source: NEMO/branches/2019/dev_r10984_HPC-13_IRRMANN_BDY_optimization/RELEASE_NOTES.rst @ 11998

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Review inclusion of RELEASE_NOTES in the index and several changes in formatting

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1*************
2Release Notes
3*************
4
5New sea-ice component SI3 (in place of LIMx)
6============================================
7
8- Physics
9
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>`)
14
15- Numerics
16
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)
20
21- Performance: all thermodynamics in 1D and reduced mpp communications
22- Usability (users & developers friendly)
23
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
31
32AGRIF for embedded zooms
33========================
34
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
40
41Enhancements
42============
43
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)
54
55Test Cases
56==========
57
58The first test cases available for now are:
59
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
67
68New Reference configurations
69============================
70
71``AGRIF_DEMO``: 2 interlocked zooms (1:4 & 1:3) in the Nordic Seas + 1 zoom (1:1) at the equator
72
73``SPITZ12``: regional configuration around the Svalbard archipelago
74
75Wave coupling
76=============
77
78Coupled interface to external wave model
79
80Large scale wave interaction process added in momentum and tracer equations
81
82Passive tracer TOP and biogeochemical PISCES components
83=======================================================
84
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:
91
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)
96
97High Performance Computing (HPC): performances improvements
98===========================================================
99
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
105
106Simplification and robustness
107=============================
108
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: ``domain_cfg.nc`` file, or ``usr_def`` module)
119
120Collaborative Development Environment
121=====================================
122
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
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