= NEMO Release notes

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Last edition: '''[[Wikinfo(changed_ts)]]''' by '''[[Wikinfo(changed_by)]]'''

{{{#!comment
TO BE ADDED (was before 3.2 but version to be checked):

        transition to full native FORTRAN 90, deep code restructuring and drastic reduction of CPP keys ;
        introduction of partial step representation of bottom topography [Barnier et al. 2006, Le Sommer et al. 2009, Penduff et al. 2007] ;
        partial reactivation of a terrain-following vertical coordinate (s- and hybrid s-z) with the addition of several options for pressure gradient computation 5 ;
        more choices for the treatment of the free surface : full explicit, split-explicit or filtered schemes, and suppression of the rigid-lid option ;
        non linear free surface associated with the rescaled height coordinate z* or s;
        additional schemes for vector and flux forms of the momentum advection ;
        additional advection schemes for tracers ;
        online diagnostics : tracers trend in the mixed layer and vorticity balance ;
        rewriting of the I/O management with the use of an I/O server ;
        generalized ocean-ice-atmosphere-CO2 coupling interface, interfaced with OASIS 3 coupler ;
        surface module (SBC) that simplify the way the ocean is forced and include two bulk formulea (CLIO and CORE) and which includes an on-the-fly in- terpolation of input forcing fields ;
        major changes in the TKE schemes : it now includes a Langmuir cell pa- rameterization [Axell 2002], the Mellor and Blumberg [2004] surface wave breaking parameterization, and has a time discretization which is energeti- cally consistent with the ocean model equations [Burchard 2002, Marsaleix et al. 2008] ;
        tidal mixing parametrisation (bottom intensification) + Indonesian specific tidal mixing [Koch-Larrouy et al. 2007] ;
}}}
== 2005-2006 From Tag nemo_v1 to nemo_v2

=== New science:

* Add the 1D configuration option
* KPP turbulent closure scheme implementation
* Implement CFC tracers and p4z
* Add new surface pressure gradient algorithms and its interface to Open Boundary Conditions module
* First implementation of AGRIF 2 ways nesting tool
* Implement overturning computation for main basins
* Implement ice damping in buffer zones
* Implement 1D on-line & off-line passive tracers
* Implement new tracers advection scheme UBS
* Implement computation of mean trends in the mixed layer taking into account the asselin time filter

=== New High Performance Computing:

* Implementation of a hierarchy of debugging levels
* Rewriting of NEMO-TOP biogeochemistry component
* Remove some of the bio models (p3zd,npzd, hamocc3, age, gosac)
* Switch to IOIPSL-3-0 new input output library
* Switch rigid lid to option rather than default
* Re-organization of coordinate definition, scale factors are now 3d by default, include file for partial steps has been removed
* Implement IO Manager module
* Enables bit comparison between single and multiple processor runs
* Implement OASIS3 and OASIS4 interfaces to buid coupled ocean-atmosphere configurations

== 2007 From tag nemo_v2 to nemo_2_3

=== New science:

* Implement non linear free surface (variable volume)
* Implement Kriest parameterization in NEMO-TOP
* Implement AGRIF 2 ways nesting for passive tracers
* Implement quickest scheme for tracers

=== New High Performance Computing:

== 2008 From tag nemo_v2.3 to nemo_v3_1

=== New science:

* Open Boundaries BDY package as unstructured boundaries, and OBCs pakage entirely cleaned and documented,
* New TKE physics
* New sea-ice NEMO-LIM 3.0 (key_lim3) component including: ice-thickness categories, EVP rheology on C-Grid, ice salinity variations interfaced with the new surface module

=== New High Performance Computing:

* New surface module in NEMO-OPA
* Namelists entire re-organisation, improve readability and coherence
* Improvement of IOManager now able to handle long simulations and so to manage successive input files from one year to an other
* Improvements of AGRIF performance and users interface
* improved vectorial performances (~5%) of the rheology module in LIM 2.0
* TOP reorganisation with one directory by model Fully written in Fortran 90, include all SMS models ( PISCES, LOBSTER, CFC ...) and interface for users developemnt through the MY_TRC directory)
* Update IOM modules for OFFLINE tracers
* Interpolation On the Fly
* Passive tracers used with AGRIF package

== 2009 From tag nemo_v3_1 to nemo_v3_2

''This release has been mainly designed for climate models, with enhanced coupling interface and implementation of AR5 diagnostics.''

=== New science:

* tidal mixing parametrization (bottom intensification) + Indonesian specific tidal mixing
* RGB light penetration and optional use of ocean color
* vvl option has been restored, including revisit free-surface time-splitting algorithm to reach stability and satisfying result and have vvl option available for all type of coordinates (z, zps, s)
* TKE change in the surface boundary condition, especially in coupled mode (mean stress module send by the atmosphere)

=== New High Performance Computing:

* the way to handle outputs has been improved
* implementation of IOM for output with the following functionalities : allows to output at few frequencies during same simulation, e.g both monthly and daily; output vectors/scalars is also available (for a strait transport calculation or for a vertical profile associated to buoys location for instance), and make easier the way to add an output everywhere in the code
* Suppression of rigid-lid option and no more island specific treatment
* Cleaning of lib_mpp
* SHMEM option has been removed
* north fold treatment is now done once for all in a new routine lbcnfd.F909 instead of being duplicated
* suppression of redundant east-west communication phase (ORCA grid case)

== 2010 From tag nemo_v3_2 to nemo_v3_3
* introduction of a modified leapfrog-Asselin filter time stepping scheme [Leclair and Madec 2009] ;
* additional scheme for iso-neutral mixing [Griffies et al. 1998], although it is still a ”work in progress” ;
* a rewriting of the bottom boundary layer scheme, following Campin and Goosse [1999] ;
* addition of a Generic Length Scale vertical mixing scheme, following Um- lauf and Burchard [2003] ;
* addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics ;
* addition of a diurnal cycle on solar radiation [Bernie et al. 2007] ; river runoffs added through a non-zero depth, and having its own temperature and salinity ;
* CORE II normal year forcing set as the default forcing of ORCA2-LIM configuration ;
* generalisation of the use of fldread.F90 for all input fields (ocean climatology, sea-ice damping...) ;
* addition of an on-line observation and model comparison (thanks to NEMOVAR project) ;
* optional application of an assimilation increment (thanks to NEMOVAR project) ;
* coupling interface adjusted for WRF atmospheric model ;
* C-grid ice rheology now available for both LIM-2 and LIM-3[Bouillon et al. 2009] ;
* LIM-3 ice-ocean momentum coupling applied to LIM-2 ;
* a deep re-writting and simplification of the off-line tracer component (OFF SRC) ;
* the merge of passive and active advection and diffusion modules ;
* Use of the Flexible Configuration Manager (FCM) to build configurations, generate the Makefile and produce the executable ;
* Linear-tangent and Adjoint component (TAM) added, phased with v3.0

In addition, several minor modifications in the coding have been introduced with the constant concern of improving the model performance.

== 2011 From tag nemo_v3_3 to nemo_v3_4

This is a major release and the documentation has been updated in consequence.

=== Major improvements

==== New physics and numerics

* new pressure gradient suitable for s-coordinate 
* completion of Griffies iso-neutral diffusion 
* back to a semi-implicit bottom friction 
* add Pacanowski-Philander scheme for computation of Ekman depth 
* add a new bulk formulae (so called MFS)
* introduce a drag coefficient compute by wave model 
* add tidal potential forcing 
* Netpune effect parametrization
* point to point MPI communication for north fold 
* allow sub timestepping for biogeochemistry models when using non-linear free surfac
* Improvement in PISCES (light limitation ; quota model for iron ; use Pa in gas exchange ; fldread for all data ; calcite dissolution & calcon salinity dependence )

==== Configurations, diagnostics and tools

* suppression of POMME configuration
* addition of a regional configuration AMM12
* improvement of format for lagrangian floats
* online computing of transport across sections
* tidal harmonic analysis 
* tools to prepare input files for observation operator
* timing functionality 

==== System simplification

* simplification of dynamic allocation
* end of merge TRA/TRA (no more separate 3d arrays for tracers, only 4d)
* suppression of obsolete hpg options
* more flexible definition of BDY input data
* simplification of interfaces toward biogeochemical models
* interface with CICE in coupled mode
* Use of fldread to read/interpolate data for passive tracers and dynamical input data for OFFLINE configurations

 
== 2012 From nemo_v3_4 to nemo_v3_5

Brief overview of the v3_5_alpha majors improvements and developments:

    The new Input/Output server XIOS is a major evolution including a versatile xml interface, the dedicated processors for I/O functionality allowing improved scalability, and a large performance improvement on massively parallel platforms. This option is now set as the default one. The previous IOIPSL code and interface are kept as backup options at this stage.
=== Interfaces:
* Ocean/ice/biogeochemistry/atmosphere: revisit heat/salt(tracers)/mass fluxes ; new levitating & embedded sea-ice (for LIM & CICE)
* AGRIF is now sea-ice (LIM) compatible using a new AGRIF package shared with other GCMs
* Compilation with external biogeochemistry model
* Improved CICE-NEMO interface
* ICB module (Bigg et al 1997, Martin and Adcroft 2010): icebergs as lagrangian floats (~200,000!) allowing improved fresh water input especially in the Southern ocean
* SAS: Stand Alone Surface module allowing testing of forcing set with bulk formulae, to run sea-ice models without ocean, to run ICB icebergs module alone, and to test AGRIF with sea-ice
* Biogeochemical component NEMO-TOP: PISCES will now include the LOBSTER functionalities, becoming more general and allowing a simplification and reduction of code size
* Open boundaries module: merging the two existing options (OBC and BDY) has made some important progress (end of the work expected for 2013)
* Wave-NEMO interface module has been further developed with the introduction of the reading of the 2D stoke drift and wave number and the on-line computation of the 3D stoke drift current.

Also:

* A new vertical sigma coordinate stretching function (Siddorn and Furner OM 2012r)
    Smagorinsky eddy coefficients: Smagorinsky type diffusivity/viscosity for lateral mixing has been introduced
* Analytical tropical cyclones taken in account using track and magnitude observations (Vincent et al. JGR 2012a,b)
* MUSCL: an option for local up-stream advection schemes which are useful in case of rivers, straits and in proximity of open lateral boundary conditions. The possibility to switch from MUSCL to a standard up-stream scheme has been included in the MUSCL advection routine
* NEMO-OBS: observation operators. Add a model equivalent of SST at night
* Log layer for bottom friction is now added (sigma coordinates only)
* Evolution of SETTE validation tool

== 2014 From nemo_v3_5 to nemo_v3_6

Includes all the developments of 3_5 (especially the new XIOS IO system) , and new features:

* Open boundaries: completion of BDY/OBC merge
* Solved 2 time stepping issues
* Faster split-explicit time stepping, Z-tilde ALE coordinates, implicit bottom friction
* First version of Configuration Manager
* Major evolution of LIM sea-ice model (including towards LIM2/LIM3 merge)
* Standalone OBS component and improvements in OBS&ASM
* Coupled interface for next IPCC requirements (multi category sea-ice, calving and iceberg module)
* Runoff improved and SBC with BGC
* MPP assessment and optimisation
* Standard Fox Kemper parametrisation
* First steps of wave coupling
* On line coarsening of ocean I/O
* Solar flux filtering at daily frequency to force BGC component
* Atmospheric forcing at land-ocean interface

== 2015: From nemo_v3_6 to nemo_v3_6_STABLE: the release from CMIP6 experiments:

Main new features

* Coupled interface for next IPCC requirements (multi category sea-ice, calving and iceberg module)
* Runoff improved and SBC with BGC
* Solar flux filtering at daily frequency to force BGC component
* Major evolution of LIM sea-ice model (including LIM3 in mono category, i.e. similar to LIM2)
* On line coarsening of ocean I/O
* Ocean and ice allowed to be explicitly coupled through OASIS, using StandAlone Surface module)
* First steps of wave coupling
* MPI optimisation
* XIOS new IO system
* Standard Fox Kemper parametrisation
* Atmospheric forcing at land-ocean interface
* Open boundaries: completion of BDY/OBC merge
* Solved 2 time stepping issues
* Faster split-explicit time stepping, Z-tilde ALE coordinates, implicit bottom friction
* First version of Configuration Manager
* Standalone OBS component and improvements in OBS&ASM

==== Features becoming obsolete:

* LIM2 (replaced by LIM3 monocategory)

==== List of associated branches

* On line coarsening of biogeochemistry