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2 | \chapter*{Introduction} |
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3 | |
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4 | %\chaptertoc |
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5 | |
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6 | %\paragraph{Changes record} ~\\ |
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20 | |
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21 | The \textbf{N}ucleus for \textbf{E}uropean \textbf{M}odelling of the \textbf{O}cean (\NEMO) is |
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22 | a framework of ocean related engines, namely the aforementioned for |
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23 | the ocean dynamics and thermodynamics, |
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24 | \SIcube \footnote{\textbf{S}ea-\textbf{I}ce modelling \textbf{I}ntegrated \textbf{I}nitiative} |
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25 | for the sea-ice dynamics and thermodynamics, |
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26 | \TOP \footnote{\textbf{T}racer in the \textbf{O}cean \textbf{P}aradigm} for |
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27 | the biogeochemistry (both transport and sources minus sinks |
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28 | (\PISCES \footnote{ |
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29 | \textbf{P}elagic \textbf{I}nteractions \textbf{S}cheme for |
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30 | \textbf{C}arbon and \textbf{E}cosystem \textbf{S}tudies |
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31 | } |
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32 | )). |
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33 | The ocean component has been developed from the legacy of |
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34 | the \OPA \footnote{\textbf{O}c\'{e}an \textbf{PA}rall\'{e}lis\'{e} (French)} |
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35 | model, described in \citet{madec.delecluse.ea_NPM98}. |
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36 | This model has been used for a wide range of applications, both regional or global, |
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37 | as a forced ocean model and as a model coupled with the sea-ice and/or the atmosphere. |
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38 | |
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39 | This manual provides information about the physics represented by the ocean component of \NEMO\ and |
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40 | the rationale for the choice of numerical schemes and the model design. |
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41 | For the use of framework, |
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42 | a guide which gathers the \texttt{README} files spread out in the source code can be build and |
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43 | exported in a web or printable format (see \path{./doc/rst}). |
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44 | Also a online copy is available on the \href{http://forge.ipsl.jussieu.fr/nemo}{forge platform}. |
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45 | |
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46 | %% ================================================================================================= |
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47 | \section*{Manual outline} |
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48 | |
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49 | \subsection*{Chapters} |
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50 | |
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51 | The manual mirrors the organization of the model and it is organised in as follows: |
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52 | after the presentation of the continuous equations |
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53 | (primitive equations with temperature and salinity, and an equation of seawater) in the next chapter, |
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54 | the following chapters refer to specific terms of the equations each associated with |
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55 | a group of modules. |
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56 | |
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57 | \begin{description} |
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58 | \item [\nameref{chap:PE}] presents the equations and their assumptions, the vertical coordinates used, |
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59 | and the subgrid scale physics. |
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60 | The equations are written in a curvilinear coordinate system, with a choice of vertical coordinates |
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61 | ($z$, $s$, \zstar, \sstar, \ztilde, \stilde, and a mix of them). |
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62 | Momentum equations are formulated in vector invariant or flux form. |
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63 | Dimensional units in the meter, kilogram, second (MKS) international system are used throughout. |
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64 | The following chapters deal with the discrete equations. |
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65 | \item [\nameref{chap:STP}] presents the model time stepping environment. |
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66 | it is a three level scheme in which the tendency terms of the equations are evaluated either |
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67 | centered in time, or forward, or backward depending of the nature of the term. |
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68 | \item [\nameref{chap:DOM}] presents the model \textbf{DOM}ain. |
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69 | It is discretised on a staggered grid (Arakawa C grid) with masking of land areas. |
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70 | Vertical discretisation used depends on both how the bottom topography is represented and whether |
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71 | the free surface is linear or not. |
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72 | Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with |
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73 | linear free surface (level position are then fixed in time). |
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74 | In non-linear free surface, the corresponding rescaled height coordinate formulation |
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75 | (\zstar or \sstar) is used |
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76 | (the level position then vary in time as a function of the sea surface heigh). |
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77 | \item [\nameref{chap:TRA} and \nameref{chap:DYN}] describe the discretisation of |
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78 | the prognostic equations for the active \textbf{TRA}cers (potential temperature and salinity) and |
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79 | the momentum (\textbf{DYN}amic). |
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80 | Explicit, split-explicit and filtered free surface formulations are implemented. |
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81 | A number of numerical schemes are available for momentum advection, |
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82 | for the computation of the pressure gradients, as well as for the advection of tracers |
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83 | (second or higher order advection schemes, including positive ones). |
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84 | \item [\nameref{chap:SBC}] can be implemented as prescribed fluxes, |
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85 | or bulk formulations for the surface fluxes (wind stress, heat, freshwater). |
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86 | The model allows penetration of solar radiation. |
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87 | There is an optional geothermal heating at the ocean bottom. |
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88 | Within the \NEMO\ system the ocean model is interactively coupled with |
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89 | a sea ice model (\SIcube) and a biogeochemistry model (\PISCES). |
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90 | Interactive coupling to Atmospheric models is possible via the \OASIS\ coupler. |
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91 | Two-way nesting is also available through an interface to the \AGRIF\ package, |
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92 | \ie\ \textbf{A}daptative \textbf{G}rid \textbf{R}efinement in \textbf{F}ortran |
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93 | \citep{debreu.vouland.ea_CG08}. |
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94 | The interface code for coupling to an alternative sea ice model (\CICE) has now been upgraded so that |
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95 | it works for both global and regional domains. |
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96 | \item [\nameref{chap:LBC}] presents the \textbf{L}ateral |
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97 | \textbf{B}oun\textbf{D}ar\textbf{Y} \textbf{C}onditions. |
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98 | Global configurations of the model make use of the ORCA tripolar grid, |
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99 | with special north fold boundary condition. |
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100 | Free-slip or no-slip boundary conditions are allowed at land boundaries. |
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101 | Closed basin geometries as well as periodic domains and open boundary conditions are possible. |
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102 | \item [\nameref{chap:LDF} and \nameref{chap:ZDF}] describe the physical parameterisations |
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103 | (\textbf{L}ateral \textbf{D}i\textbf{F}fusion and vertical \textbf{Z} \textbf{D}i\textbf{F}fusion) |
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104 | The model includes an implicit treatment of vertical viscosity and diffusivity. |
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105 | The lateral Laplacian and biharmonic viscosity and diffusion can be rotated following |
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106 | a geopotential or neutral direction. |
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107 | There is an optional eddy induced velocity \citep{gent.mcwilliams_JPO90} with |
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108 | a space and time variable coefficient \citet{treguier.held.ea_JPO97}. |
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109 | The model has vertical harmonic viscosity and diffusion with a space and time variable coefficient, |
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110 | with options to compute the coefficients with \citet{blanke.delecluse_JPO93}, |
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111 | \citet{pacanowski.philander_JPO81}, or \citet{umlauf.burchard_JMR03} mixing schemes. |
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112 | \item [\nameref{chap:DIA}] describes model \textbf{I}n-\textbf{O}utputs \textbf{M}anagement and |
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113 | specific online \textbf{DIA}gnostics. |
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114 | The diagnostics includes the output of all the tendencies of the momentum and tracers equations, |
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115 | the output of tracers \textbf{TR}en\textbf{D}s averaged over the time evolving mixed layer, |
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116 | the output of the tendencies of the barotropic vorticity equation, |
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117 | the computation of on-line \textbf{FLO}ats trajectories... |
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118 | \item [\nameref{chap:OBS}] describes a tool which reads in \textbf{OBS}ervation files |
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119 | (profile temperature and salinity, sea surface temperature, sea level anomaly and |
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120 | sea ice concentration) and calculates an interpolated model equivalent value at |
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121 | the observation location and nearest model timestep. |
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122 | Originally developed of data assimilation, it is a fantastic tool for model and data comparison. |
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123 | \item [\nameref{chap:ASM}] describes how increments produced by |
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124 | data \textbf{A}s\textbf{S}i\textbf{M}ilation may be applied to the model equations. |
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125 | \item [\nameref{chap:MISC}] (including solvers) |
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126 | \item [\nameref{chap:CFG}] provides finally a brief introduction to |
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127 | the pre-defined model configurations |
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128 | (water column model \texttt{C1D}, ORCA and GYRE families of configurations). |
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129 | \end{description} |
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130 | |
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131 | %% ================================================================================================= |
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132 | \subsection*{Appendices} |
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133 | |
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134 | \begin{description} |
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135 | \item [\nameref{apdx:s_coord}] |
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136 | \item [\nameref{apdx:diff_oper}] |
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137 | \item [\nameref{apdx:invariants}] |
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138 | \item [\nameref{apdx:triads}] |
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139 | \item [\nameref{apdx:DOMAINcfg}] |
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140 | \item [\nameref{apdx:coding}] |
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141 | \end{description} |
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