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r9407 r10368 8 8 \chapter{Introduction} 9 9 10 The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean 11 related engines, namely OPA\footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the 12 ocean dynamics and thermodynamics, LIM\footnote{LIM = Louvain la-neuve Ice 13 Model} for the sea-ice dynamics and thermodynamics, TOP\footnote{TOP = Tracer 14 in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources 15 minus sinks (LOBSTER\footnote{LOBSTER = Lodyc Ocean Biogeochemical SysTem for 16 Ecosystem and Resources}, PISCES\footnote{PISCES = Pelagic Interactions Scheme for 17 Carbon and Ecosystem Studies}). It is intended to be a flexible tool for studying 18 the ocean and its interactions with the other components of the earth climate system 19 (atmosphere, sea-ice, biogeochemical tracers, ...) over a wide range of space and time scales. 20 This documentation provides information about the physics represented by the ocean 21 component of \NEMO and the rationale for the choice of numerical schemes and 22 the model design. More specific information about running the model on different 23 computers, or how to set up a configuration, are found on the \NEMO web site 24 (www.nemo-ocean.eu). 25 26 The ocean component of \NEMO has been developed from the OPA model, 27 release 8.2, described in \citet{Madec1998}. This model has been used for a wide 28 range of applications, both regional or global, as a forced ocean model and as a 29 model coupled with the sea-ice and/or the atmosphere. 30 31 This manual is organised in as follows. \autoref{chap:PE} presents the model basics, 32 $i.e.$ the equations and their assumptions, the vertical coordinates used, and the 33 subgrid scale physics. This part deals with the continuous equations of the model 34 (primitive equations, with temperature, salinity and an equation of seawater). 35 The equations are written in a curvilinear coordinate system, with a choice of vertical 36 coordinates ($z$, $s$, \textit{z*}, \textit{s*}, $\tilde{z}$, $\tilde{s}$, and a mixture of them). 37 Momentum equations are formulated in vector invariant or flux form. 38 Dimensional units in the meter, kilogram, second (MKS) international system 39 are used throughout. 40 41 The following chapters deal with the discrete equations. \autoref{chap:STP} presents the 42 time domain. The model time stepping environment is a three level scheme in which 43 the tendency terms of the equations are evaluated either centered in time, or forward, 44 or backward depending of the nature of the term. 45 \autoref{chap:DOM} presents the space domain. The model is discretised on a staggered 46 grid (Arakawa C grid) with masking of land areas. Vertical discretisation used depends 47 on both how the bottom topography is represented and whether the free surface is linear or not. 48 Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used 49 with linear free surface (level position are then fixed in time). In non-linear free surface, 50 the corresponding rescaled height coordinate formulation (\textit{z*} or \textit{s*}) is used 51 (the level position then vary in time as a function of the sea surface heigh). 52 The following two chapters (\autoref{chap:TRA} and \autoref{chap:DYN}) describe the discretisation of the 53 prognostic equations for the active tracers and the momentum. Explicit, split-explicit 54 and filtered free surface formulations are implemented. 55 A number of numerical schemes are available for momentum advection, for the computation 56 of the pressure gradients, as well as for the advection of tracers (second or higher 57 order advection schemes, including positive ones). 58 59 Surface boundary conditions (\autoref{chap:SBC}) can be implemented as prescribed 60 fluxes, or bulk formulations for the surface fluxes (wind stress, heat, freshwater). The 61 model allows penetration of solar radiation There is an optional geothermal heating at 62 the ocean bottom. Within the \NEMO system the ocean model is interactively coupled 63 with a sea ice model (LIM) and with biogeochemistry models (PISCES, LOBSTER). 64 Interactive coupling to Atmospheric models is possible via the OASIS coupler 65 \citep{OASIS2006}. Two-way nesting is also available through an interface to the 66 AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}. 67 The interface code for coupling to an alternative sea ice model (CICE, \citet{Hunke2008}) 68 has now been upgraded so that it works for both global and regional domains, although AGRIF 69 is still not available. 70 71 Other model characteristics are the lateral boundary conditions (\autoref{chap:LBC}). 72 Global configurations of the model make use of the ORCA tripolar grid, with special north 73 fold boundary condition. Free-slip or no-slip boundary conditions are allowed at land 74 boundaries. Closed basin geometries as well as periodic domains and open boundary 75 conditions are possible. 76 77 Physical parameterisations are described in \autoref{chap:LDF} and \autoref{chap:ZDF}. The 78 model includes an implicit treatment of vertical viscosity and diffusivity. The lateral 79 Laplacian and biharmonic viscosity and diffusion can be rotated following a geopotential 80 or neutral direction. There is an optional eddy induced velocity \citep{Gent1990} with a 81 space and time variable coefficient \citet{Treguier1997}. The model has vertical harmonic 82 viscosity and diffusion with a space and time variable coefficient, with options to compute 83 the coefficients with \citet{Blanke1993}, \citet{Pacanowski_Philander_JPO81}, 10 The Nucleus for European Modelling of the Ocean (\NEMO) is a framework of ocean related engines, 11 namely OPA\footnote{OPA = Oc\'{e}an PArall\'{e}lis\'{e}} for the ocean dynamics and thermodynamics, 12 LIM\footnote{LIM = Louvain la-neuve Ice Model} for the sea-ice dynamics and thermodynamics, 13 TOP\footnote{TOP = Tracer in the Ocean Paradigm} for the biogeochemistry (both transport (TRP) and sources 14 minus sinks (LOBSTER\footnote{LOBSTER = Lodyc Ocean Biogeochemical SysTem for Ecosystem and Resources}, 15 PISCES\footnote{PISCES = Pelagic Interactions Scheme for Carbon and Ecosystem Studies})). 16 It is intended to be a flexible tool for studying the ocean and its interactions with the other components of 17 the earth climate system (atmosphere, sea-ice, biogeochemical tracers, ...) over 18 a wide range of space and time scales. 19 This documentation provides information about the physics represented by the ocean component of \NEMO and 20 the rationale for the choice of numerical schemes and the model design. 21 More specific information about running the model on different computers, or how to set up a configuration, 22 are found on the \NEMO web site (www.nemo-ocean.eu). 23 24 The ocean component of \NEMO has been developed from the OPA model, release 8.2, described in \citet{Madec1998}. 25 This model has been used for a wide range of applications, both regional or global, 26 as a forced ocean model and as a model coupled with the sea-ice and/or the atmosphere. 27 28 This manual is organised in as follows. 29 \autoref{chap:PE} presents the model basics, $i.e.$ the equations and their assumptions, 30 the vertical coordinates used, and the subgrid scale physics. 31 This part deals with the continuous equations of the model 32 (primitive equations, with temperature, salinity and an equation of seawater). 33 The equations are written in a curvilinear coordinate system, with a choice of vertical coordinates 34 ($z$, $s$, \textit{z*}, \textit{s*}, $\tilde{z}$, $\tilde{s}$, and a mixture of them). 35 Momentum equations are formulated in vector invariant or flux form. 36 Dimensional units in the meter, kilogram, second (MKS) international system are used throughout. 37 38 The following chapters deal with the discrete equations. 39 \autoref{chap:STP} presents the time domain. 40 The model time stepping environment is a three level scheme in which the tendency terms of 41 the equations are evaluated either centered in time, or forward, or backward depending of the nature of the term. 42 \autoref{chap:DOM} presents the space domain. 43 The model is discretised on a staggered grid (Arakawa C grid) with masking of land areas. 44 Vertical discretisation used depends on both how the bottom topography is represented and 45 whether the free surface is linear or not. 46 Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used with 47 linear free surface (level position are then fixed in time). 48 In non-linear free surface, 49 the corresponding rescaled height coordinate formulation (\textit{z*} or \textit{s*}) is used 50 (the level position then vary in time as a function of the sea surface heigh). 51 The following two chapters (\autoref{chap:TRA} and \autoref{chap:DYN}) describe the discretisation of 52 the prognostic equations for the active tracers and the momentum. 53 Explicit, split-explicit and filtered free surface formulations are implemented. 54 A number of numerical schemes are available for momentum advection, for the computation of the pressure gradients, 55 as well as for the advection of tracers (second or higher order advection schemes, including positive ones). 56 57 Surface boundary conditions (\autoref{chap:SBC}) can be implemented as prescribed fluxes, 58 or bulk formulations for the surface fluxes (wind stress, heat, freshwater). 59 The model allows penetration of solar radiation. 60 There is an optional geothermal heating at the ocean bottom. 61 Within the \NEMO system the ocean model is interactively coupled with a sea ice model (LIM) and 62 with biogeochemistry models (PISCES, LOBSTER). 63 Interactive coupling to Atmospheric models is possible via the OASIS coupler \citep{OASIS2006}. 64 Two-way nesting is also available through an interface to the AGRIF package 65 (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}. 66 The interface code for coupling to an alternative sea ice model (CICE, \citet{Hunke2008}) has now been upgraded so 67 that it works for both global and regional domains, although AGRIF is still not available. 68 69 Other model characteristics are the lateral boundary conditions (\autoref{chap:LBC}). 70 Global configurations of the model make use of the ORCA tripolar grid, with special north fold boundary condition. 71 Free-slip or no-slip boundary conditions are allowed at land boundaries. 72 Closed basin geometries as well as periodic domains and open boundary conditions are possible. 73 74 Physical parameterisations are described in \autoref{chap:LDF} and \autoref{chap:ZDF}. 75 The model includes an implicit treatment of vertical viscosity and diffusivity. 76 The lateral Laplacian and biharmonic viscosity and diffusion can be rotated following 77 a geopotential or neutral direction. 78 There is an optional eddy induced velocity \citep{Gent1990} with a space and time variable coefficient 79 \citet{Treguier1997}. 80 The model has vertical harmonic viscosity and diffusion with a space and time variable coefficient, 81 with options to compute the coefficients with \citet{Blanke1993}, \citet{Pacanowski_Philander_JPO81}, 84 82 or \citet{Umlauf_Burchard_JMS03} mixing schemes. 85 83 \vspace{1cm} … … 90 88 91 89 \noindent \index{CPP keys} CPP keys \newline 92 Some CPP keys are implemented in the FORTRAN code to allow code selection at compiling step. This selection of code at compilation time reduces the reliability of the whole platform since it changes the code from one set of CPP keys to the other. It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time. 90 Some CPP keys are implemented in the FORTRAN code to allow code selection at compiling step. 91 This selection of code at compilation time reduces the reliability of the whole platform since 92 it changes the code from one set of CPP keys to the other. 93 It is used only when the addition/suppression of the part of code highly changes the amount of memory at run time. 93 94 Usual coding looks like : 94 95 \begin{forlines} … … 101 102 \noindent \index{Namelist} Namelists 102 103 103 The namelist allows to input variables (character, logical, real and integer) into the code. There is one namelist file for each component of NEMO (dynamics, sea-ice, biogeochemistry...) containing all the FOTRAN namelists needed. The implementation in NEMO uses a two step process. For each FORTRAN namelist, two files are read: 104 \begin{enumerate} 105 \item A reference namelist (in \path{CONFIG/SHARED/namelist_ref}) is read first. This file contains all the namelist variables which are initialised to default values 106 \item A configuration namelist (in \path{CONFIG/CFG_NAME/EXP00/namelist_cfg}) is read aferwards. This file contains only the namelist variables which are changed from default values, and overwrites those. 104 The namelist allows to input variables (character, logical, real and integer) into the code. 105 There is one namelist file for each component of NEMO (dynamics, sea-ice, biogeochemistry...) 106 containing all the FOTRAN namelists needed. 107 The implementation in NEMO uses a two step process. For each FORTRAN namelist, two files are read: 108 \begin{enumerate} 109 \item 110 A reference namelist (in \path{CONFIG/SHARED/namelist_ref}) is read first. 111 This file contains all the namelist variables which are initialised to default values 112 \item 113 A configuration namelist (in \path{CONFIG/CFG_NAME/EXP00/namelist_cfg}) is read aferwards. 114 This file contains only the namelist variables which are changed from default values, and overwrites those. 107 115 \end{enumerate} 108 116 A template can be found in \path{NEMO/OPA_SRC/module.example}. 109 The effective namelist, taken in account during the run, is stored at execution time in an output\_namelist\_dyn (or \_ice or \_top) file. 110 \vspace{1cm} 117 The effective namelist, taken in account during the run, is stored at execution time in 118 an output\_namelist\_dyn (or \_ice or \_top) file. 119 \vspace{1cm} 111 120 112 121 %%gm end 113 122 114 123 Model outputs management and specific online diagnostics are described in \autoref{chap:DIA}. 115 The diagnostics includes the output of all the tendencies of the momentum and tracers equations, 116 the output of tracers tendencies averaged over the time evolving mixed layer, the output of 117 the tendencies of the barotropic vorticity equation, the computation of on-line floats trajectories... 118 \autoref{chap:OBS} describes a tool which reads in observation files (profile temperature 119 and salinity, sea surface temperature, sea level anomaly and sea ice concentration) 120 and calculates an interpolated model equivalent value at the observation location 121 and nearest model timestep. Originally developed of data assimilation, it is a fantastic 122 tool for model and data comparison. \autoref{chap:ASM} describes how increments 123 produced by data assimilation may be applied to the model equations. 124 Finally, \autoref{chap:CFG} provides a brief introduction to the pre-defined model 125 configurations (water column model, ORCA and GYRE families of configurations). 126 127 The model is implemented in \textsc{Fortran 90}, with preprocessing (C-pre-processor). 128 It runs under UNIX. It is optimized for vector computers and parallelised by domain 129 decomposition with MPI. All input and output is done in NetCDF (Network Common Data 130 Format) with a optional direct access format for output. To ensure the clarity and 131 readability of the code it is necessary to follow coding rules. The coding rules for OPA 132 include conventions for naming variables, with different starting letters for different types 133 of variables (real, integer, parameter\ldots). Those rules are briefly presented in 134 \autoref{apdx:D} and a more complete document is available on the \NEMO web site. 135 136 The model is organized with a high internal modularity based on physics. For example, 137 each trend ($i.e.$, a term in the RHS of the prognostic equation) for momentum and 138 tracers is computed in a dedicated module. To make it easier for the user to find his way 139 around the code, the module names follow a three-letter rule. For example, \mdl{traldf} 140 is a module related to the TRAcers equation, computing the Lateral DiFfussion. 124 The diagnostics includes the output of all the tendencies of the momentum and tracers equations, 125 the output of tracers tendencies averaged over the time evolving mixed layer, 126 the output of the tendencies of the barotropic vorticity equation, 127 the computation of on-line floats trajectories... 128 \autoref{chap:OBS} describes a tool which reads in observation files 129 (profile temperature and salinity, sea surface temperature, sea level anomaly and sea ice concentration) 130 and calculates an interpolated model equivalent value at the observation location and nearest model timestep. 131 Originally developed of data assimilation, it is a fantastic tool for model and data comparison. 132 \autoref{chap:ASM} describes how increments produced by data assimilation may be applied to the model equations. 133 Finally, \autoref{chap:CFG} provides a brief introduction to the pre-defined model configurations 134 (water column model, ORCA and GYRE families of configurations). 135 136 The model is implemented in \textsc{Fortran 90}, with preprocessing (C-pre-processor). 137 It runs under UNIX. 138 It is optimized for vector computers and parallelised by domain decomposition with MPI. 139 All input and output is done in NetCDF (Network Common Data Format) with a optional direct access format for output. 140 To ensure the clarity and readability of the code it is necessary to follow coding rules. 141 The coding rules for OPA include conventions for naming variables, 142 with different starting letters for different types of variables (real, integer, parameter\ldots). 143 Those rules are briefly presented in \autoref{apdx:D} and a more complete document is available on 144 the \NEMO web site. 145 146 The model is organized with a high internal modularity based on physics. 147 For example, each trend ($i.e.$, a term in the RHS of the prognostic equation) for momentum and tracers 148 is computed in a dedicated module. 149 To make it easier for the user to find his way around the code, the module names follow a three-letter rule. 150 For example, \mdl{traldf} is a module related to the TRAcers equation, computing the Lateral DiFfussion. 141 151 %The complete list of module names is presented in \autoref{apdx:D}. %====>>>> to be done ! 142 Furthermore, modules are organized in a few directories that correspond to their category, 152 Furthermore, modules are organized in a few directories that correspond to their category, 143 153 as indicated by the first three letters of their name (\autoref{tab:chap}). 144 154 145 The manual mirrors the organization of the model. 146 After the presentation of the continuous equations (\autoref{chap:PE}), the following chapters 147 refer to specific terms of the equations each associated with a group of modules (\autoref{tab:chap}). 155 The manual mirrors the organization of the model. 156 After the presentation of the continuous equations (\autoref{chap:PE}), 157 the following chapters refer to specific terms of the equations each associated with 158 a group of modules (\autoref{tab:chap}). 148 159 149 160 150 161 %--------------------------------------------------TABLE-------------------------------------------------- 151 162 \begin{table}[!t] 152 %\begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline 153 \caption{ \protect\label{tab:chap} Organization of Chapters mimicking the one of the model directories. } 154 \begin{center} \begin{tabular}{|l|l|l|} \hline 155 \autoref{chap:STP} & - & model time STePping environment \\ \hline 156 \autoref{chap:DOM} & DOM & model DOMain \\ \hline 157 \autoref{chap:TRA} & TRA & TRAcer equations (potential temperature and salinity) \\ \hline 158 \autoref{chap:DYN} & DYN & DYNamic equations (momentum) \\ \hline 159 \autoref{chap:SBC} & SBC & Surface Boundary Conditions \\ \hline 160 \autoref{chap:LBC} & LBC & Lateral Boundary Conditions (also OBC and BDY) \\ \hline 161 \autoref{chap:LDF} & LDF & Lateral DiFfusion (parameterisations) \\ \hline 162 \autoref{chap:ZDF} & ZDF & vertical (Z) DiFfusion (parameterisations) \\ \hline 163 \autoref{chap:DIA} & DIA & I/O and DIAgnostics (also IOM, FLO and TRD) \\ \hline 164 \autoref{chap:OBS} & OBS & OBServation and model comparison \\ \hline 165 \autoref{chap:ASM} & ASM & ASsiMilation increment \\ \hline 166 \autoref{chap:MISC} & SOL & Miscellaneous topics (including solvers) \\ \hline 167 \autoref{chap:CFG} & - & predefined configurations (including C1D) \\ \hline 168 \end{tabular} 169 \end{center} \end{table} 163 % \begin{center} \begin{tabular}{|p{143pt}|l|l|} \hline 164 \caption{ \protect\label{tab:chap} Organization of Chapters mimicking the one of the model directories. } 165 \begin{center} 166 \begin{tabular}{|l|l|l|} \hline 167 \autoref{chap:STP} & - & model time STePping environment \\ \hline 168 \autoref{chap:DOM} & DOM & model DOMain \\ \hline 169 \autoref{chap:TRA} & TRA & TRAcer equations (potential temperature and salinity) \\ \hline 170 \autoref{chap:DYN} & DYN & DYNamic equations (momentum) \\ \hline 171 \autoref{chap:SBC} & SBC & Surface Boundary Conditions \\ \hline 172 \autoref{chap:LBC} & LBC & Lateral Boundary Conditions (also OBC and BDY) \\ \hline 173 \autoref{chap:LDF} & LDF & Lateral DiFfusion (parameterisations) \\ \hline 174 \autoref{chap:ZDF} & ZDF & vertical (Z) DiFfusion (parameterisations) \\ \hline 175 \autoref{chap:DIA} & DIA & I/O and DIAgnostics (also IOM, FLO and TRD) \\ \hline 176 \autoref{chap:OBS} & OBS & OBServation and model comparison \\ \hline 177 \autoref{chap:ASM} & ASM & ASsiMilation increment \\ \hline 178 \autoref{chap:MISC} & SOL & Miscellaneous topics (including solvers) \\ \hline 179 \autoref{chap:CFG} & - & predefined configurations (including C1D) \\ \hline 180 \end{tabular} 181 \end{center} 182 \end{table} 170 183 %-------------------------------------------------------------------------------------------------------------- 171 184 172 185 173 186 \subsubsection{Changes between releases} 174 NEMO/OPA, like all research tools, is in perpetual evolution. The present document describes175 the OPA version include in the release 3.4 of NEMO. This release differs significantly 176 from version 8, documented in \citet{Madec1998}.\\187 NEMO/OPA, like all research tools, is in perpetual evolution. 188 The present document describes the OPA version include in the release 3.4 of NEMO. 189 This release differs significantly from version 8, documented in \citet{Madec1998}.\\ 177 190 178 191 $\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\ 179 192 \begin{enumerate} 180 \item transition to full native \textsc{Fortran} 90, deep code restructuring and drastic 181 reduction of CPP keys; 182 \item introduction of partial step representation of bottom topography \citep{Barnier_al_OD06, Le_Sommer_al_OM09, Penduff_al_OS07}; 183 \item partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$) 184 with the addition of several options for pressure gradient computation \footnote{Partial 185 support of $s$-coordinate: there is presently no support for neutral physics in $s$- 186 coordinate and for the new options for horizontal pressure gradient computation with 187 a non-linear equation of state.}; 188 \item more choices for the treatment of the free surface: full explicit, split-explicit or filtered 189 schemes, and suppression of the rigid-lid option; 190 \item non linear free surface associated with the rescaled height coordinate 191 \textit{z*} or \textit{s}; 192 \item additional schemes for vector and flux forms of the momentum advection; 193 \item additional advection schemes for tracers; 194 \item implementation of the AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}; 195 \item online diagnostics : tracers trend in the mixed layer and vorticity balance; 196 \item rewriting of the I/O management with the use of an I/O server; 197 \item generalized ocean-ice-atmosphere-CO2 coupling interface, interfaced with OASIS 3 coupler ; 198 \item surface module (SBC) that simplify the way the ocean is forced and include two 199 bulk formulea (CLIO and CORE) and which includes an on-the-fly interpolation of input forcing fields ; 200 \item RGB light penetration and optional use of ocean color 201 \item major changes in the TKE schemes: it now includes a Langmuir cell parameterization \citep{Axell_JGR02}, 202 the \citet{Mellor_Blumberg_JPO04} surface wave breaking parameterization, and has a time discretization 203 which is energetically consistent with the ocean model equations \citep{Burchard_OM02, Marsaleix_al_OM08}; 204 \item tidal mixing parametrisation (bottom intensification) + Indonesian specific tidal mixing \citep{Koch-Larrouy_al_GRL07}; 205 \item introduction of LIM-3, the new Louvain-la-Neuve sea-ice model (C-grid rheology and 206 new thermodynamics including bulk ice salinity) \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b} 193 \item 194 transition to full native \textsc{Fortran} 90, deep code restructuring and drastic reduction of CPP keys; 195 \item 196 introduction of partial step representation of bottom topography 197 \citep{Barnier_al_OD06, Le_Sommer_al_OM09, Penduff_al_OS07}; 198 \item 199 partial reactivation of a terrain-following vertical coordinate ($s$- and hybrid $s$-$z$) with 200 the addition of several options for pressure gradient computation 201 \footnote{Partial support of $s$-coordinate: there is presently no support for neutral physics in 202 $s$-coordinate and for the new options for horizontal pressure gradient computation with 203 a non-linear equation of state. 204 }; 205 \item 206 more choices for the treatment of the free surface: full explicit, split-explicit or filtered schemes, 207 and suppression of the rigid-lid option; 208 \item 209 non linear free surface associated with the rescaled height coordinate \textit{z*} or \textit{s}; 210 \item 211 additional schemes for vector and flux forms of the momentum advection; 212 \item 213 additional advection schemes for tracers; 214 \item 215 implementation of the AGRIF package (Adaptative Grid Refinement in \textsc{Fortran}) \citep{Debreu_al_CG2008}; 216 \item 217 online diagnostics : tracers trend in the mixed layer and vorticity balance; 218 \item 219 rewriting of the I/O management with the use of an I/O server; 220 \item 221 generalized ocean-ice-atmosphere-CO2 coupling interface, interfaced with OASIS 3 coupler; 222 \item 223 surface module (SBC) that simplify the way the ocean is forced and include two bulk formulea (CLIO and CORE) and 224 which includes an on-the-fly interpolation of input forcing fields; 225 \item 226 RGB light penetration and optional use of ocean color 227 \item 228 major changes in the TKE schemes: it now includes a Langmuir cell parameterization \citep{Axell_JGR02}, 229 the \citet{Mellor_Blumberg_JPO04} surface wave breaking parameterization, and has a time discretization which 230 is energetically consistent with the ocean model equations \citep{Burchard_OM02, Marsaleix_al_OM08}; 231 \item 232 tidal mixing parametrisation (bottom intensification) + Indonesian specific tidal mixing 233 \citep{Koch-Larrouy_al_GRL07}; 234 \item 235 introduction of LIM-3, the new Louvain-la-Neuve sea-ice model 236 (C-grid rheology and new thermodynamics including bulk ice salinity) 237 \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b} 207 238 \end{enumerate} 208 239 209 240 \vspace{1cm} 210 $\bullet$ The main modifications from NEMO/OPA v3.2 and v3.3 are :\\ 211 \begin{enumerate} 212 \item introduction of a modified leapfrog-Asselin filter time stepping scheme \citep{Leclair_Madec_OM09}; 213 \item additional scheme for iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress"; 214 \item a rewriting of the bottom boundary layer scheme, following \citet{Campin_Goosse_Tel99}; 215 \item addition of a Generic Length Scale vertical mixing scheme, following \citet{Umlauf_Burchard_JMS03}; 216 \item addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics; 217 \item addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07}; 218 \item river runoffs added through a non-zero depth, and having its own temperature and salinity; 219 \item CORE II normal year forcing set as the default forcing of ORCA2-LIM configuration ; 220 \item generalisation of the use of \mdl{fldread} for all input fields (ocean climatology, sea-ice damping...) ; 221 \item addition of an on-line observation and model comparison (thanks to NEMOVAR project); 222 \item optional application of an assimilation increment (thanks to NEMOVAR project); 223 \item coupling interface adjusted for WRF atmospheric model; 224 \item C-grid ice rheology now available fro both LIM-2 and LIM-3 \citep{Bouillon_al_OM09}; 225 \item LIM-3 ice-ocean momentum coupling applied to LIM-2 ; 226 \item a deep re-writting and simplification of the off-line tracer component (OFF\_SRC) ; 227 \item the merge of passive and active advection and diffusion modules ; 228 \item Use of the Flexible Configuration Manager (FCM) to build configurations, generate the Makefile and produce the executable ; 229 \item Linear-tangent and Adjoint component (TAM) added, phased with v3.0 230 \end{enumerate} 231 \vspace{1cm} 232 In addition, several minor modifications in the coding have been introduced with the constant 233 concern of improving the model performance. 234 235 \vspace{1cm} 241 $\bullet$ The main modifications from NEMO/OPA v3.2 and v3.3 are :\\ 242 \begin{enumerate} 243 \item 244 introduction of a modified leapfrog-Asselin filter time stepping scheme 245 \citep{Leclair_Madec_OM09}; 246 \item 247 additional scheme for iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress"; 248 \item 249 a rewriting of the bottom boundary layer scheme, following \citet{Campin_Goosse_Tel99}; 250 \item 251 addition of a Generic Length Scale vertical mixing scheme, following \citet{Umlauf_Burchard_JMS03}; 252 \item 253 addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics; 254 \item 255 addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07}; 256 \item 257 river runoffs added through a non-zero depth, and having its own temperature and salinity; 258 \item 259 CORE II normal year forcing set as the default forcing of ORCA2-LIM configuration; 260 \item 261 generalisation of the use of \mdl{fldread} for all input fields (ocean climatology, sea-ice damping...); 262 \item 263 addition of an on-line observation and model comparison (thanks to NEMOVAR project); 264 \item 265 optional application of an assimilation increment (thanks to NEMOVAR project); 266 \item 267 coupling interface adjusted for WRF atmospheric model; 268 \item 269 C-grid ice rheology now available fro both LIM-2 and LIM-3 \citep{Bouillon_al_OM09}; 270 \item 271 LIM-3 ice-ocean momentum coupling applied to LIM-2; 272 \item 273 a deep re-writting and simplification of the off-line tracer component (OFF\_SRC); 274 \item 275 the merge of passive and active advection and diffusion modules; 276 \item 277 Use of the Flexible Configuration Manager (FCM) to build configurations, 278 generate the Makefile and produce the executable; 279 \item 280 Linear-tangent and Adjoint component (TAM) added, phased with v3.0 281 \end{enumerate} 282 \vspace{1cm} 283 In addition, several minor modifications in the coding have been introduced with the constant concern of 284 improving the model performance. 285 286 \vspace{1cm} 236 287 $\bullet$ The main modifications from NEMO/OPA v3.3 and v3.4 are :\\ 237 288 \begin{enumerate} 238 \item finalisation of above iso-neutral mixing \citep{Griffies_al_JPO98}"; 289 \item finalisation of above iso-neutral mixing \citep{Griffies_al_JPO98}"; 239 290 \item "Neptune effect" parametrisation; 240 \item horizontal pressure gradient suitable for s-coordinate; 291 \item horizontal pressure gradient suitable for s-coordinate; 241 292 \item semi-implicit bottom friction; 242 \item finalisation of the merge of passive and active tracers advection-diffusion modules; 293 \item finalisation of the merge of passive and active tracers advection-diffusion modules; 243 294 \item a new bulk formulae (so-called MFS); 244 \item use fldread for the off-line tracer component (OFF\_SRC) ;295 \item use fldread for the off-line tracer component (OFF\_SRC); 245 296 \item use MPI point to point communications for north fold; 246 \item diagnostic of transport ;297 \item diagnostic of transport; 247 298 \end{enumerate} 248 299
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