source: NEMO/branches/2019/dev_r10503_XIOS_RW_doc/RELEASE_NOTES.rst @ 10508

Last change on this file since 10508 was 10279, checked in by nicolasmartin, 23 months ago

Various improvments for quick start guide

  • implementation of Rtd theme (Read the Docs) with custom layout and style file
  • add reviewed BibTeX entries for NEMO references with DOI (manuals, guide, development strategy)
  • enhancement of bibliography management and configuration file for guide building
  • standardisation of headings markup
  • numerous edits
File size: 11.1 KB
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1**********************
2What's new in NEMO 4.0
3**********************
4
5.. contents::
6   :local:
7     
8Original sea-ice component SI\ :sup:`3`\
9========================================
10
11| Meeting in 2017, the `sea ice working group`_ decided to gather sea ice developers and
12  scientific expertise within the NEMO community in order to build a unified model.
13  The replacement of LIM (Louvain-la-Neuve Ice Model) has required the backport of
14  the desired functionalities from each of CICE, GELATO and LIM into a common code in the NEMO framework.
15| This new model has been named SI\ :sup:`3`\ ("sea ice cubed") and
16  means "**Sea Ice modelling Integrated Initiative**".
17
18- Physics
19
20  * Landfast ice: simple grounding with a "release" stress (not fully operational)
21  * Lateral melting
22  * Melt ponds: constant or `Holland 2012`_ formulation (and soon topographic melt ponds)
23  * Ice-atm. drags from `Lupkes 2012`_ (depending on ice concentration) or `Lupkes 2014`_
24    (Depending on sea ice concentration and atm. stability)
25- Numerics
26
27  * Advection: Ultimate-Macho scheme
28  * Rheology: adaptive EVP (`Kimmritz 2016`_)
29  * Coupling interface: conductivity as surface forcing instead of heat fluxes (Met Office requirement)
30- Performance
31
32  * All thermodynamics in 1D
33  * Reduced mpp communications
34- Users & developers friendly
35
36  * Comprehensive set of outputs (universal units and understandable names + includes limp)
37  * New architecture and namelist
38  * All processes can be decoupled from each other (switch on/off)
39  * Ice categories bounds can be defined by the user or set automatically
40  * For open boundaries, the number of ice categories from the forcing model can be different
41    from the number of categories in the regional simulation
42  * Fully compatible with AGRIF
43
44First Test Cases
45================
46
47Define and install a separate repository for test cases to all easy contributions from the NEMO Users Community
48
49Core components
50===============
51
52Passive tracer TOP and biogeochemical PISCES components
53-------------------------------------------------------
54
55- The passive tracers transport component was redesigned toward a modular structure and
56  users can enable each module directly through logical flags in namelist_top (no more Fortran macros!).
57- TOP on-line user documentation is available on NEMO Trac platform (`TOP User Quick Guide`_)
58- TOP currently accounts for the following 5 modules:
59
60  * ``CFC`` contains inorganic carbon tracers (CFC11/CFC12/SF6)
61  * ``MY_TRC`` is a template for new modules (or external couplings)
62  * ``AGE`` deals with water age tracking
63  * ``C14`` as a radiocarbon passive tracer
64  * ``PISCES`` the companion ecosystem model
65- A generalized infrastructure was developed to handle the prescription of either surface, coastal, or
66  open boundaries conditions for each passive tracer.
67- PISCES model contains new developments and modifications:
68
69  * Particulate Organic Carbon (POC) component comes with a new liability scheme,
70    while the former Kriest parameterisation was superseded;
71  * A complex iron chemistry scheme is now available, with an improved description of ligands for
72    the marine iron cycle
73  * Carbonate chemistry is based on MOCSY 2.0 routines (see `Orr and Epitalon 2015`_),
74    by complying also with CMIP6 standards.
75  * Ecosystem components can be optionally modelled by means of explicit nutrient quotas (PISCES-QUOTA)
76
77AGRIF (embedded zooms)
78----------------------
79
80The NEMO 4.0 includes new capabilities, configurations and test cases with AGRIF:
81
82.. role:: underline
83   :class: underline
84
85:underline:`New capabilities from NEMO 3.6 to NEMO 4.0`
86
87AGRIF is continuously maintained so that it could be activated with all NEMO components (OPA, sea-ice, TOP).
88Depending on NEMO version, it is nevertheless not the case so that some options may not be compatible with
89the use of online grid refinement.
90Check out the table below to know the status according to the NEMO release you may use.
91
92:underline:`Status of available options with AGRIF (if not listed, option is compatible with AGRIF)`:
93
94+--------------------------------------------------------+----------------+---------------------+
95|                                                        | NEMO 3.6       | NEMO 4.0            |
96+========================================================+================+=====================+
97| LIM2                                                   | yes            | ``-``               |
98+--------------------------------------------------------+----------------+---------------------+
99| LIM3/SI3                                               | no             | yes                 |
100+--------------------------------------------------------+----------------+---------------------+
101| TOP                                                    | yes            | yes                 |
102+--------------------------------------------------------+----------------+---------------------+
103| GLS vertical mixing                                    | no             | yes                 |
104+--------------------------------------------------------+----------------+---------------------+
105| z*                                                     | no             | yes                 |
106+--------------------------------------------------------+----------------+---------------------+
107| z~                                                     | no             | no                  |
108+--------------------------------------------------------+----------------+---------------------+
109| Lagrangian icebergs                                    | no             | no                  |
110+--------------------------------------------------------+----------------+---------------------+
111| East-west periodic and/or north fold bcs in zooms      | no             | no                  |
112+--------------------------------------------------------+----------------+---------------------+
113| Online timing                                          | no             | no                  |
114+--------------------------------------------------------+----------------+---------------------+
115| Stochastic parameterization                            | no             | no                  |
116+--------------------------------------------------------+----------------+---------------------+
117| Vertical coordinate change in zooms (``key_vertical``) | no             | yes, but not tested |
118+--------------------------------------------------------+----------------+---------------------+
119| Number of ghost cells                                  | 1 (hard coded) | 3 (parameter)       |
120+--------------------------------------------------------+----------------+---------------------+
121
122[Important notice concerning the change of ghost cells number]
123
124The default number of ghost cells (i.e. the number of cells that serve as open boundary data provision) has been
125increased from 1 to 3 in NEMO 4.0.
126This allows to properly handle boundary conditions for numerical schemes that
127have a discretization order greater than 2.
128On the user point of view this does not change anything++ except in the definition of level 1 grids in
129the ``AGRIF_FixedGrids.in`` file.
130In order to retrieve exactly the position of a nested grid in NEMO 4.0 one has to shift indices by
1312 points to the south-west.
132Taking the ``ICEDYN`` example above for NEMO 4.0, the "old" NEMO 3.6 corresponding file would contain::
133
134   1
135   36 65 36 65 3 3 3
136   0
137
138++ Child grid output files are now greater by 4 points in each direction.
139
140- Now compatible with new sea ice component and z* coordinate
141- Extended ghost cells area to properly handle scheme with spatial order >2
142- Added vertical refinement (beta)
143- Nesting tools for setup now up to date and working
144
145Adding of 3 Reference Configurations
146------------------------------------
147
148- ``AGRIF_DEMO``: 2 interlocked zooms (1:4 & 1:3) in the Nordic Seas + 1 zoom (1:1) at the equator
149- ``ORCA2_OFF_TRC``: a benchmark simulation environment to deal with inert carbon tracers dynamics by
150  exploiting the offline coupling with NEMO.
151- ``SPITZ12``: regional configuration around the Svalbard archipelago.
152
153Misc. improvments
154=================
155
156Physics
157-------
158
159- Bulk formulae : move to aerobulk package (`Brodeau 2017`_), i.e. NCAR, COARE and ECMWF bulk
160  (remove Clio and MFS bulk)
161- Fix for tracer conservation with split explicit free surface
162- Wetting and drying
163- iso-neutral mixing (iso and triad operators): add the Method of Stabilizing Correction (MSC)
164  (more accurate calculation) + add a bilaplacian case
165- Lateral physics (LDF): scale aware setting of eddy viscosity and diffusivity
166- Wave coupling: large scale wave interaction process added in momentum and tracer equations
167- Remove the acceleration of convergence
168
169Numerics
170--------
171
172- Added tidal self attraction and loading either read from a file or from usual "scalar" approximation
173- Vertical physics (ZDF) (modularity, share shear production calculation between TKE and GKS,
174  removal of all ZDF CPP keys, removal of avmu & avmv, minimization of MPP comm.: ~15 removed)
175- Remove the split-explicit ZDF scheme for both TRA and DYN
176- Lateral physics (LDF): simplification of user interface and removal of CPP keys
177- Add a 4th order centered (CEN) and Flux Corrected Transport (FCT) tracer advection
178  (using a 4th compact in the vertical)
179- Generalised lbc_lnk and lbc_nfd
180- Configuration interface completely rewritten (DOM module mainly suppressed,
181  and in place: domain_cfg.nc file, or usr_def module)
182- Vorticity: 2 new energy conserving scheme:  ENT with Coriolis defined at T-point
183  (better for Flux form) and EET a variant of EEN where e3t is used instead of e3f
184  (solved the issue with e3f specification but is not enstrophy conserving)
185- Wave coupling: coupled interface to external wave model
186
187Performances
188------------
189
190- MPI Message passing recoded to reduce number of MPI communications (suppression of redundant communications,
191  gather multiple communications into one)
192- Back to standard dynamical allocation (remove of wrk_alloc/dealloc statements)
193- XIOS software for IOs version 2 as default, and optionally available for restarts
194- Unify mppini
195- Use non uniform jpi/jpj with dynamic allocation to avoid ghost rows/columns
196
197Environment
198-----------
199
200- Revised structure of namelist_ref/_cfg and default reference values.
201- Reorganisation of SVN repository to be compliant with usual directory tree and facilitate building of
202  NEMO executable
203- Improvements of reliability through automatic and regular testing of the changes made in repository
204
205.. _sea ice working group:       http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups/SI3
206.. _TOP User Quick Guide:        http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups/top-dg/TOP-UserQuickGuide
207
208.. The following references should be in the manual bibliographies and referenced via 'bibliography' directive
209.. _Brodeau 2017:                http://doi.org/10.1175/JPO-D-16-0169.1
210.. _Holland 2012:                http://doi.org/10.1175/JCLI-D-11-00078.1
211.. _Lupkes 2012:                 http://doi.org/10.1029/2012JD017630
212.. _Lupkes 2014:                 http://doi.org/10.1002/2014JD022418
213.. _Kimmritz 2016:               http://doi.org/10.1016/j.ocemod.2016.03.004
214.. _Orr and Epitalon 2015:       http://doi.org/10.5194/gmd-8-485-2015
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