Changeset 7669 for branches/2016
- Timestamp:
- 2017-02-10T18:16:26+01:00 (7 years ago)
- Location:
- branches/2016/dev_merge_2016/DOC
- Files:
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- 4 edited
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Namelists/namcfg (modified) (1 diff)
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TexFiles/Chapters/Chap_CFG.tex (modified) (9 diffs)
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TexFiles/Chapters/Chap_DOM.tex (modified) (4 diffs)
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TexFiles/Preamble.tex (modified) (1 diff)
Legend:
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branches/2016/dev_merge_2016/DOC/Namelists/namcfg
r6289 r7669 2 2 &namcfg ! parameters of the configuration 3 3 !----------------------------------------------------------------------- 4 cp_cfg = "default" ! name of the configuration 5 cp_cfz = "no zoom" ! name of the zoom of configuration 6 jp_cfg = 0 ! resolution of the configuration 7 jpidta = 10 ! 1st lateral dimension ( >= jpi ) 8 jpjdta = 12 ! 2nd " " ( >= jpj ) 9 jpkdta = 31 ! number of levels ( >= jpk ) 10 jpiglo = 10 ! 1st dimension of global domain --> i =jpidta 11 jpjglo = 12 ! 2nd - - --> j =jpjdta 12 jpizoom = 1 ! left bottom (i,j) indices of the zoom 13 jpjzoom = 1 ! in data domain indices 14 jperio = 0 ! lateral cond. type (between 0 and 6) 15 ! = 0 closed ; = 1 cyclic East-West 16 ! = 2 equatorial symmetric ; = 3 North fold T-point pivot 17 ! = 4 cyclic East-West AND North fold T-point pivot 18 ! = 5 North fold F-point pivot 19 ! = 6 cyclic East-West AND North fold F-point pivot 4 ln_read_cfg = .false. ! (=T) read the domain configuration file 5 ! ! (=F) user defined configuration ==>>> see usrdef(_...) modules 6 cn_domcfg = "domain_cfg" ! domain configuration filename 7 ! 8 ln_write_cfg= .false. ! (=T) create the domain configuration file 9 cn_domcfg_out = "domain_cfg_out" ! newly created domain configuration filename 10 ! 20 11 ln_use_jattr = .false. ! use (T) the file attribute: open_ocean_jstart, if present 21 12 ! ! in netcdf input files, as the start j-row for reading 22 13 / -
branches/2016/dev_merge_2016/DOC/TexFiles/Chapters/Chap_CFG.tex
r7412 r7669 22 22 thus allowing the user to verify that the code is performing in a manner consistent with that 23 23 we are running. This form of verification is critical as one adopts the code for his or her particular 24 research purposes. The test cases also provide a sense for some of the options available24 research purposes. The reference configurations also provide a sense for some of the options available 25 25 in the code, though by no means are all options exercised in the reference configurations. 26 26 27 Configuration is defined mainly through the \ngn{namcfg} namelist variables: 27 Configuration is defined mainly through the \ngn{namcfg} namelist variables: 28 \sfcomment {Here change namcfg part of namelist. Configuration is defined throughout domain\_cfg.nc file now} 29 28 30 %------------------------------------------namcfg---------------------------------------------------- 29 31 \namdisplay{namcfg} … … 83 85 the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model 84 86 (ORCA-LIM-PISCES), using various resolutions. 85 The appropriate \textit{\&namcfg} namelist is available in \textit{CONFIG/ORCA2\_LIM/EXP00/namelist\_cfg}86 for ORCA2 and in \textit{CONFIG/SHARED/README\_ other\_configurations\_namelist\_namcfg}87 The appropriate namelist is available in \textit{CONFIG/ORCA2\_LIM3\_PISCES/EXP00/namelist\_cfg} 88 for ORCA2 and in \textit{CONFIG/SHARED/README\_configs\_namcfg\_namdom} \sfcomment {not really true, they are obsolete namelists, where find these informations?} 87 89 for other resolutions 88 90 … … 151 153 The NEMO system is provided with five built-in ORCA configurations which differ in the 152 154 horizontal resolution. The value of the resolution is given by the resolution at the Equator 153 expressed in degrees. Each of configuration is set through the \textit{\ngn{namcfg}} namelist, 154 which sets the grid size and configuration 155 name parameters (Tab. \ref{Tab_ORCA}). 156 . 155 expressed in degrees. Each of configuration is set through the \textit{domain\_cfg} file, 156 which sets the grid size and configuration name parameters \sfcomment {I would like to change tab_ORCA but I can not find it, wrong jp_cfg} 157 (Tab. \ref{Tab_ORCA}). 158 159 160 157 161 158 162 %--------------------------------------------------TABLE-------------------------------------------------- 159 163 \begin{table}[!t] \begin{center} 160 164 \begin{tabular}{p{4cm} c c c c} 161 Horizontal Grid & \np{ jp\_cfg} & \np{jpiglo} & \np{jpjglo} & \\165 Horizontal Grid & \np{ORCA\_index} & \np{jpiglo} & \np{jpjglo} & \\ 162 166 \hline \hline 163 167 \~4\deg & 4 & 92 & 76 & \\ … … 172 176 \caption{ \label{Tab_ORCA} 173 177 Set of predefined parameters for ORCA family configurations. 174 In all cases, the name of the configuration is set to "orca" ($i.e.$ \np{cp\_cfg}~=~orca).}178 In all cases, the flag for configurations of ORCA family is set to 1 in \textit{domain\_cfg} } 175 179 \end{center} 176 180 \end{table} … … 191 195 For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, 192 196 otherwise 46 are used. In the other ORCA configurations, 31 levels are used 193 (see Tab.~\ref{Tab_orca_zgr} and Fig.~\ref{Fig_zgr}).197 (see Tab.~\ref{Tab_orca_zgr} \sfcomment{HERE I need to put new table for ORCA2 values} and Fig.~\ref{Fig_zgr}). 194 198 195 199 Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution. … … 209 213 210 214 ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas 211 current area ( \key{agrif} defined) and, by setting the appropriate variables in 212 \textit{\&namcfg}, see \textit{CONFIG/SHARED/namelist\_ref} 215 current area ( \key{agrif} defined) and, by setting the appropriate variables, see \textit{CONFIG/SHARED/namelist\_ref} 213 216 a regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations 214 217 using sponge layers at open boundaries. … … 247 250 uniformly applied to the whole domain. 248 251 249 The GYRE configuration is set through the \textit{\&namcfg} namelist defined in the reference 250 configuration \textit{CONFIG/GYRE/EXP00/namelist\_cfg}. Its horizontal resolution 251 (and thus the size of the domain) is determined by setting \np{jp\_cfg} : \\ 252 \np{jpiglo} $= 30 \times$ \np{jp\_cfg} + 2 \\ 253 \np{jpjglo} $= 20 \times$ \np{jp\_cfg} + 2 \\ 252 The GYRE configuration is set like an analytical configuration, through \np{ln\_read\_cfg\textit{=true}} in \textit{namcfg} namelist defined in the reference configuration \textit{CONFIG/GYRE/EXP00/namelist\_cfg}. Its horizontal resolution 253 (and thus the size of the domain) is determined by setting \np{nn\_GYRE} in \ngn{namusr\_def}: \\ 254 \np{jpiglo} $= 30 \times$ \np{nn\_GYRE} + 2 \\ 255 \np{jpjglo} $= 20 \times$ \np{nn\_GYRE} + 2 \\ 254 256 Obviously, the namelist parameters have to be adjusted to the chosen resolution, see the Configurations 255 257 pages on the NEMO web site (Using NEMO\/Configurations) . … … 259 261 its resolution and as it does not requires any input file. For example, keeping a same model size 260 262 on each processor while increasing the number of processor used is very easy, even though the 261 physical integrity of the solution can be compromised. 263 physical integrity of the solution can be compromised. Benchmark is activate via \np{ln\_bench\textit{=true}} in \ngn{namusr\_def} in namelist \textit{CONFIG/GYRE/EXP00/namelist\_cfg}. 262 264 263 265 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> … … 270 272 %>>>>>>>>>>>>>>>>>>>>>>>>>>>> 271 273 272 % -------------------------------------------------------------------------------------------------------------273 % EEL family configuration274 % -------------------------------------------------------------------------------------------------------------275 \section{EEL family: periodic channel}276 \label{MISC_config_EEL}277 278 \begin{description}279 \item[eel\_r2] to be described....280 \item[eel\_r5]281 \item[eel\_r6]282 \end{description}283 The appropriate \textit{\&namcfg} namelists are available in284 \textit{CONFIG/SHARED/README\_other\_configurations\_namelist\_namcfg}285 274 % ------------------------------------------------------------------------------------------------------------- 286 275 % AMM configuration -
branches/2016/dev_merge_2016/DOC/TexFiles/Chapters/Chap_DOM.tex
r6997 r7669 18 18 19 19 \newpage 20 $\ $\newline % force a new li gne20 $\ $\newline % force a new line 21 21 22 22 Having defined the continuous equations in Chap.~\ref{PE} and chosen a time … … 26 26 directory routines as well as the DOM (DOMain) directory. 27 27 28 $\ $\newline % force a new li gn28 $\ $\newline % force a new line 29 29 30 30 % ================================================================ … … 268 268 269 269 The total size of the computational domain is set by the parameters \np{jpiglo}, 270 \np{jpjglo} and \np{jpk dta} in the $i$, $j$ and $k$ directions respectively. They are270 \np{jpjglo} and \np{jpkglo} in the $i$, $j$ and $k$ directions respectively. They are 271 271 given as namelist variables in the \ngn{namcfg} namelist. 272 273 Note that are other namelist variables in the \ngn{namcfg} namelist that refer to 274 the domain size. 275 The two variables \np{jpidta} and \np{jpjdta} may be larger than \np{jpiglo}, \np{jpjglo} 276 when the user wants to use only a sub-region of a given configuration. This is 277 the "zoom" capability described in \S\ref{MISC_zoom}. In most applications of 278 the model, $jpidta=jpiglo$, $jpjdta=jpjglo$, and $jpizoom=jpjzoom=1$. Parameters 279 $jpi$ and $jpj$ refer to the size of each processor subdomain when the code is 280 run in parallel using domain decomposition (\key{mpp\_mpi} defined, see 281 \S\ref{LBC_mpp}). 282 283 284 $\ $\newline % force a new lign 272 %%% 273 %%% 274 %%% 275 Parameters $jpi$ and $jpj$ refer to the size of each processor subdomain when the code is 276 run in parallel using domain decomposition (\key{mpp\_mpi} defined, see \S\ref{LBC_mpp}). 277 278 279 $\ $\newline % force a new line 280 281 %%% 282 \sfcomment {Hereafter I want to create new subsection 4.2: "fields needed by opa engine or something like this" 283 and add list of fields : 284 case 1: read in domain.nc 285 case 2: defined in userdef\_hrg\/zgr.F90 286 longitude, latitude, domaine size 287 number of points 288 factor scales (e1, e2, e3) 289 coriolis 290 k\_top, k\_bottom (first and last ocean level) 291 periodicity 292 } 293 %%% 294 295 % ================================================================ 296 % Domain: List of fields needed 297 % ================================================================ 298 \section [Domain: Needed fields] 299 {Domain: Needed fields} 300 \label{DOM_fields} 301 The ocean mesh ($i.e.$ the position of all the scalar and vector points) is defined 302 by the transformation that gives $(\lambda,\varphi,z)$ as a function of $(i,j,k)$. 303 The grid-points are located at integer or integer and a half values of as indicated 304 in Table~\ref{Tab_cell}. The associated scale factors are defined using the 305 analytical first derivative of the transformation \eqref{Eq_scale_factors}. These 306 definitions are done in two modules given by example, \mdl{userdef\_hgr} and \mdl{userdef\_zgr}, which 307 provide the horizontal and vertical meshes, respectively. Otherwise all needed fields can be read in file \np{cn\_domcfg} specified in \ngn{namcfg}. 308 309 The needed fields for domain are: 310 311 geographic position : 312 313 longitude : glamt , glamu , glamv and glamf (at T, U, V and F point) 314 315 latitude : gphit , gphiu , gphiv and gphif (at T, U, V and F point) 316 317 Coriolis parameter (if domain not on the sphere): ff\_f and ff\_t (at T and F point) 318 319 Scale factors : e1t, e1u, e1v and e1f (on i direction), 320 321 e2t, e2u, e2v and e2f (on j direction) 322 323 and ie1e2u\_v, e1e2u , e1e2v 324 325 %%% 326 \sfcomment { 327 say something about ie1e2u\_v, e1e2u , e1e2v 328 329 and add list of fields : 330 case 1: read in domain.nc 331 case 2: defined in userdef\_hrg\/zgr.F90 332 longitude, latitude, domaine size 333 number of points 334 factor scales (e1, e2, e3) 335 coriolis 336 k\_top, k\_bottom (first and last ocean level) 337 periodicity 338 ---- 339 int ORCA ; 340 int ORCA\_index ; 341 int jpiglo ; j, k 342 int jperio ; 343 int ln_zco ; zps, sco 344 int ln_isfcav ; 345 double glamt(t, y, x) ; u,v,f 346 double gphit(t, y, x) ; u,v,f 347 double e1t(t, y, x) ; u,v,w, 348 double e2t(t, y, x) ; u,v,w 349 double ff\_f(t, y, x) ; double ff\_t(t, y, x) ; 350 double e3t\_1d(t, z) ; 351 double e3w\_1d(t, z) ; 352 double e3t\_0(t, z, y, x) ; u0, v0 , w0 353 ---- 354 } 355 356 % ------------------------------------------------------------------------------------------------------------- 357 % Needed fields 358 % ------------------------------------------------------------------------------------------------------------- 359 %\subsection{List of needed fields to build DOMAIN} 360 %\label{DOM_fields_list} 361 285 362 286 363 % ================================================================ … … 436 513 the output grid written when $\np{nn\_msh} \not=0$ is no more equal to the input grid. 437 514 438 $\ $\newline % force a new li gn515 $\ $\newline % force a new line 439 516 440 517 % ================================================================ -
branches/2016/dev_merge_2016/DOC/TexFiles/Preamble.tex
r6998 r7669 138 138 \newcommand{\sgacomment}[1]{} % command to "commented out" portions of 139 139 \newcommand{\gmcomment}[1]{} % command to "commented out" portions of 140 \newcommand{\sfcomment}[1]{} % command to "commented out" portions of 140 141 % % text that span line breaks 141 142 %Red (NR) or Yellow(WARN)
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