1 | ====================== |
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2 | What's new in NEMO 4.0 |
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3 | ====================== |
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4 | |
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5 | .. contents:: |
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6 | :local: |
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7 | |
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8 | Original sea-ice component SI\ :sup:`3`\ |
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9 | ======================================== |
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10 | |
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11 | | Meeting in 2017, the `sea ice working group`_ decided to gather sea ice developers and |
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12 | scientific expertise within the NEMO community in order to build a unified model. |
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13 | The replacement of LIM (Louvain-la-Neuve Ice Model) has required the backport of |
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14 | the desired functionalities from each of CICE, GELATO and LIM into a common code in the NEMO framework. |
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15 | | This new model has been named SI\ :sup:`3`\ ("sea ice cubed") and |
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16 | means "**Sea Ice modelling Integrated Initiative**". |
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17 | |
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18 | - Physics |
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19 | |
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20 | * Landfast ice: simple grounding with a "release" stress (not fully operational) |
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21 | * Lateral melting |
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22 | * Melt ponds: constant or `Holland 2012`_ formulation (and soon topographic melt ponds) |
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23 | * Ice-atm. drags from `Lupkes 2012`_ (depending on ice concentration) or `Lupkes 2014`_ |
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24 | (Depending on sea ice concentration and atm. stability) |
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25 | - Numerics |
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26 | |
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27 | * Advection: Ultimate-Macho scheme |
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28 | * Rheology: adaptive EVP (`Kimmritz 2016`_) |
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29 | * Coupling interface: conductivity as surface forcing instead of heat fluxes (Met Office requirement) |
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30 | - Performance |
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31 | |
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32 | * All thermodynamics in 1D |
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33 | * Reduced mpp communications |
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34 | - Users & developers friendly |
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35 | |
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36 | * Comprehensive set of outputs (universal units and understandable names + includes limp) |
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37 | * New architecture and namelist |
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38 | * All processes can be decoupled from each other (switch on/off) |
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39 | * Ice categories bounds can be defined by the user or set automatically |
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40 | * For open boundaries, the number of ice categories from the forcing model can be different |
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41 | from the number of categories in the regional simulation |
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42 | * Fully compatible with AGRIF |
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43 | |
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44 | First Test Cases |
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45 | ================ |
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46 | |
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47 | Define and install a separate repository for test cases to all easy contributions from the NEMO Users Community |
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48 | |
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49 | +-------------------+--------------------------------------------------------+------------------------------------+ |
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50 | | Name | Purpose | References | |
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51 | +===================+=================+======================================+====================================+ |
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52 | | ``CANAL`` | East-west periodic canal of variable size with several | | |
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53 | | | initial states and associated geostrophic currents | | |
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54 | | | (zonal jets or vortex). | | |
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55 | +-------------------+--------------------------------------------------------+------------------------------------+ |
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56 | | ``ICEDYN`` | East-west + north-south periodic channel. | | |
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57 | | | The common configuration includes an AGRIF zoom (1:3) | | |
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58 | | | in the middle of the basin to test how an ice patch is | | |
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59 | | | advected through it but one can also test the | | |
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60 | | | advection schemes (Prather and Ultimate-Macho) by | | |
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61 | | | removing the ``key_agrif`` in the CPP keys. | | |
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62 | +-------------------+--------------------------------------------------------+------------------------------------+ |
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63 | | ``ISOMIP`` | Simple box configuration with an iceshelf with simple | `Hunter 2006`_ | |
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64 | | | geometry on top. | | |
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65 | | | The purpose of this test case is to evaluate the | | |
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66 | | | impact of various schemes and new development with | | |
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67 | | | iceshelf cavities. | | |
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68 | +-------------------+--------------------------------------------------------+------------------------------------+ |
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69 | | ``LOCK_EXCHANGE`` | Classical fluid dynamics experiment that has been | - `Haidvogel and Beckmann 1999`_ | |
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70 | | | adapted for testing advection schemes in ocean | - `Burchard and Bolding 2002`_ | |
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71 | | | circulation models. | - `Ilıcak 2012`_ | |
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72 | | | This experiment can in particular illustrate the | | |
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73 | | | impact of different choices of numerical schemes | | |
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74 | | | and/or subgrid closures on spurious interior mixing. | | |
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75 | +-------------------+--------------------------------------------------------+------------------------------------+ |
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76 | | ``OVERFLOW`` | Adapted from the non-rotating overflow configuration | - `Haidvogel and Beckmann 1999`_ | |
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77 | | | Illustrates the impact of different choices of | - `Ilıcak 2012`_ | |
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78 | | | numerical schemes and/or subgrid closures on spurious | | |
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79 | | | interior mixing close to bottom topography. | | |
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80 | +-------------------+--------------------------------------------------------+------------------------------------+ |
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81 | | ``VORTEX`` | Illustrates the propagation of an anticyclonic eddy | - `Debreu 2012`_ | |
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82 | | | over a Beta plan and flat bottom. | - `Penven 2006`_ | |
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83 | | | It is implemented here with an online refined | - `Spall and Holland 1991`_ | |
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84 | | | subdomain (thanks to AGRIF library) out of which the | | |
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85 | | | vortex propagates and serves as a benchmark to | | |
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86 | | | diagnose nesting errors. | | |
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87 | +-------------------+--------------------------------------------------------+------------------------------------+ |
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88 | | ``WAD`` | Set of simple closed basin geometries for testing the | | |
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89 | | | wetting and drying capabilities. | | |
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90 | | | Examples range from a closed channel with EW linear | | |
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91 | | | bottom slope to a parabolic EW channel with a Gaussian | | |
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92 | | | ridge. | | |
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93 | +-------------------+--------------------------------------------------------+------------------------------------+ |
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94 | |
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95 | ----------- |
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96 | Improvments |
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97 | ----------- |
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98 | |
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99 | Core components |
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100 | =============== |
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101 | |
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102 | Passive tracer TOP and biogeochemical PISCES components |
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103 | ------------------------------------------------------- |
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104 | |
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105 | - The passive tracers transport component was redesigned toward a modular structure and |
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106 | users can enable each module directly through logical flags in namelist_top (no more Fortran macros!). |
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107 | - TOP on-line user documentation is available on NEMO Trac platform (`TOP User Quick Guide`_) |
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108 | - TOP currently accounts for the following 5 modules: |
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109 | |
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110 | * ``CFC`` contains inorganic carbon tracers (CFC11/CFC12/SF6) |
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111 | * ``MY_TRC`` is a template for new modules (or external couplings) |
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112 | * ``AGE`` deals with water age tracking |
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113 | * ``C14`` as a radiocarbon passive tracer |
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114 | * ``PISCES`` the companion ecosystem model |
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115 | - A generalized infrastructure was developed to handle the prescription of either surface, coastal, or |
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116 | open boundaries conditions for each passive tracer. |
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117 | - PISCES model contains new developments and modifications: |
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118 | |
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119 | * Particulate Organic Carbon (POC) component comes with a new liability scheme, |
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120 | while the former Kriest parameterisation was superseded; |
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121 | * A complex iron chemistry scheme is now available, with an improved description of ligands for |
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122 | the marine iron cycle |
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123 | * Carbonate chemistry is based on MOCSY 2.0 routines (see `Orr and Epitalon 2015`_), |
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124 | by complying also with CMIP6 standards. |
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125 | * Ecosystem components can be optionally modelled by means of explicit nutrient quotas (PISCES-QUOTA) |
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126 | |
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127 | AGRIF (embedded zooms) |
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128 | ---------------------- |
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129 | |
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130 | The NEMO 4.0 includes new capabilities, configurations and test cases with AGRIF: |
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131 | |
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132 | .. role:: underline |
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133 | :class: underline |
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134 | |
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135 | :underline:`New capabilities from NEMO 3.6 to NEMO 4.0` |
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136 | |
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137 | AGRIF is continuously maintained so that it could be activated with all NEMO components (OPA, sea-ice, TOP). |
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138 | Depending on NEMO version, it is nevertheless not the case so that some options may not be compatible with |
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139 | the use of online grid refinement. |
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140 | Check out the table below to know the status according to the NEMO release you may use. |
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141 | |
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142 | :underline:`Status of available options with AGRIF (if not listed, option is compatible with AGRIF)`: |
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143 | |
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144 | +--------------------------------------------------------+----------------+---------------------+ |
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145 | | | NEMO 3.6 | NEMO 4.0 | |
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146 | +========================================================+================+=====================+ |
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147 | | LIM2 | yes | ``-`` | |
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148 | +--------------------------------------------------------+----------------+---------------------+ |
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149 | | LIM3/SI3 | no | yes | |
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150 | +--------------------------------------------------------+----------------+---------------------+ |
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151 | | TOP | yes | yes | |
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152 | +--------------------------------------------------------+----------------+---------------------+ |
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153 | | GLS vertical mixing | no | yes | |
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154 | +--------------------------------------------------------+----------------+---------------------+ |
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155 | | z* | no | yes | |
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156 | +--------------------------------------------------------+----------------+---------------------+ |
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157 | | z~ | no | no | |
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158 | +--------------------------------------------------------+----------------+---------------------+ |
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159 | | Lagrangian icebergs | no | no | |
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160 | +--------------------------------------------------------+----------------+---------------------+ |
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161 | | East-west periodic and/or north fold bcs in zooms | no | no | |
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162 | +--------------------------------------------------------+----------------+---------------------+ |
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163 | | Online timing | no | no | |
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164 | +--------------------------------------------------------+----------------+---------------------+ |
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165 | | Stochastic parameterization | no | no | |
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166 | +--------------------------------------------------------+----------------+---------------------+ |
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167 | | Vertical coordinate change in zooms (``key_vertical``) | no | yes, but not tested | |
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168 | +--------------------------------------------------------+----------------+---------------------+ |
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169 | | Number of ghost cells | 1 (hard coded) | 3 (parameter) | |
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170 | +--------------------------------------------------------+----------------+---------------------+ |
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171 | |
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172 | [Important notice concerning the change of ghost cells number] |
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173 | |
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174 | The default number of ghost cells (i.e. the number of cells that serve as open boundary data provision) has been |
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175 | increased from 1 to 3 in NEMO 4.0. |
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176 | This allows to properly handle boundary conditions for numerical schemes that |
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177 | have a discretization order greater than 2. |
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178 | On the user point of view this does not change anything++ except in the definition of level 1 grids in |
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179 | the ``AGRIF_FixedGrids.in`` file. |
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180 | In order to retrieve exactly the position of a nested grid in NEMO 4.0 one has to shift indices by |
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181 | 2 points to the south-west. |
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182 | Taking the ``ICEDYN`` example above for NEMO 4.0, the "old" NEMO 3.6 corresponding file would contain:: |
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183 | |
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184 | 1 |
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185 | 36 65 36 65 3 3 3 |
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186 | 0 |
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187 | |
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188 | ++ Child grid output files are now greater by 4 points in each direction. |
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189 | |
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190 | - Now compatible with new sea ice component and z* coordinate |
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191 | - Extended ghost cells area to properly handle scheme with spatial order >2 |
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192 | - Added vertical refinement (beta) |
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193 | - Nesting tools for setup now up to date and working |
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194 | |
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195 | Adding of 3 Reference Configurations |
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196 | ------------------------------------ |
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197 | |
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198 | - ``AGRIF_DEMO``: 2 interlocked zooms (1:4 & 1:3) in the Nordic Seas + 1 zoom (1:1) at the equator |
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199 | - ``ORCA2_OFF_TRC``: a benchmark simulation environment to deal with inert carbon tracers dynamics by |
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200 | exploiting the offline coupling with NEMO. |
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201 | - ``SPITZ12``: regional configuration around the Svalbard archipelago. |
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202 | |
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203 | Misc. improvments |
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204 | ================= |
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205 | |
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206 | Physics |
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207 | ------- |
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208 | |
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209 | - Bulk formulae : move to aerobulk package (`Brodeau 2017`_), i.e. NCAR, COARE and ECMWF bulk |
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210 | (remove Clio and MFS bulk) |
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211 | - Fix for tracer conservation with split explicit free surface |
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212 | - Wetting and drying |
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213 | - iso-neutral mixing (iso and triad operators): add the Method of Stabilizing Correction (MSC) |
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214 | (more accurate calculation) + add a bilaplacian case |
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215 | - Lateral physics (LDF): scale aware setting of eddy viscosity and diffusivity |
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216 | - Wave coupling: large scale wave interaction process added in momentum and tracer equations |
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217 | - Remove the acceleration of convergence |
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218 | |
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219 | Numerics |
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220 | -------- |
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221 | |
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222 | - Added tidal self attraction and loading either read from a file or from usual "scalar" approximation |
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223 | - Vertical physics (ZDF) (modularity, share shear production calculation between TKE and GKS, |
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224 | removal of all ZDF CPP keys, removal of avmu & avmv, minimization of MPP comm.: ~15 removed) |
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225 | - Remove the split-explicit ZDF scheme for both TRA and DYN |
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226 | - Lateral physics (LDF): simplification of user interface and removal of CPP keys |
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227 | - Add a 4th order centered (CEN) and Flux Corrected Transport (FCT) tracer advection |
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228 | (using a 4th compact in the vertical) |
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229 | - Generalised lbc_lnk and lbc_nfd |
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230 | - Configuration interface completely rewritten (DOM module mainly suppressed, |
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231 | and in place: domain_cfg.nc file, or usr_def module) |
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232 | - Vorticity: 2 new energy conserving scheme: ENT with Coriolis defined at T-point |
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233 | (better for Flux form) and EET a variant of EEN where e3t is used instead of e3f |
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234 | (solved the issue with e3f specification but is not enstrophy conserving) |
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235 | - Wave coupling: coupled interface to external wave model |
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236 | |
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237 | Performances |
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238 | ------------ |
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239 | |
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240 | - MPI Message passing recoded to reduce number of MPI communications (suppression of redundant communications, |
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241 | gather multiple communications into one) |
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242 | - Back to standard dynamical allocation (remove of wrk_alloc/dealloc statements) |
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243 | - XIOS software for IOs version 2 as default, and optionally available for restarts |
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244 | - Unify mppini |
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245 | - Use non uniform jpi/jpj with dynamic allocation to avoid ghost rows/columns |
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246 | |
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247 | Environment |
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248 | ----------- |
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249 | |
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250 | - Revised structure of namelist_ref/_cfg and default reference values. |
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251 | - Reorganisation of SVN repository to be compliant with usual directory tree and facilitate building of |
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252 | NEMO executable |
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253 | - Improvements of reliability through automatic and regular testing of the changes made in repository |
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254 | |
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255 | .. _sea ice working group: http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups/SI3 |
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256 | .. _TOP User Quick Guide: http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups/top-dg/TOP-UserQuickGuide |
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257 | |
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258 | .. _Hunter 2006: http://staff.acecrc.org.au/~bkgalton/ISOMIP/test_cavities.pdf |
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259 | .. _Brodeau 2017: http://doi.org/10.1175/JPO-D-16-0169.1 |
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260 | .. _Haidvogel and Beckmann 1999: http://hdl.handle.net/10013/epic.11761 |
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261 | .. _Burchard and Bolding 2002: http://www.researchgate.net/publication/258128069_GETM_A_General_Estuarine_Transport_Model_Scientific_Documentation |
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262 | .. _Ilıcak 2012: http://doi.org/10.1016/j.ocemod.2011.10.003 |
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263 | .. _Debreu 2012: http://doi.org/10.1016/j.ocemod.2012.03.003 |
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264 | .. _Penven 2006: http://doi.org/10.1016/j.ocemod.2005.05.002 |
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265 | .. _Spall and Holland 1991: http://www.researchgate.net/publication/232101325_A_Nested_Primitive_Equation_Model_for_Oceanic_Applications |
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266 | .. _Holland 2012: http://doi.org/10.1175/JCLI-D-11-00078.1 |
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267 | .. _Lupkes 2012: http://doi.org/10.1029/2012JD017630 |
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268 | .. _Lupkes 2014: http://doi.org/10.1002/2014JD022418 |
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269 | .. _Kimmritz 2016: http://doi.org/10.1016/j.ocemod.2016.03.004 |
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270 | .. _Orr and Epitalon 2015: http://doi.org/10.5194/gmd-8-485-2015 |
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