Changeset 7669


Ignore:
Timestamp:
2017-02-10T18:16:26+01:00 (4 years ago)
Author:
flavoni
Message:

starting update of tex book for new configurations interface

Location:
branches/2016/dev_merge_2016/DOC
Files:
4 edited

Legend:

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  • branches/2016/dev_merge_2016/DOC/Namelists/namcfg

    r6289 r7669  
    22&namcfg        !   parameters of the configuration 
    33!----------------------------------------------------------------------- 
    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      ! 
    2011   ln_use_jattr = .false.  !  use (T) the file attribute: open_ocean_jstart, if present 
    21                            !  in netcdf input files, as the start j-row for reading 
     12   !                       !  in netcdf input files, as the start j-row for reading 
    2213/ 
  • branches/2016/dev_merge_2016/DOC/TexFiles/Chapters/Chap_CFG.tex

    r7412 r7669  
    2222thus allowing the user to verify that the code is performing in a manner consistent with that  
    2323we 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 available  
     24research purposes. The reference configurations also provide a sense for some of the options available  
    2525in the code, though by no means are all options exercised in the reference configurations. 
    2626 
    27 Configuration is defined mainly through the \ngn{namcfg} namelist variables: 
     27Configuration 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 
    2830%------------------------------------------namcfg---------------------------------------------------- 
    2931\namdisplay{namcfg} 
     
    8385the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model  
    8486(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}  
     87The appropriate namelist is available in \textit{CONFIG/ORCA2\_LIM3\_PISCES/EXP00/namelist\_cfg}  
     88for ORCA2 and in \textit{CONFIG/SHARED/README\_configs\_namcfg\_namdom}  \sfcomment {not really true, they are obsolete namelists, where find these informations?}  
    8789for other resolutions 
    8890 
     
    151153The NEMO system is provided with five built-in ORCA configurations which differ in the  
    152154horizontal 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 . 
     155expressed in degrees. Each of configuration is set through the \textit{domain\_cfg} file,  
     156which 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 
    157161 
    158162%--------------------------------------------------TABLE-------------------------------------------------- 
    159163\begin{table}[!t]     \begin{center} 
    160164\begin{tabular}{p{4cm} c c c c} 
    161 Horizontal Grid                         & \np{jp\_cfg} &  \np{jpiglo} & \np{jpjglo} &       \\   
     165Horizontal Grid                         & \np{ORCA\_index} &  \np{jpiglo} & \np{jpjglo} &       \\   
    162166\hline  \hline 
    163167\~4\deg     &        4         &         92     &      76      &       \\ 
     
    172176\caption{ \label{Tab_ORCA}    
    173177Set 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). } 
     178In all cases, the flag for configurations of ORCA family is set to 1 in \textit{domain\_cfg} } 
    175179\end{center} 
    176180\end{table} 
     
    191195For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels,  
    192196otherwise 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}). 
    194198 
    195199Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution.  
     
    209213 
    210214ORCA\_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} 
     215current area ( \key{agrif}  defined) and, by setting the appropriate variables, see \textit{CONFIG/SHARED/namelist\_ref} 
    213216a regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations 
    214217using sponge layers at open boundaries.  
     
    247250uniformly applied to the whole domain. 
    248251 
    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   \\ 
     252The 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   \\ 
    254256Obviously, the namelist parameters have to be adjusted to the chosen resolution, see the Configurations  
    255257pages on the NEMO web site (Using NEMO\/Configurations) . 
     
    259261its resolution and as it does not requires any input file. For example, keeping a same model size  
    260262on each processor while increasing the number of processor used is very easy, even though the  
    261 physical integrity of the solution can be compromised. 
     263physical 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}. 
    262264 
    263265%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    270272%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    271273 
    272 % ------------------------------------------------------------------------------------------------------------- 
    273 %       EEL family configuration 
    274 % ------------------------------------------------------------------------------------------------------------- 
    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 in   
    284 \textit{CONFIG/SHARED/README\_other\_configurations\_namelist\_namcfg} 
    285274% ------------------------------------------------------------------------------------------------------------- 
    286275%       AMM configuration 
  • branches/2016/dev_merge_2016/DOC/TexFiles/Chapters/Chap_DOM.tex

    r6997 r7669  
    1818 
    1919\newpage 
    20 $\ $\newline    % force a new ligne 
     20$\ $\newline    % force a new line 
    2121 
    2222Having defined the continuous equations in Chap.~\ref{PE} and chosen a time  
     
    2626directory routines as well as the DOM (DOMain) directory.  
    2727 
    28 $\ $\newline    % force a new lign 
     28$\ $\newline    % force a new line 
    2929 
    3030% ================================================================ 
     
    268268 
    269269The total size of the computational domain is set by the parameters \np{jpiglo},  
    270 \np{jpjglo} and \np{jpkdta} in the $i$, $j$ and $k$ directions respectively. They are  
     270\np{jpjglo} and \np{jpkglo} in the $i$, $j$ and $k$ directions respectively. They are  
    271271given 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%%% 
     275Parameters $jpi$ and $jpj$ refer to the size of each processor subdomain when the code is  
     276run in parallel using domain decomposition (\key{mpp\_mpi} defined, see \S\ref{LBC_mpp}). 
     277 
     278 
     279$\ $\newline    % force a new line 
     280 
     281%%% 
     282\sfcomment {Hereafter I want to create new subsection 4.2: "fields needed by opa engine or something like this" 
     283and add list of fields : 
     284case 1: read in domain.nc 
     285case 2: defined in userdef\_hrg\/zgr.F90 
     286longitude, latitude, domaine size  
     287number of points 
     288factor scales (e1, e2, e3) 
     289coriolis 
     290k\_top, k\_bottom (first and last ocean level) 
     291periodicity 
     292} 
     293%%% 
     294 
     295% ================================================================ 
     296% Domain: List of fields needed 
     297% ================================================================ 
     298\section  [Domain: Needed fields] 
     299      {Domain: Needed fields} 
     300\label{DOM_fields} 
     301The ocean mesh ($i.e.$ the position of all the scalar and vector points) is defined  
     302by the transformation that gives $(\lambda,\varphi,z)$ as a function of $(i,j,k)$.  
     303The grid-points are located at integer or integer and a half values of as indicated  
     304in Table~\ref{Tab_cell}. The associated scale factors are defined using the   
     305analytical first derivative of the transformation \eqref{Eq_scale_factors}. These  
     306definitions are done in two modules given by example, \mdl{userdef\_hgr} and \mdl{userdef\_zgr}, which  
     307provide the horizontal and vertical meshes, respectively. Otherwise all needed fields can be read in file \np{cn\_domcfg} specified in \ngn{namcfg}. 
     308  
     309The needed fields for domain are:  
     310 
     311geographic position : 
     312 
     313longitude : glamt , glamu , glamv and glamf  (at T, U, V and F point) 
     314 
     315latitude : gphit , gphiu , gphiv and gphif (at T, U, V and F point) 
     316 
     317Coriolis parameter (if domain not on the sphere):  ff\_f  and  ff\_t (at T and F point) 
     318 
     319Scale 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 { 
     327say something about ie1e2u\_v, e1e2u , e1e2v 
     328 
     329and add list of fields : 
     330case 1: read in domain.nc 
     331case 2: defined in userdef\_hrg\/zgr.F90 
     332longitude, latitude, domaine size 
     333number of points 
     334factor scales (e1, e2, e3) 
     335coriolis 
     336k\_top, k\_bottom (first and last ocean level) 
     337periodicity 
     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 
    285362 
    286363% ================================================================ 
     
    436513the output grid written when $\np{nn\_msh} \not=0$ is no more equal to the input grid. 
    437514 
    438 $\ $\newline    % force a new lign 
     515$\ $\newline    % force a new line 
    439516 
    440517% ================================================================ 
  • branches/2016/dev_merge_2016/DOC/TexFiles/Preamble.tex

    r6998 r7669  
    138138\newcommand{\sgacomment}[1]{}    % command to "commented out" portions of 
    139139\newcommand{\gmcomment}[1]{}     % command to "commented out" portions of 
     140\newcommand{\sfcomment}[1]{}     % command to "commented out" portions of 
    140141%                                               % text that span line breaks 
    141142%Red (NR) or Yellow(WARN) 
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