Changeset 10595 for NEMO/trunk/RELEASE_NOTES.rst
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NEMO/trunk/RELEASE_NOTES.rst
r10592 r10595 1 ************* *********2 What's new in NEMO 4.0 3 ************* *********1 ************* 2 RELEASE NOTES 3 ************* 4 4 5 5 .. contents:: 6 6 :local: 7 8 Original sea-ice component SI\ :sup:`3`\9 ========================================10 7 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**". 8 New sea-ice component SI3 (in place of LIMx) 9 ============================================ 16 10 17 11 - 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>`) 18 17 19 * Landfast ice: simple grounding with a "release" stress (not fully operational)20 * Lateral melting21 * 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)24 18 - 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 25 33 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 34 AGRIF for embedded zooms 35 ======================== 30 36 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 34 42 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 43 Enhancements 44 ============ 42 45 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) 45 60 46 Define and install a separate repository for test cases to all easy contributions from the NEMO Users Community 61 Test Cases 62 ========== 47 63 48 Core components 49 =============== 64 The 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 82 New 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 88 Wave coupling 89 ============= 90 91 Coupled interface to external wave model 92 Large scale wave interaction process added in momentum and tracer equations 50 93 51 94 Passive tracer TOP and biogeochemical PISCES components 52 ------------------------------------------------------- 95 ======================================================= 53 96 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>` 57 99 - 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) 58 112 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: 113 High Performance Computing (HPC): performances improvements 114 =========================================================== 67 115 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 75 121 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 ----------- 122 Simplification and robustness 123 ============================= 195 124 196 125 - 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) 200 136 201 .. _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 137 Collaborative Development Environment 138 ===================================== 203 139 204 .. 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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