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Changelog – NEMO

Version 16 (modified by nicolasmartin, 4 years ago) (diff)



Last edition: Wikinfo(changed_ts)? by Wikinfo(changed_by)?

2019 v4.0 (Jan. 2019)

  • New sea-ice component SI3 (in place of LIMx)
    • Improvements in physics
      • Lateral melting
      • Melt ponds: constant or Holland et al. 2012 formulation (and soon topographic melt ponds)
      • Ice-atm. drags from Lupkes et al. 2012 (depending on ice concentration) or Lupkes et al. 2015 (depending on sea ice concentration and atm. stability)
      • Landfast ice (Lemieux et al. 2016)
    • Improvements in numerics
      • Advection: Ultimate-Macho scheme
      • Rheology: adaptive EVP (Kimmritz et al. 2017)
      • Coupling interface: conductivity as surface forcing instead of heat fluxes (Met-Office requirement)
    • Improvements in performance
      • All thermodynamics in 1D
      • Reduced mpp communications
    • Users & developers friendly
      • Comprehensive set of outputs (universal units and understandable names + includes cmip)
      • New architecture and namelist
      • All processes can be decoupled from each other (switch on/off)
      • Ice categories bounds can be defined by the user or set automatically
      • For open boundaries, the number of ice categories from the forcing model can be different from the number of categories in the regional simulation
      • Fully compatible with AGRIF
      • Revised documentation
  • AGRIF for embedded zooms:
    • Now compatible with new sea ice component
    • Now compatible with z* coordinate
    • Extended ghost cells area to properly handle scheme with spatial order >2
    • Added vertical refinement (beta)
    • Nesting tools for setup now up to date and working
  • Enhancements
    • Fix for tracer conservation with split explicit free surface
    • Bulk formulae : move to aerobulk package (Brodeau et al. 2016), i.e. NCAR, COARE and ECMWF bulk (remove Clio and MFS bulk)
    • Wetting and drying
    • Added tidal self attraction and loading either read from a file or from usual "scalar" approximation
    • Add a 4th order centered (CEN) and Flux Corrected Transport (FCT) tracer advection (using a 4th compact in the vertical)
    • iso-neutral mixing (iso and triad operators): add the Method of Stabilizing Correction (MSC) (more accurate calculation) + add a bilaplacian case
    • Lateral physics (LDF): scale aware setting of eddy viscosity and diffusivity
    • Vorticity: 2 new energy conserving scheme: ENT with Coriolis defined at T-point (better for Flux form) and EET a variant of EEN where e3t is used instead of e3f (solved the issue with e3f specification but is not enstrophy conserving)
  • Test Cases
    • The test cases are academic setups allowing to explore specific features. They can also be useful for schools and trainings.
    • Test cases are avaiable from | NEMO Consortium github
    • The first test cases available at release time are:
      • CANAL: east-west periodic canal of variable size with several initial states and associated geostrophic currents (zonal jets or vortex)
      • ICE_AGRIF : east-west + north-south periodic channel. The common configuration includes an AGRIF zoom (1:3) in the middle of the basin to test how an ice patch is advected through it but one can also test the advection schemes (Prather and Ultimate-Macho) by removing the key_agrif in the cpp keys.
      • ISOMIP: simple box configuration with an ice shelf with simple geometry on top. The purpose of this test case is to evaluate the impact of various schemes and new development with iceshelf cavities. The exact original setup is described here.
      • LOCK-EXCHANGE:classical fluid dynamics experiment that has been adapted by Haidvogel and Beckmann (1999) for testing advection schemes in ocean circulation models. It has been used by several authors including Burchard and Bolding (2002) and Ilıcak et al. (2012). The LOCK EXCHANGE experiment can in particular illustrate the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing
      • OVERFLOW: illustrates the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing close to bottom topography. It is adapted from the non-rotating overflow configuration described in Haidvogel and Beckmann (1999) and further used by Ilıcak et al. (2012)
      • VORTEX: illustrates the propagation of an anticyclonic eddy over a Beta plan and flat bottom. It is implemented here with an online refined subdomain (thanks to AGRIF library) out of which the vortex propagates. It serves as a benchmark to diagnose nesting errors as in Debreu et al. (2012), Penven et al. (2006) and Spall and Holland (1991)
      • WAD: a set of simple closed basin geometries for testing the Wetting and drying capabilities. Examples range from a closed channel with EW linear bottom slope to a parabolic EW channel with a Gaussian ridge.
  • New Reference configurations
    • AGRIF_DEMO: 2 interlocked zooms (1:4 & 1:3) in the Nordic Seas + 1 zoom (1:1) at the equator
    • SPITZ12: regional configuration around the Svalbard archipelago
  • Wave coupling
    • Coupled interface to external wave model
    • Large scale wave interaction process added in momentum and tracer equations
  • Passive tracer TOP and biogeochemical PISCES components
    • The passive tracers transport component was redesigned toward a modular structure and users can enable each module directly through logical flags in namelist_top (no more fortran macros!).
    • TOP on-line user documentation is available on NEMO Trac platform (TOP-UserQuickGuide)
    • TOP currently accounts for the following 5 modules: CFC contains inorganic carbon tracers (CFC11/CFC12/SF6), MY_TRC is a template for new modules (or external couplings), AGE deals with water age tracking, C14 as a radiocarbon passive tracer, and the companion ecosystem model PISCES.
    • A generalized infrastructure was developed to handle the prescription of either surface, coastal, or open boundaries conditions for each passive tracer.
    • A new configuration, named ORCA2_OFF_TRC, was created to provide a benchmark simulation environment to deal with inert carbon tracers dynamics by exploiting the offline coupling with NEMO.
    • PISCES model contains new developments and modifications:
      • Particulate Organic Carbon (POC) component comes with a new liability scheme, while the former Kriest parametrisation was superseded;
      • A complex iron chemistry scheme is now available, with an improved description of ligands for the marine iron cycle
      • Carbonate chemistry is based on MOCSY 2.0 routines (see Orr and Epitalon, 2015), by complying also with CMIP6 standards.
      • Ecosystem components can be optionally modelled by means of explicit nutrient quotas (PISCES-QUOTA)
  • High Performance Computing: performances improvements
    • Reduce number of MPI communications (suppression of redundant communications, gather multiple communications into one)
    • Use of MPI-3 asynchronous routines for performance (use key_mpi2 if MPI-3 not available)
    • Back to standard dynamical allocation (remove of wrk_alloc/dealloc statements)
    • XIOS software for IOs version 2.5 as default, and optionally available for restarts
  • Simplification and robustness
    • Revised structure of namelist_ref/_cfg and default reference values.
    • Lateral physics (LDF): simplification of user interface and removal of CPP keys
    • Vertical physics (ZDF) (modularity, share shear production calculation between TKE and GKS, removal of all ZDF CPP keys, removal of avmu & avmv, minimization of MPP comm.: ~15 removed)
    • Remove the split-explicit ZDF scheme for both TRA and DYN
    • Remove the acceleration of convergence
    • Generalised lbc_lnk and lbc_nfd
    • Unify mppini
    • Use non uniform jpi/jpj with dynamic allocation to avoid ghost rows/columns
    • MPI Message passing re coded
    • Configuration interface completely rewritten (DOM module mainly suppressed , and in place: file, or usr_def module)
  • Collaborative Development Environment
    • Access to information on NEMO wiki reorganised through portals for users/developers/System Team and complete refactoring of all wiki pages and their layout
    • Reorganisation of svn repository to be compliant with usual directory tree and facilitate building of NEMO executable
    • Define and install a separate repository for test cases to all easy contributions from the NEMO Users Community
    • Forums created
    • NEMO public web site has been cleaned and is now much nicer (using Wordpress rather than EzP)
    • New mailing lists have been set up
    • Improvements of reliability through automatic and regular testing of the changes made in repository

2015 v3.6 stable - CMIP6 (Jun. 2015)

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

2014 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

2012 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.


  • 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.


  • 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

2011 v3.4 (Feb. 2012)

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

2010 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” ;
  • 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 ;
  • Deep re-writting and simplification of the off-line tracer component (OFF SRC) ;
  • 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.

2009 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, 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

  • 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.F90 instead of being duplicated
  • Suppression of redundant east-west communication phase (ORCA grid case)

2008 v3.1

New science

  • Open Boundaries BDY package as unstructured boundaries, and OBC package 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 development through the MY_TRC directory)
  • Update IOM modules for OFFLINE tracers
  • Interpolation On the Fly
  • Passive tracers used with AGRIF package

2007 v2.3

New science

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

New High Performance Computing

2005-2006 v2.0

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