build: global/regional and idealized.

- create ./cfgs/your_config
- case 1: regional or global 
    => ln_read_cfg = .true. in ./cfgs/your_config/EXP00/namelist_cfg (i.e. read domain_cfg.nc)
- case 2: idealized 
    =>in ./cfgs/your_config/EXP00/namelist_cfg :
      ln_read_cfg = .false. (need to define usrdef_hgr.F90 and usrdef_zgr.F90) 
      ln_usr = .true.       (need to define usrdef_sbc.F90)    
    => copy ./src/OCE/USR in ./cfgs/your_config/MY_SRC routines nedeed to set up domain, forcing fields and initial state
    
  Routines in NEMOGCM/NEMO/OCE/USR define analytically the domain, the initial state and the surface boundary conditions for the reference configuration GYRE.
     •   usrdef_hgr.F90 and usrdef_zgr.F90 : define horizontal and vertical grid
     •   usrdef_sbc.F90    : provides at each time-step the surface boundary condition, i.e. the momentum, heat and freshwater fluxes
     •   usrdef_istate.F90 : defines initialization of the dynamics and tracers
     •   usrdef_fmask.F90  : used just in ORCA CONFIGURATIONS for alteration of f-point land/ocean mask in some straits 
     •   usrdef_closea.F90 : used just in ORCA CONFIGURATIONS for specific treatments associated with closed seas
     •   usrdef_nam.F90    : set the domain characteristics of a user configuration

  Other analytical examples are given in ./tests.

===========================================
== The domain_cfg.nc file must contain : ==
===========================================
   int ORCA  , ORCA_index            : configuration name, configuration resolution
   int jpiglo, jpjglo , jpkglo       : global domain sizes 
   int jperio                        : lateral global domain b.c. 
   int ln_zco, ln_zps, ln_sco        : flags for z-coordinate, z-coordinate with partial steps and s-coordinate 
   int ln_isfcav                     : flag  for ice shelf cavities 
   double glamt, glamu, glamv, glamf : geographic position 
   double gphit, gphiu, gphiv, gphif : geographic position
   double iff, ff_f, ff_t            : Coriolis parameter (if not on the sphere)
   double e1t, e1u, e1v, e1f         : horizontal scale factors
   double e2t, e2u, e2v, e2f         : horizontal scale factors
   double ie1e2u_v, e1e2u, e1e2v     : U and V surfaces (if grid size reduction in some straits)
   double e3t_1d, e3w_1d             : reference vertical scale factors at T and W points
   double e3t_0, e3u_0, e3v_0, e3f_0, e3w_0 : vertical scale factors 3D coordinate at T,U,V,F and W points
   double e3uw_0,e3vw_0              : vertical scale factors 3D coordinate at UW and VW points
   int bottom_level, top_level       : last wet T-points, 1st wet T-points (for ice shelf cavities)

=======================================
= HOW TO CREATE domain_cfg.nc file : ==
=======================================
Two options are possible :

 - users can create with his own tool the domain_cfg.nc with all mandatory fields.  

 - tool is available in ./tools/DOMAINcfg based on NEMO 3.6 version. See ./tools/DOMAINcfg/README.

.. role:: rstblue
.. role:: rstgrey
.. role:: rstgreen

================
NEMO Ocean Model
================

NEMO_ (Nucleus for European Modelling of the Ocean) is a state-of-the-art modelling framework of 
ocean related engines for oceanographic research, operational oceanography, seasonal forecast and 
[paleo]climate studies.

The NEMO ocean model has 3 major components:

- :rstblue:`OPA` is fundamental to all users by modelling the ocean [thermo]dynamics and 
  solving the primitive equations;
- :rstgrey:`LIM` for sea-ice simulates ice [thermo]dynamics, brine inclusions and 
  subgrid-scale thickness variations;
- :rstgreen:`TOP-PISCES` models biogeochemistry with TOP for 
  the on/offline oceanic tracers transport and PISCES for the biogeochemical processes.

These physical engines are described in their respective `reference publications`_.

They are complemented by a 2-way nesting software (AGRIF_) and 
a versatile data assimilation interface with 3 different modules
(linear-tangent TAM, observational operators OBS, and increment ASM).

------------
Applications
------------

| Distributed under CeCILL license (GNU GPL compatible - see ``LICENSE``), 
  the framework offers several builtins reference configurations to 
  check your computing architecture and evaluate the model skills and performances (``./cfgs``).
| The end user could also find some idealized test cases on the web to serve as examples and 
  to study particular processes.

A set of tools is also provided to setup your own configuration and 
[pre|post]process your data (``./tools``).

-------
Options
-------

For writing diagnostics in a efficient way, NEMO make use of XIOS_ server which 
controlled the outputs using XML input file.

To enable Earth system modelling, NEMO can be interfaced via 
OASIS_ coupleur to external components such as atmospheric models or 
alternative models of sea-ice or biogeochemistry.

-------------
Documentation
-------------

The NEMO reference manual can be generated from the LaTeX source code (``./doc``), 
either in PDF or in HTML format, but it mights require some additionnal installations.

In any case, both formats are available online on the `NEMO website`__.

---------------------
Community development
---------------------

| The NEMO Consortium gathering 6 European institutes organises the sustainable development in order to 
  keep a reliable evolving system since 2008.
| It defined the multiyear development strategy which is implemented by the NEMO System Team.

--------
Acronyms
--------

AGRIF
 Adaptive Grid Refinement In Fortran

LIM
 Louvain-la-Neuve Ice Model

OPA
 "Océan PArallélisé" (french)

PISCES
 Pelagic Interactions Scheme for Carbon and Ecosystem Studies

TAM
 Tangent Adjoint Model

TOP
 Tracers in Ocean Paradigm

XIOS
 XML Input Output Server

----

.. _AGRIF:                  http://agrif.imag.fr
.. _Forge:                  http://forge.ipsl.jussieu.fr/nemo
.. _NEMO:                   http://www.nemo-ocean.eu
.. _OASIS:                  http://verc.enes.org/oasis
.. _reference publications: http://www.nemo-ocean.eu/bibliography/documentation
.. _XIOS:                   http://forge.ipsl.jussieu.fr/ioserver

.. __:  NEMO_