Changeset 3101 for branches/2011/dev_NOC_UKMO_MERGE/DOC
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- 2011-11-14T18:39:45+01:00 (13 years ago)
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branches/2011/dev_NOC_UKMO_MERGE/DOC/TexFiles/Biblio/Biblio.bib
r3094 r3101 1275 1275 url = {http://dx.doi.org/10.1016/j.ocemod.2009.12.003}, 1276 1276 issn = {1463-5003}, 1277 } 1278 1279 @ARTICLE{HollowayOM86, 1280 author = {Greg Holloway}, 1281 title = {A Shelf Wave/Topographic Pump Drives Mean Coastal Circulation (part I)}, 1282 journal = OM, 1283 year = {1986}, 1284 volume = {68}, 1285 } 1286 1287 @ARTICLE{HollowayJPO92, 1288 author = {Greg Holloway}, 1289 title = {Representing Topographic Stress for Large-Scale Ocean Models}, 1290 journal = JPO, 1291 year = {1992}, 1292 volume = {22}, 1293 pages = {1033--1046}, 1294 } 1295 1296 @ARTICLE{HollowayJPO94, 1297 author = {Michael Eby and Greg Holloway}, 1298 title = {Sensitivity of a Large-Scale Ocean Model to a Parameterization of Topographic Stress}, 1299 journal = JPO, 1300 year = {1994}, 1301 volume = {24}, 1302 pages = {2577--2587}, 1303 } 1304 1305 @ARTICLE{HollowayJGR09, 1306 author = {Greg Holloway and Zeliang Wang}, 1307 title = {Representing eddy stress in an Arctic Ocean model}, 1308 journal = JGR, 1309 year = {2009}, 1310 doi = {10.1029/2008JC005169}, 1311 } 1312 1313 @ARTICLE{HollowayOM08, 1314 author = {Mathew Maltrud and Greg Holloway}, 1315 title = {Implementing biharmonic neptune in a global eddying ocean model}, 1316 journal = OM, 1317 year = {2008}, 1318 volume = {21}, 1319 pages = {22--34}, 1277 1320 } 1278 1321 -
branches/2011/dev_NOC_UKMO_MERGE/DOC/TexFiles/Chapters/Chap_DYN.tex
r2541 r3101 633 633 $\bullet$ Rotated axes scheme (rot) \citep{Thiem_Berntsen_OM06} (\np{ln\_dynhpg\_rot}=true) 634 634 635 Note that expression \eqref{Eq_dynhpg_sco} is used when the variable volume 635 $\bullet$ Pressure Jacobian scheme (prj) \citep{Thiem_Berntsen_OM06} (\np{ln\_dynhpg\_prj}=true) 636 637 Note that expression \eqref{Eq_dynhpg_sco} is commonly used when the variable volume 636 638 formulation is activated (\key{vvl}) because in that case, even with a flat bottom, 637 639 the coordinate surfaces are not horizontal but follow the free surface 638 \citep{Levier2007}. The other pressure gradient options are not yet available. 640 \citep{Levier2007}. Only the pressure jacobian scheme (\np{ln\_dynhpg\_prj}=true) is available as an 641 alternative to the default \np{ln\_dynhpg\_sco}=true when \key{vvl} is active. The pressure Jacobian scheme uses 642 a constrained cubic spline to reconstruct the density profile across the water column. This method 643 maintains the monotonicity between the density nodes and is of a higher order than the linear 644 interpolation method. The pressure can be calculated by analytical integration of the density profile and 645 a pressure Jacobian method is used to solve the horizontal pressure gradient. This method should 646 provide a more accurate calculation of the horizontal pressure gradient than the standard scheme. 639 647 640 648 %-------------------------------------------------------------------------------------------------------------- … … 1162 1170 1163 1171 % ================================================================ 1172 % Neptune effect 1173 % ================================================================ 1174 \section [Neptune effect (\textit{dynnept})] 1175 {Neptune effect (\mdl{dynnept})} 1176 \label{DYN_nept} 1177 1178 The "Neptune effect" (thus named in \citep{HollowayOM86}) is a 1179 parameterisation of the potentially large effect of topographic form stress 1180 (caused by eddies) in driving the ocean circulation. Originally developed for 1181 low-resolution models, in which it was applied via a Laplacian (second-order) 1182 diffusion-like term in the momentum equation, it can also be applied in eddy 1183 permitting or resolving models, in which a more scale-selective bilaplacian 1184 (fourth-order) implementation is preferred. This mechanism has a 1185 significant effect on boundary currents (including undercurrents), and the 1186 upwelling of deep water near continental shelves. 1187 1188 The theoretical basis for the method can be found in 1189 \citep{HollowayJPO92}, including the explanation of why form stress is not 1190 necessarily a drag force, but may actually drive the flow. 1191 \citep{HollowayJPO94} demonstrate the effects of the parameterisation in 1192 the GFDL-MOM model, at a horizontal resolution of about 1.8 degrees. 1193 \citep{HollowayOM08} demonstrate the biharmonic version of the 1194 parameterisation in a global run of the POP model, with an average horizontal 1195 grid spacing of about 32km. 1196 1197 The NEMO implementation is a simplified form of that supplied by 1198 Greg Holloway, the testing of which was described in \citep{HollowayJGR09}. 1199 The major simplification is that a time invariant Neptune velocity 1200 field is assumed. This is computed only once, during start-up, and 1201 made available to the rest of the code via a module. Vertical 1202 diffusive terms are also ignored, and the model topography itself 1203 is used, rather than a separate topographic dataset as in 1204 \citep{HollowayOM08}. This implementation is only in the iso-level 1205 formulation, as is the case anyway for the bilaplacian operator. 1206 1207 The velocity field is derived from a transport stream function given by: 1208 1209 \begin{equation} \label{Eq_dynnept_sf} 1210 \psi = -fL^2H 1211 \end{equation} 1212 1213 where $L$ is a latitude-dependant length scale given by: 1214 1215 \begin{equation} \label{Eq_dynnept_ls} 1216 L = l_1 + (l_2 -l_1)\left ( {1 + \cos 2\phi \over 2 } \right ) 1217 \end{equation} 1218 1219 where $\phi$ is latitude and $l_1$ and $l_2$ are polar and equatorial length scales respectively. 1220 Neptune velocity components, $u^*$, $v^*$ are derived from the stremfunction as: 1221 1222 \begin{equation} \label{Eq_dynnept_vel} 1223 u^* = -{1\over H} {\partial \psi \over \partial y}\ \ \ ,\ \ \ v^* = {1\over H} {\partial \psi \over \partial x} 1224 \end{equation} 1225 1226 \smallskip 1227 %----------------------------------------------namdom---------------------------------------------------- 1228 \namdisplay{namdyn_nept} 1229 %-------------------------------------------------------------------------------------------------------- 1230 \smallskip 1231 1232 The Neptune effect is enabled when \np{ln\_neptsimp}=true (default=false). 1233 \np{ln\_smooth\_neptvel} controls whether a scale-selective smoothing is applied 1234 to the Neptune effect flow field (default=false) (this smoothing method is as 1235 used by Holloway). \np{rn\_tslse} and \np{rn\_tslsp} are the equatorial and 1236 polar values respectively of the length-scale parameter $L$ used in determining 1237 the Neptune stream function \eqref{Eq_dynnept_sf} and \eqref{Eq_dynnept_ls}. 1238 Values at intermediate latitudes are given by a cosine fit, mimicking the 1239 variation of the deformation radius with latitude. The default values of 12km 1240 and 3km are those given in \citep{HollowayJPO94}, appropriate for a coarse 1241 resolution model. The finer resolution study of \citep{HollowayOM08} increased 1242 the values of L by a factor of $\sqrt 2$ to 17km and 4.2km, thus doubling the 1243 stream function for a given topography. 1244 1245 The simple formulation for ($u^*$, $v^*$) can give unacceptably large velocities 1246 in shallow water, and \citep{HollowayOM08} add an offset to the depth in the 1247 denominator to control this problem. In this implementation we offer instead (at 1248 the suggestion of G. Madec) the option of ramping down the Neptune flow field to 1249 zero over a finite depth range. The switch \np{ln\_neptramp} activates this 1250 option (default=false), in which case velocities at depths greater than 1251 \np{rn\_htrmax} are unaltered, but ramp down linearly with depth to zero at a 1252 depth of \np{rn\_htrmin} (and shallower). 1253 1254 % ================================================================ -
branches/2011/dev_NOC_UKMO_MERGE/DOC/TexFiles/Chapters/Chap_MISC.tex
r2541 r3101 253 253 Note this implementation may be sensitive to the optimization level. 254 254 255 \subsection{MPP scalability} 256 \label{MISC_mppsca} 257 258 The default method of communicating values across the north-fold in distributed memory applications 259 (\key{mpp\_mpi}) uses a \textsc{MPI\_ALLGATHER} function to exchange values from each processing 260 region in the northern row with every other processing region in the northern row. This enables a 261 global width array containing the top 4 rows to be collated on every northern row processor and then 262 folded with a simple algorithm. Although conceptually simple, this "All to All" communication will 263 hamper performance scalability for large numbers of northern row processors. From version 3.4 264 onwards an alternative method is available which only performs direct "Peer to Peer" communications 265 between each processor and its immediate "neighbours" across the fold line. This is achieved by 266 using the default \textsc{MPI\_ALLGATHER} method during initialisation to help identify the "active" 267 neighbours. Stored lists of these neighbours are then used in all subsequent north-fold exchanges to 268 restrict exchanges to those between associated regions. The collated global width array for each 269 region is thus only partially filled but is guaranteed to be set at all the locations actually 270 required by each individual for the fold operation. This alternative method should give identical 271 results to the default \textsc{ALLGATHER} method and is recommended for large values of \np{jpni}. 272 The new method is activated by setting \np{ln\_nnogather} to be true ({\bf nammpp}). The 273 reproducibility of results using the two methods should be confirmed for each new, non-reference 274 configuration. 255 275 256 276 % ================================================================ -
branches/2011/dev_NOC_UKMO_MERGE/DOC/TexFiles/Chapters/Chap_ZDF.tex
r2541 r3101 1 1 % ================================================================ 2 % Chapter ÑVertical Ocean Physics (ZDF)2 % Chapter Vertical Ocean Physics (ZDF) 3 3 % ================================================================ 4 4 \chapter{Vertical Ocean Physics (ZDF)} … … 539 539 the clipping factor is of crucial importance for the entrainment depth predicted in 540 540 stably stratified situations, and that its value has to be chosen in accordance 541 with the algebraic model for the turbulent ßuxes. The clipping is only activated541 with the algebraic model for the turbulent fluxes. The clipping is only activated 542 542 if \np{ln\_length\_lim}=true, and the $c_{lim}$ is set to the \np{rn\_clim\_galp} value. 543 543 … … 981 981 reduced as necessary to ensure stability; these changes are not reported. 982 982 983 Limits on the bottom friction coefficient are not imposed if the user has elected to 984 handle the bottom friction implicitly (see \S\ref{ZDF_bfr_imp}). The number of potential 985 breaches of the explicit stability criterion are still reported for information purposes. 986 987 % ------------------------------------------------------------------------------------------------------------- 988 % Implicit Bottom Friction 989 % ------------------------------------------------------------------------------------------------------------- 990 \subsection{Implicit Bottom Friction (\np{ln\_bfrimp}$=$\textit{T})} 991 \label{ZDF_bfr_imp} 992 993 An optional implicit form of bottom friction has been implemented to improve 994 model stability. We recommend this option for shelf sea and coastal ocean applications, especially 995 for split-explicit time splitting. This option can be invoked by setting \np{ln\_bfrimp} 996 to \textit{true} in the \textit{nambfr} namelist. This option requires \np{ln\_zdfexp} to be \textit{false} 997 in the \textit{namzdf} namelist. 998 999 This implementation is realised in \mdl{dynzdf\_imp} and \mdl{dynspg\_ts}. In \mdl{dynzdf\_imp}, the 1000 bottom boundary condition is implemented implicitly. 1001 1002 \begin{equation} \label{Eq_dynzdf_bfr} 1003 \left.{\left( {\frac{A^{vm} }{e_3 }\ \frac{\partial \textbf{U}_h}{\partial k}} \right)} \right|_{mbk} 1004 = \binom{c_{b}^{u}u^{n+1}_{mbk}}{c_{b}^{v}v^{n+1}_{mbk}} 1005 \end{equation} 1006 1007 where $mbk$ is the layer number of the bottom wet layer. superscript $n+1$ means the velocity used in the 1008 friction formula is to be calculated, so, it is implicit. 1009 1010 If split-explicit time splitting is used, care must be taken to avoid the double counting of 1011 the bottom friction in the 2-D barotropic momentum equations. As NEMO only updates the barotropic 1012 pressure gradient and Coriolis' forcing terms in the 2-D barotropic calculation, we need to remove 1013 the bottom friction induced by these two terms which has been included in the 3-D momentum trend 1014 and update it with the latest value. On the other hand, the bottom friction contributed by the 1015 other terms (e.g. the advection term, viscosity term) has been included in the 3-D momentum equations 1016 and should not be added in the 2-D barotropic mode. 1017 1018 The implementation of the implicit bottom friction in \mdl{dynspg\_ts} is done in two steps as the 1019 following: 1020 1021 \begin{equation} \label{Eq_dynspg_ts_bfr1} 1022 \frac{\textbf{U}_{med}-\textbf{U}^{m-1}}{2\Delta t}=-g\nabla\eta-f\textbf{k}\times\textbf{U}^{m}+c_{b} 1023 \left(\textbf{U}_{med}-\textbf{U}^{m-1}\right) 1024 \end{equation} 1025 \begin{equation} \label{Eq_dynspg_ts_bfr2} 1026 \frac{\textbf{U}^{m+1}-\textbf{U}_{med}}{2\Delta t}=\textbf{T}+ 1027 \left(g\nabla\eta^{'}+f\textbf{k}\times\textbf{U}^{'}\right)- 1028 2\Delta t_{bc}c_{b}\left(g\nabla\eta^{'}+f\textbf{k}\times\textbf{u}_{b}\right) 1029 \end{equation} 1030 1031 where $\textbf{T}$ is the vertical integrated 3-D momentum trend. We assume the leap-frog time-stepping 1032 is used here. $\Delta t$ is the barotropic mode time step and $\Delta t_{bc}$ is the baroclinic mode time step. 1033 $c_{b}$ is the friction coefficient. $\eta$ is the sea surface level calculated in the barotropic loops 1034 while $\eta^{'}$ is the sea surface level used in the 3-D baroclinic mode. $\textbf{u}_{b}$ is the bottom 1035 layer horizontal velocity. 1036 1037 1038 1039 983 1040 % ------------------------------------------------------------------------------------------------------------- 984 1041 % Bottom Friction with split-explicit time splitting 985 1042 % ------------------------------------------------------------------------------------------------------------- 986 \subsection{Bottom Friction with split-explicit time splitting }1043 \subsection{Bottom Friction with split-explicit time splitting (\np{ln\_bfrimp}$=$\textit{F})} 987 1044 \label{ZDF_bfr_ts} 988 1045 … … 993 1050 {\key{dynspg\_flt}). Extra attention is required, however, when using 994 1051 split-explicit time stepping (\key{dynspg\_ts}). In this case the free surface 995 equation is solved with a small time step \np{ nn\_baro}*\np{rn\_rdt}, while the three996 dimensional prognostic variables are solved with a longer time step that is a997 multiple of \np{rn\_rdt}. The trend in the barotropic momentum due to bottom1052 equation is solved with a small time step \np{rn\_rdt}/\np{nn\_baro}, while the three 1053 dimensional prognostic variables are solved with the longer time step 1054 of \np{rn\_rdt} seconds. The trend in the barotropic momentum due to bottom 998 1055 friction appropriate to this method is that given by the selected parameterisation 999 1056 ($i.e.$ linear or non-linear bottom friction) computed with the evolving velocities … … 1018 1075 \end{enumerate} 1019 1076 1020 Note that the use of an implicit formulation 1077 Note that the use of an implicit formulation within the barotropic loop 1021 1078 for the bottom friction trend means that any limiting of the bottom friction coefficient 1022 1079 in \mdl{dynbfr} does not adversely affect the solution when using split-explicit time 1023 1080 splitting. This is because the major contribution to bottom friction is likely to come from 1024 the barotropic component which uses the unrestricted value of the coefficient. 1025 1026 The implicit formulation takes the form: 1081 the barotropic component which uses the unrestricted value of the coefficient. However, if the 1082 limiting is thought to be having a major effect (a more likely prospect in coastal and shelf seas 1083 applications) then the fully implicit form of the bottom friction should be used (see \S\ref{ZDF_bfr_imp} ) 1084 which can be selected by setting \np{ln\_bfrimp} $=$ \textit{true}. 1085 1086 Otherwise, the implicit formulation takes the form: 1027 1087 \begin{equation} \label{Eq_zdfbfr_implicitts} 1028 1088 \bar{U}^{t+ \rdt} = \; \left [ \bar{U}^{t-\rdt}\; + 2 \rdt\;RHS \right ] / \left [ 1 - 2 \rdt \;c_b^{u} / H_e \right ] … … 1091 1151 The essential goal of the parameterization is to represent the momentum 1092 1152 exchange between the barotropic tides and the unrepresented internal waves 1093 induced by the tidal ßow over rough topography in a stratified ocean.1153 induced by the tidal flow over rough topography in a stratified ocean. 1094 1154 In the current version of \NEMO, the map is built from the output of 1095 1155 the barotropic global ocean tide model MOG2D-G \citep{Carrere_Lyard_GRL03}. -
branches/2011/dev_NOC_UKMO_MERGE/DOC/TexFiles/Namelist/nambfr
r2540 r3101 9 9 ln_bfr2d = .false. ! horizontal variation of the bottom friction coef (read a 2D mask file ) 10 10 rn_bfrien = 50. ! local multiplying factor of bfr (ln_bfr2d=T) 11 ln_bfrimp = .false. ! implicit bottom friction (requires ln_zdfexp = .false. if true) 11 12 / -
branches/2011/dev_NOC_UKMO_MERGE/DOC/TexFiles/Namelist/namdyn_hpg
r2540 r3101 9 9 ln_hpg_djc = .false. ! s-coordinate (Density Jacobian with Cubic polynomial) 10 10 ln_hpg_rot = .false. ! s-coordinate (ROTated axes scheme) 11 ln_hpg_prj = .false. ! s-coordinate (Pressure Jacobian scheme) 11 12 rn_gamma = 0.e0 ! weighting coefficient (wdj scheme) 12 13 ln_dynhpg_imp = .false. ! time stepping: semi-implicit time scheme (T) -
branches/2011/dev_NOC_UKMO_MERGE/DOC/TexFiles/Namelist/namtra_ldf
r2540 r3101 9 9 ln_traldf_hor = .false. ! horizontal (geopotential) (require "key_ldfslp" when ln_sco=T) 10 10 ln_traldf_iso = .true. ! iso-neutral (require "key_ldfslp") 11 ln_traldf_grif = .false. ! griffies skew flux formulation (require "key_ldfslp") ! UNDER TEST, DO NOT USE 12 ln_traldf_gdia = .false. ! griffies operator strfn diagnostics (require "key_ldfslp") ! UNDER TEST, DO NOT USE 11 ln_traldf_grif = .false. ! griffies skew flux formulation (require "key_ldfslp") 12 ln_traldf_gdia = .false. ! griffies operator strfn diagnostics (require "key_ldfslp") 13 ln_triad_iso = .false. ! griffies operator calculates triads twice => pure lateral mixing in ML (require "key_ldfslp") 14 ln_botmix_grif = .false. ! griffies operator with lateral mixing on bottom (require "key_ldfslp") 13 15 ! ! Coefficient 14 16 rn_aht_0 = 2000. ! horizontal eddy diffusivity for tracers [m2/s]
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