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Changeset 11713 for NEMO/trunk/RELEASE_NOTES.rst – NEMO

2019-10-17T17:49:19+02:00 (3 years ago)

Revamp TOP README and implement a TODO list
Review tracers.rst by adding snippets of source files
Add drafthtml target for Makefile related to draft building tag for sphinx-build to
display todo items at the top of the guide homepage


  • Use dedicated :file: role instead of ... for file or directory
  • Update BibTeX entries of NEMO reference publications by using :title: role
  • Dump of RELEASE_NOTES.rst
  • New file todos.rst to list all items declared with todo directive
  • Modify to add a conditional test for draft tag
1 edited


  • NEMO/trunk/RELEASE_NOTES.rst

    r10600 r11713  
    5 New sea-ice component SI3 (in place of LIMx) 
    6 ============================================ 
     5.. todo:: 
    8 - Physics 
    10   - Lateral melting 
    11   - Melt ponds: constant or :doi:`Holland et al. 2012<10.1175/JCLI-D-11-00078.1>` formulation (and soon topographic melt ponds) 
    12   - Ice-atm. drags from :doi:`Lupkes et al. 2012<10.1029/2012JD017630>` (depending on ice concentration) or :doi:`Lupkes et al. 2015<10.1002/2014JD022418>` (depending on sea ice concentration and atm. stability) 
    13   - Landfast ice (:doi:`Lemieux et al. 2016<10.1002/2016JC012006>`) 
    15 - Numerics 
    17   - Advection: Ultimate-Macho scheme 
    18   - Rheology: adaptive EVP (:doi:`Kimmritz et al. 2017<10.1016/j.ocemod.2016.03.004>`) 
    19   - Coupling interface: conductivity as surface forcing instead of heat fluxes (Met Office requirement) 
    21 - Performance: all thermodynamics in 1D and reduced mpp communications 
    22 - Usability (users & developers friendly) 
    24   - Comprehensive set of outputs (universal units and understandable names + includes CMIP) 
    25   - New architecture and namelist 
    26   - All processes can be decoupled from each other (switch on/off) 
    27   - Ice categories bounds can be defined by the user or set automatically 
    28   - For open boundaries, the number of ice categories from the forcing model can be different from the number of categories in the regional simulation 
    29   - Fully compatible with AGRIF_ 
    30   - Revised documentation  
    32 AGRIF for embedded zooms 
    33 ======================== 
    35 - Now compatible with new sea ice component 
    36 - Now compatible with z* coordinate 
    37 - Extended ghost cells area to properly handle scheme with spatial order >2 
    38 - Added vertical refinement (beta) 
    39 - Nesting tools for setup now up to date and working  
    41 Enhancements 
    42 ============ 
    44 - Fix for tracer conservation with split explicit free surface 
    45 - Bulk formulae : move to aerobulk package (:doi:`Brodeau et al. 2016<10.1175/JPO-D-16-0169.1>`), i.e. NCAR, COARE and ECMWF bulk (remove Clio and MFS bulk) 
    46 - Wetting and drying 
    47 - Added tidal self attraction and loading either read from a file or from usual "scalar" approximation 
    48 - Add a 4th order centered (CEN) and Flux Corrected Transport (FCT) tracer advection 
    49   (using a 4th compact in the vertical) 
    50 - iso-neutral mixing (iso and triad operators): 
    51   add the Method of Stabilizing Correction (MSC) (more accurate calculation) + add a bilaplacian case 
    52 - Lateral physics (``LDF``): scale aware setting of eddy viscosity and diffusivity 
    53 - 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)  
    55 Test Cases 
    56 ========== 
    58 The first test cases available for now are: 
    60 - ``CANAL``: east-west periodic canal of variable size with several initial states and associated geostrophic currents (zonal jets or vortex) 
    61 - ``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 
    62 - ``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 
    63 - ``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 :doi:`Ilıcak et al. (2012)<10.1016/j.ocemod.2011.10.003>`. The ``LOCK EXCHANGE`` experiment can in particular illustrate the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing 
    64 - ``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 :doi:`Ilıcak et al. (2012)<10.1016/j.ocemod.2011.10.003>` 
    65 - ``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 :doi:`Debreu et al. (2012)<10.1016/j.ocemod.2012.03.003>`, :doi:`Penven et al. (2006)<10.1016/j.ocemod.2005.05.002>` and :doi:`Spall and Holland (1991)<10.1175/1520-0485(1991)021<0205:ANPEMF>2.0.CO;2>` 
    66 - ``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 
    68 New Reference configurations 
    69 ============================ 
    71 ``AGRIF_DEMO``: 2 interlocked zooms (1:4 & 1:3) in the Nordic Seas + 1 zoom (1:1) at the equator 
    73 ``SPITZ12``: regional configuration around the Svalbard archipelago  
    75 Wave coupling 
    76 ============= 
    78 Coupled interface to external wave model 
    80 Large scale wave interaction process added in momentum and tracer equations  
    82 Passive tracer TOP and biogeochemical PISCES components 
    83 ======================================================= 
    85 - 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!) 
    86 - :doc:`TOP on-line user documentation<tracers>` 
    87 - 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`` 
    88 - A generalized infrastructure was developed to handle the prescription of either surface, coastal, or open boundaries conditions for each passive tracer 
    89 - 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 
    90 - PISCES model contains new developments and modifications: 
    92   - Particulate Organic Carbon (POC) component comes with a new liability scheme, while the former Kriest parametrisation was superseded 
    93   - A complex iron chemistry scheme is now available, with an improved description of ligands for the marine iron cycle 
    94   - Carbonate chemistry is based on MOCSY 2.0 routines (see :doi:`10.5194/gmd-8-485-2015 <Orr and Epitalon, 2015>`), by complying also with CMIP6 standards 
    95   - Ecosystem components can be optionally modelled by means of explicit nutrient quotas (PISCES-QUOTA)  
    97 High Performance Computing (HPC): performances improvements 
    98 =========================================================== 
    100 - Reduce number of MPI communications 
    101   (suppression of redundant communications, gather multiple communications into one) 
    102 - Use of MPI-3 asynchronous routines for performance (use ``key_mpi2`` if MPI-3 not available) 
    103 - Back to standard dynamical allocation (remove of wrk_alloc/dealloc statements) 
    104 - :xios:`XIOS software<>` for IOs version 2.5 as default, and optionally available for restarts  
    106 Simplification and robustness 
    107 ============================= 
    109 - Revised structure of ``namelist_ref`` / ``namelist_cfg`` and default reference values 
    110 - Lateral physics (``LDF``): simplification of user interface and removal of CPP keys 
    111 - 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) 
    112 - Remove the split-explicit ZDF scheme for both ``TRA`` and ``DYN`` 
    113 - Remove the acceleration of convergence 
    114 - Generalised ``lbc_lnk`` and ``lbc_nfd`` 
    115 - Unify mppini 
    116 - Use non uniform jpi/jpj with dynamic allocation to avoid ghost rows/columns 
    117 - MPI Message passing re coded 
    118 - Configuration interface completely rewritten (``DOM`` module mainly suppressed , and in place: ```` file, or ``usr_def`` module)  
    120 Collaborative Development Environment 
    121 ===================================== 
    123 - Access to information on wiki reorganised through portals for users/developers/System Team and complete refactoring of all pages and their layout 
    124 - Reorganisation of SVN repository to be compliant with usual directory tree and facilitate building of the executable 
    125 - Define and install a separate repository for test cases to all easy contributions from the community 
    126 - :forge:`Forums<discussion>` created 
    127 - :website:`Public web site<>` has been revamped and cleaned using Wordpress 
    128 - New mailing lists have been set up 
    129 - Improvements of reliability through automatic and regular testing of the changes made in repository  
     7   Complete "Release Notes" 
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