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branches/nemo_v3_3_beta/DOC/TexFiles/Chapters/Introduction.tex
r2282 r2349 37 37 are used throughout. 38 38 39 The following chapters deal with the discrete equations. Chapter~\ref{DOM} presents the 40 space and time domain. The model is discretised on a staggered grid (Arakawa C grid) 41 with masking of land areas and uses a Leap-frog environment for time-stepping. Vertical 42 discretisation used depends on both how the bottom topography is represented and 39 The following chapters deal with the discrete equations. Chapter~\ref{STP} presents the 40 time domain. The model time stepping environment is a three level scheme in which 41 the tendency terms of the equations are evaluated either centered in time, or forward, 42 or backward depending of the nature of the term. 43 Chapter~\ref{DOM} presents the space domain. The model is discretised on a staggered grid 44 (Arakawa C grid) with masking of land areas and uses a Leap-frog environment for time-stepping. 45 Vertical discretisation used depends on both how the bottom topography is represented and 43 46 whether the free surface is linear or not. Full step or partial step $z$-coordinate or 44 47 $s$- (terrain-following) coordinate is used with linear free surface (level position are then … … 47 50 function of the sea surface heigh). The following two chapters (\ref{TRA} and \ref{DYN}) 48 51 describe the discretisation of the prognostic equations for the active tracers and the 49 momentum. Explicit, split-explicit and implicit free surface formulations are implemented50 as well as rigid-lid case. A number of numerical schemes are available for momentum51 advection, for the computation of the pressure gradients, as well as for the advection of52 tracers (second or higherorder advection schemes, including positive ones).52 momentum. Explicit, split-explicit and filtered free surface formulations are implemented. 53 A number of numerical schemes are available for momentum advection, for the computation 54 of the pressure gradients, as well as for the advection of tracers (second or higher 55 order advection schemes, including positive ones). 53 56 54 57 Surface boundary conditions (chapter~\ref{SBC}) can be implemented as prescribed … … 58 61 with a sea ice model (LIM) and with biogeochemistry models (PISCES, LOBSTER). 59 62 Interactive coupling to Atmospheric models is possible via the OASIS coupler 60 \citep{OASIS2006}. 63 \citep{OASIS2006}. Two-way nesting is also available through an interface to the 64 AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}. 61 65 62 66 Other model characteristics are the lateral boundary conditions (chapter~\ref{LBC}). … … 72 76 space and time variable coefficient \citet{Treguier1997}. The model has vertical harmonic 73 77 viscosity and diffusion with a space and time variable coefficient, with options to compute 74 the coefficients with \citet{Blanke1993}, \citet{Large_al_RG94}, or \citet{Pacanowski_Philander_JPO81} mixing75 schemes.78 the coefficients with \citet{Blanke1993}, \citet{Large_al_RG94}, \citet{Pacanowski_Philander_JPO81}, 79 or \citet{Umlauf_Burchard_JMS03} mixing schemes. 76 80 77 Specific online diagnostics (not documented yet) are available in the model: output of all 81 Chapter~\ref{OBS} describes a tool which reads in observation files (profile temperature and salinity, 82 sea surface temperature, sea level anomaly and sea ice concentration) and calculates an interpolated 83 model equivalent value at the observation location and nearest model timestep. Originally 84 developed of data assimilation, it is a fantastic tool for model and data comparison. 85 Other Specific online diagnostics (not documented yet) are available in the model: output of all 78 86 the tendencies of the momentum and tracers equations, output of tracers tendencies 79 averaged over the time evolving mixed layer. 87 averaged over the time evolving mixed layer, output of the tendencies of the barotropic 88 vorticity equation, on-line floats trajectories... 80 89 81 90 The model is implemented in \textsc{Fortran 90}, with preprocessing (C-pre-processor). … … 85 94 readability of the code it is necessary to follow coding rules. The coding rules for OPA 86 95 include conventions for naming variables, with different starting letters for different types 87 of variables (real, integer, parameter\ldots). Those rules are presented in a document88 available on the \NEMO web site.96 of variables (real, integer, parameter\ldots). Those rules are briefly presented in 97 Appendix~\ref{Apdx_D} and a more complete document is available on the \NEMO web site. 89 98 90 99 The model is organized with a high internal modularity based on physics. For example, 91 100 each trend ($i.e.$, a term in the RHS of the prognostic equation) for momentum and 92 101 tracers is computed in a dedicated module. To make it easier for the user to find his way 93 around the code, the module names follow a three-letter rule. For example, \mdl{tra dmp}94 is a module related to the TRAcers equation, computing the DaMPing. The complete list95 of module names is presented in Appendix~\ref{Apdx_D}. Furthermore, modules are96 organized in a few directories that correspond to their category, as indicated by the first 97 three letters of their name.102 around the code, the module names follow a three-letter rule. For example, \mdl{traldf} 103 is a module related to the TRAcers equation, computing the Lateral DiFfussion. 104 The complete list of module names is presented in Appendix~\ref{Apdx_D}. 105 Furthermore, modules are organized in a few directories 106 that correspond to their category, as indicated by the first three letters of their name. 98 107 99 The manual mirrors the organization of the model. After the presentation of the100 continuous equations (Chapter \ref{PE}), the following chapters refer to specific terms of101 the equations each associated with a group of modules .108 The manual mirrors the organization of the model. 109 After the presentation of the continuous equations (Chapter \ref{PE}), the following chapters 110 refer to specific terms of the equations each associated with a group of modules . 102 111 103 112 … … 105 114 %\begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline 106 115 \begin{center} \begin{tabular}{|l|l|l|} \hline 116 Chapter \ref{STP} & - & model time STePping environment \\ \hline 107 117 Chapter \ref{DOM} & DOM & model DOMain \\ \hline 108 118 Chapter \ref{TRA} & TRA & TRAcer equations (potential temperature and salinity) \\ \hline 109 119 Chapter \ref{DYN} & DYN & DYNamic equations (momentum) \\ \hline 110 120 Chapter \ref{SBC} & SBC & Surface Boundary Conditions \\ \hline 111 Chapter \ref{LBC} & LBC & Lateral Boundary Conditions \\ \hline121 Chapter \ref{LBC} & LBC & Lateral Boundary Conditions (also OBC and BDY) \\ \hline 112 122 Chapter \ref{LDF} & LDF & Lateral DiFfusion (parameterisations) \\ \hline 113 Chapter \ref{ZDF} & ZDF & Vertical DiFfusion \\ \hline 114 Chapter \ref{MISC} & ... & Miscellaneous topics \\ \hline 123 Chapter \ref{ZDF} & ZDF & vertical (Z) DiFfusion \\ \hline 124 Chapter \ref{OBS} & OBS & OBServation and model comparison \\ \hline 125 Chapter \ref{ASM} & ASM & ASsimilation increment \\ \hline 126 Chapter \ref{MISC} & ... & Miscellaneous topics (DIA, DTA, IOM, SOL, TRD, FLO...) \\ \hline 115 127 \end{tabular} \end{center} 116 128 \end{table} 117 129 118 In the current release (v3.0), the LBC directory does not yet exist.119 When created LBC will contain the OBC directory (Open Boundary Condition),120 and the \mdl{lbclnk}, \mdl{mppini} and \mdl{lib\_mpp} modules.121 122 130 \vspace{1cm} Nota Bene : \vspace{0.25cm} 123 131 124 OPA, like all research tools, is in perpetual evolution. The present document describes 125 the OPA version include in the release 3.2 of NEMO. This release differs significantly 126 from version 8, documented in \citet{Madec1998}. The main modifications are :\\ 132 \subsubsection{Changes between releases} 133 NEMO/OPA, like all research tools, is in perpetual evolution. The present document describes 134 the OPA version include in the release 3.3 of NEMO. This release differs significantly 135 from version 8, documented in \citet{Madec1998}. 136 137 $\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\ 127 138 (1) transition to full native \textsc{Fortran} 90, deep code restructuring and drastic 128 139 reduction of CPP keys; \\ 129 (2) introduction of partial step representation of bottom topography \citep{Barnier_al_OD06 }; \\140 (2) introduction of partial step representation of bottom topography \citep{Barnier_al_OD06, Le_Sommer_al_OM09, Penduff_al_OS07}; \\ 130 141 (3) partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$) 131 142 with the addition of several options for pressure gradient computation \footnote{Partial … … 148 159 new thermodynamics including bulk ice salinity) \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b} 149 160 150 In addition, several minor modifications in the coding have been introduced with the constant concern of improving performance on both scalar and vector computers. 161 \vspace{1cm} 162 $\bullet$ The main modifications from NEMO/OPA v3.2 and v3.2 are :\\ 163 (1) introduction of a modified leapfrog-Asselin filter time stepping scheme \citep{Leclair_Madec_OM09}; \\ 164 (2) additional scheme for iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress"; \\ 165 (3) a rewriting of the bottom boundary scheme, following \citet{Campin_Goosse_Tel99}; \\ 166 (4) addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics; \\ 167 (5) addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07}; \\ 168 (6) addition of an on-line observation and model comparison (thanks to NEMOVAR project); \\ 169 (7) optional application of an assimilation increment (thanks to NEMOVAR project); \\ 170 (8) introduction of ..... 151 171 172 \vspace{1cm} 173 In addition, several minor modifications in the coding have been introduced with the constant 174 concern of improving the model performance. 175
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