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Changeset 10595 for NEMO – NEMO

Changeset 10595 for NEMO


Ignore:
Timestamp:
2019-01-28T16:48:52+01:00 (5 years ago)
Author:
nicolasmartin
Message:

Same mistake as previously, forget to add the modified target file of the symbolic link

File:
1 edited

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  • NEMO/trunk/RELEASE_NOTES.rst

    r10592 r10595  
    1 ********************** 
    2 What's new in NEMO 4.0 
    3 ********************** 
     1************* 
     2RELEASE NOTES 
     3************* 
    44 
    55.. contents:: 
    66   :local: 
    7        
    8 Original sea-ice component SI\ :sup:`3`\ 
    9 ======================================== 
    107 
    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 |SI3| ("sea ice cubed") and means "**Sea Ice modelling Integrated Initiative**". 
     8New sea-ice component SI3 (in place of LIMx) 
     9============================================ 
    1610 
    1711- Physics 
     12  - Lateral melting 
     13  - Melt ponds: constant or :doi:`10.1175/JCLI-D-11-00078.1 <Holland et al. 2012>` formulation (and soon topographic melt ponds) 
     14  - Ice-atm. drags from :doi:`10.1029/2012JD017630 <Lupkes et al. 2012>` (depending on ice concentration) or 
     15    :doi:`10.1002/2014JD022418 <Lupkes et al. 2015>` (depending on sea ice concentration and atm. stability) 
     16  - Landfast ice (:doi:`10.1002/2016JC012006 <Lemieux et al. 2016>`) 
    1817 
    19   * Landfast ice: simple grounding with a "release" stress (not fully operational) 
    20   * Lateral melting 
    21   * Melt ponds: constant or `Holland 2012`_ formulation (and soon topographic melt ponds) 
    22   * Ice-atm. drags from `Lupkes 2012`_ (depending on ice concentration) or `Lupkes 2014`_ 
    23     (Depending on sea ice concentration and atm. stability) 
    2418- Numerics 
     19  - Advection: Ultimate-Macho scheme 
     20  - Rheology: adaptive EVP (:doi:`10.1016/j.ocemod.2016.03.004 <Kimmritz et al. 2017>`) 
     21  - Coupling interface: conductivity as surface forcing instead of heat fluxes (Met Office requirement) 
     22     
     23- Performance: all thermodynamics in 1D and reduced mpp communications 
     24     
     25- Usability (users & developers friendly) 
     26  - Comprehensive set of outputs (universal units and understandable names + includes cmip) 
     27  - New architecture and namelist 
     28  - All processes can be decoupled from each other (switch on/off) 
     29  - Ice categories bounds can be defined by the user or set automatically 
     30  - For open boundaries, the number of ice categories from the forcing model can be different from the number of categories in the regional simulation 
     31  - Fully compatible with AGRIF_ 
     32  - Revised documentation  
    2533 
    26   * Advection: Ultimate-Macho scheme 
    27   * Rheology: adaptive EVP (`Kimmritz 2016`_) 
    28   * Coupling interface: conductivity as surface forcing instead of heat fluxes (Met Office requirement) 
    29 - Performance 
     34AGRIF for embedded zooms 
     35======================== 
    3036 
    31   * All thermodynamics in 1D 
    32   * Reduced mpp communications 
    33 - Users & developers friendly 
     37- Now compatible with new sea ice component 
     38- Now compatible with z* coordinate 
     39- Extended ghost cells area to properly handle scheme with spatial order >2 
     40- Added vertical refinement (beta) 
     41- Nesting tools for setup now up to date and working  
    3442 
    35   * Comprehensive set of outputs (universal units and understandable names + includes limp) 
    36   * New architecture and namelist 
    37   * All processes can be decoupled from each other (switch on/off) 
    38   * Ice categories bounds can be defined by the user or set automatically 
    39   * For open boundaries, the number of ice categories from the forcing model can be different 
    40     from the number of categories in the regional simulation 
    41   * Fully compatible with AGRIF 
     43Enhancements 
     44============ 
    4245 
    43 First Test Cases 
    44 ================ 
     46- Fix for tracer conservation with split explicit free surface 
     47- Bulk formulae : move to aerobulk package (:doi:`10.1175/JPO-D-16-0169.1 <Brodeau et al. 2016>`), i.e. NCAR, COARE and ECMWF bulk 
     48                  (remove Clio and MFS bulk) 
     49- Wetting and drying 
     50- Added tidal self attraction and loading either read from a file or from usual "scalar" approximation 
     51- Add a 4th order centered (CEN) and Flux Corrected Transport (FCT) tracer advection 
     52  (using a 4th compact in the vertical) 
     53- iso-neutral mixing (iso and triad operators): 
     54  add the Method of Stabilizing Correction (MSC) (more accurate calculation) + add a bilaplacian case 
     55- Lateral physics (LDF): scale aware setting of eddy viscosity and diffusivity 
     56- Vorticity: 2 new energy conserving scheme: 
     57  ENT with Coriolis defined at T-point (better for Flux form) and 
     58  EET a variant of EEN where e3t is used instead of e3f 
     59  (solved the issue with e3f specification but is not enstrophy conserving)  
    4560 
    46 Define and install a separate repository for test cases to all easy contributions from the NEMO Users Community 
     61Test Cases 
     62========== 
    4763 
    48 Core components 
    49 =============== 
     64The first test cases available for now are: 
     65- ``CANAL``: east-west periodic canal of variable size with several initial states and associated geostrophic currents (zonal jets or vortex) 
     66- ``ICE_AGRIF``: east-west + north-south periodic channel. 
     67  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. 
     68- ``ISOMIP``: simple box configuration with an ice shelf with simple geometry on top. 
     69  The purpose of this test case is to evaluate the impact of various schemes and new development with iceshelf cavities. 
     70  The exact original setup is described ​here. 
     71- ``LOCK-EXCHANGE``:classical fluid dynamics experiment that has been adapted by Haidvogel and Beckmann (1999) for testing advection schemes in ocean circulation models. 
     72  It has been used by several authors including Burchard and Bolding (2002) and Ilıcak et al. (2012). 
     73  The LOCK EXCHANGE experiment can in particular illustrate the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing 
     74- ``OVERFLOW``: illustrates the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing close to bottom topography. 
     75  It is adapted from the non-rotating overflow configuration described in Haidvogel and Beckmann (1999) and further used by Ilıcak et al. (2012) 
     76- ``VORTEX``: illustrates the propagation of an anticyclonic eddy over a Beta plan and flat bottom. 
     77  It is implemented here with an online refined subdomain (thanks to AGRIF library) out of which the vortex propagates. 
     78  It serves as a benchmark to diagnose nesting errors as in Debreu et al. (2012), Penven et al. (2006) and Spall and Holland (1991) 
     79- ``WAD``: a set of simple closed basin geometries for testing the Wetting and drying capabilities. 
     80  Examples range from a closed channel with EW linear bottom slope to a parabolic EW channel with a Gaussian ridge.  
     81 
     82New Reference configurations 
     83============================ 
     84 
     85``AGRIF_DEMO``: 2 interlocked zooms (1:4 & 1:3) in the Nordic Seas + 1 zoom (1:1) at the equator 
     86``SPITZ12``: regional configuration around the Svalbard archipelago  
     87 
     88Wave coupling 
     89============= 
     90 
     91Coupled interface to external wave model 
     92Large scale wave interaction process added in momentum and tracer equations  
    5093 
    5194Passive tracer TOP and biogeochemical PISCES components 
    52 ------------------------------------------------------- 
     95======================================================= 
    5396 
    54 - The passive tracers transport component was redesigned toward a modular structure and 
    55   users can enable each module directly through logical flags in namelist_top (no more Fortran macros!). 
    56 - TOP on-line user documentation is available on NEMO Trac platform (`TOP User Quick Guide`_) 
     97- 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!). 
     98- :doc:`tracers <TOP on-line user documentation>` 
    5799- TOP currently accounts for the following 5 modules: 
     100  CFC contains inorganic carbon tracers (CFC11/CFC12/SF6), 
     101  MY_TRC is a template for new modules (or external couplings), 
     102  AGE deals with water age tracking, 
     103  C14 as a radiocarbon passive tracer, and 
     104  the companion ecosystem model PISCES. 
     105- A generalized infrastructure was developed to handle the prescription of either surface, coastal, or open boundaries conditions for each passive tracer. 
     106- 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. 
     107- PISCES model contains new developments and modifications: 
     108  - Particulate Organic Carbon (POC) component comes with a new liability scheme, while the former Kriest parametrisation was superseded; 
     109  - A complex iron chemistry scheme is now available, with an improved description of ligands for the marine iron cycle 
     110  - 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. 
     111  - Ecosystem components can be optionally modelled by means of explicit nutrient quotas (PISCES-QUOTA)  
    58112 
    59   * ``CFC`` contains inorganic carbon tracers (CFC11/CFC12/SF6) 
    60   * ``MY_TRC`` is a template for new modules (or external couplings) 
    61   * ``AGE`` deals with water age tracking 
    62   * ``C14`` as a radiocarbon passive tracer 
    63   * ``PISCES`` the companion ecosystem model 
    64 - A generalized infrastructure was developed to handle the prescription of either surface, coastal, or 
    65   open boundaries conditions for each passive tracer. 
    66 - PISCES model contains new developments and modifications: 
     113High Performance Computing (HPC): performances improvements 
     114=========================================================== 
    67115 
    68   * Particulate Organic Carbon (POC) component comes with a new liability scheme, 
    69     while the former Kriest parameterisation was superseded; 
    70   * A complex iron chemistry scheme is now available, with an improved description of ligands for 
    71     the marine iron cycle 
    72   * Carbonate chemistry is based on MOCSY 2.0 routines (see `Orr and Epitalon 2015`_), 
    73     by complying also with CMIP6 standards. 
    74   * Ecosystem components can be optionally modelled by means of explicit nutrient quotas (PISCES-QUOTA) 
     116- Reduce number of MPI communications 
     117  (suppression of redundant communications, gather multiple communications into one) 
     118- Use of MPI-3 asynchronous routines for performance (use key_mpi2 if MPI-3 not available) 
     119- Back to standard dynamical allocation (remove of wrk_alloc/dealloc statements) 
     120- :xios:`<XIOS software>` for IOs version 2.5 as default, and optionally available for restarts  
    75121 
    76 AGRIF (embedded zooms) 
    77 ---------------------- 
    78  
    79 The NEMO 4.0 includes new capabilities, configurations and test cases with AGRIF: 
    80  
    81 :underline:`New capabilities from NEMO 3.6 to NEMO 4.0` 
    82  
    83 AGRIF is continuously maintained so that it could be activated with all NEMO components (OPA, sea-ice, TOP). 
    84 Depending on NEMO version, it is nevertheless not the case so that some options may not be compatible with 
    85 the use of online grid refinement. 
    86 Check out the table below to know the status according to the NEMO release you may use. 
    87  
    88 :underline:`Status of available options with AGRIF (if not listed, option is compatible with AGRIF)`: 
    89  
    90 +--------------------------------------------------------+----------------+---------------------+ 
    91 |                                                        | NEMO 3.6       | NEMO 4.0            | 
    92 +========================================================+================+=====================+ 
    93 | LIM2                                                   | yes            | ``-``               | 
    94 +--------------------------------------------------------+----------------+---------------------+ 
    95 | LIM3/SI3                                               | no             | yes                 | 
    96 +--------------------------------------------------------+----------------+---------------------+ 
    97 | TOP                                                    | yes            | yes                 | 
    98 +--------------------------------------------------------+----------------+---------------------+ 
    99 | GLS vertical mixing                                    | no             | yes                 | 
    100 +--------------------------------------------------------+----------------+---------------------+ 
    101 | z*                                                     | no             | yes                 | 
    102 +--------------------------------------------------------+----------------+---------------------+ 
    103 | z~                                                     | no             | no                  | 
    104 +--------------------------------------------------------+----------------+---------------------+ 
    105 | Lagrangian icebergs                                    | no             | no                  | 
    106 +--------------------------------------------------------+----------------+---------------------+ 
    107 | East-west periodic and/or north fold bcs in zooms      | no             | no                  | 
    108 +--------------------------------------------------------+----------------+---------------------+ 
    109 | Online timing                                          | no             | no                  | 
    110 +--------------------------------------------------------+----------------+---------------------+ 
    111 | Stochastic parameterization                            | no             | no                  | 
    112 +--------------------------------------------------------+----------------+---------------------+ 
    113 | Vertical coordinate change in zooms (``key_vertical``) | no             | yes, but not tested | 
    114 +--------------------------------------------------------+----------------+---------------------+ 
    115 | Number of ghost cells                                  | 1 (hard coded) | 3 (parameter)       | 
    116 +--------------------------------------------------------+----------------+---------------------+ 
    117  
    118 [Important notice concerning the change of ghost cells number] 
    119  
    120 The default number of ghost cells (i.e. the number of cells that serve as open boundary data provision) has been 
    121 increased from 1 to 3 in NEMO 4.0. 
    122 This allows to properly handle boundary conditions for numerical schemes that 
    123 have a discretization order greater than 2. 
    124 On the user point of view this does not change anything++ except in the definition of level 1 grids in 
    125 the ``AGRIF_FixedGrids.in`` file. 
    126 In order to retrieve exactly the position of a nested grid in NEMO 4.0 one has to shift indices by 
    127 2 points to the south-west. 
    128 Taking the ``ICEDYN`` example above for NEMO 4.0, the "old" NEMO 3.6 corresponding file would contain:: 
    129  
    130    1 
    131    36 65 36 65 3 3 3 
    132    0 
    133  
    134 ++ Child grid output files are now greater by 4 points in each direction. 
    135  
    136 - Now compatible with new sea ice component and z* coordinate 
    137 - Extended ghost cells area to properly handle scheme with spatial order >2 
    138 - Added vertical refinement (beta) 
    139 - Nesting tools for setup now up to date and working 
    140  
    141 Adding of 3 Reference Configurations 
    142 ------------------------------------ 
    143  
    144 - ``AGRIF_DEMO``: 2 interlocked zooms (1:4 & 1:3) in the Nordic Seas + 1 zoom (1:1) at the equator 
    145 - ``ORCA2_OFF_TRC``: a benchmark simulation environment to deal with inert carbon tracers dynamics by 
    146   exploiting the offline coupling with NEMO. 
    147 - ``SPITZ12``: regional configuration around the Svalbard archipelago. 
    148  
    149 Misc. improvments 
    150 ================= 
    151  
    152 Physics 
    153 ------- 
    154  
    155 - Bulk formulae : move to aerobulk package (`Brodeau 2017`_), i.e. NCAR, COARE and ECMWF bulk 
    156   (remove Clio and MFS bulk) 
    157 - Fix for tracer conservation with split explicit free surface 
    158 - Wetting and drying 
    159 - iso-neutral mixing (iso and triad operators): add the Method of Stabilizing Correction (MSC) 
    160   (more accurate calculation) + add a bilaplacian case 
    161 - Lateral physics (LDF): scale aware setting of eddy viscosity and diffusivity 
    162 - Wave coupling: large scale wave interaction process added in momentum and tracer equations 
    163 - Remove the acceleration of convergence 
    164  
    165 Numerics 
    166 -------- 
    167  
    168 - Added tidal self attraction and loading either read from a file or from usual "scalar" approximation 
    169 - Vertical physics (ZDF) (modularity, share shear production calculation between TKE and GKS, 
    170   removal of all ZDF CPP keys, removal of avmu & avmv, minimization of MPP comm.: ~15 removed) 
    171 - Remove the split-explicit ZDF scheme for both TRA and DYN 
    172 - Lateral physics (LDF): simplification of user interface and removal of CPP keys 
    173 - Add a 4th order centered (CEN) and Flux Corrected Transport (FCT) tracer advection 
    174   (using a 4th compact in the vertical) 
    175 - Generalised lbc_lnk and lbc_nfd 
    176 - Configuration interface completely rewritten (DOM module mainly suppressed, 
    177   and in place: domain_cfg.nc file, or usr_def module) 
    178 - Vorticity: 2 new energy conserving scheme:  ENT with Coriolis defined at T-point 
    179   (better for Flux form) and EET a variant of EEN where e3t is used instead of e3f 
    180   (solved the issue with e3f specification but is not enstrophy conserving) 
    181 - Wave coupling: coupled interface to external wave model 
    182  
    183 Performances 
    184 ------------ 
    185  
    186 - MPI Message passing recoded to reduce number of MPI communications (suppression of redundant communications, 
    187   gather multiple communications into one) 
    188 - Back to standard dynamical allocation (remove of wrk_alloc/dealloc statements) 
    189 - XIOS software for IOs version 2 as default, and optionally available for restarts 
    190 - Unify mppini 
    191 - Use non uniform jpi/jpj with dynamic allocation to avoid ghost rows/columns 
    192  
    193 Environment 
    194 ----------- 
     122Simplification and robustness 
     123============================= 
    195124 
    196125- Revised structure of namelist_ref/_cfg and default reference values. 
    197 - Reorganisation of SVN repository to be compliant with usual directory tree and facilitate building of 
    198   NEMO executable 
    199 - Improvements of reliability through automatic and regular testing of the changes made in repository 
     126- Lateral physics (LDF): simplification of user interface and removal of CPP keys 
     127- 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) 
     128  Remove the split-explicit ZDF scheme for both TRA and DYN 
     129  Remove the acceleration of convergence 
     130  Generalised lbc_lnk and lbc_nfd 
     131  Unify mppini 
     132  Use non uniform jpi/jpj with dynamic allocation to avoid ghost rows/columns 
     133  MPI Message passing re coded 
     134  Configuration interface completely rewritten 
     135  (DOM module mainly suppressed , and in place: domain_cfg.nc file, or usr_def module)  
    200136 
    201 .. _sea ice working group:       http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups/SI3 
    202 .. _TOP User Quick Guide:        http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups/top-dg/TOP-UserQuickGuide 
     137Collaborative Development Environment 
     138===================================== 
    203139 
    204 .. The following references should be in the manual bibliographies and referenced via 'bibliography' directive 
    205 .. _Brodeau 2017:                http://doi.org/10.1175/JPO-D-16-0169.1 
    206 .. _Holland 2012:                http://doi.org/10.1175/JCLI-D-11-00078.1 
    207 .. _Lupkes 2012:                 http://doi.org/10.1029/2012JD017630 
    208 .. _Lupkes 2014:                 http://doi.org/10.1002/2014JD022418 
    209 .. _Kimmritz 2016:               http://doi.org/10.1016/j.ocemod.2016.03.004 
    210 .. _Orr and Epitalon 2015:       http://doi.org/10.5194/gmd-8-485-2015 
     140- Access to information on NEMO wiki reorganised through portals for users/developers/System Team and complete refactoring of all wiki pages and their layout 
     141- Reorganisation of SVN repository to be compliant with usual directory tree and facilitate building of NEMO executable 
     142- Define and install a separate repository for test cases to all easy contributions from the NEMO Users Community 
     143- :forge:`discussion <Forums>` created 
     144- ​:nemo:`<NEMO public web site>` has been cleaned and is now much nicer (using Wordpress instead of EzP) 
     145- New mailing lists have been set up 
     146- Improvements of reliability through automatic and regular testing of the changes made in repository  
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