Changeset 11112


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Timestamp:
2019-06-14T15:57:28+02:00 (10 months ago)
Author:
mocavero
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Update the chapter on reference configurations for 4.0 release, see #2216

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1 edited

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  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_CONFIG.tex

    r10442 r11112  
    1818\label{sec:CFG_intro} 
    1919 
    20 The purpose of this part of the manual is to introduce the \NEMO reference configurations. 
     20The purpose of this part of the manual is to introduce the NEMO reference configurations. 
    2121These configurations are offered as means to explore various numerical and physical options, 
    2222thus allowing the user to verify that the code is performing in a manner consistent with that we are running. 
     
    2424The reference configurations also provide a sense for some of the options available in the code, 
    2525though by no means are all options exercised in the reference configurations. 
     26Configuration is defined manually through the \textit{namcfg} namelist variables. 
    2627 
    2728%------------------------------------------namcfg---------------------------------------------------- 
     
    3637\label{sec:CFG_c1d} 
    3738 
    38 BE careful: to be re-written according to suppression of jpizoom and jpjzoom !!!! 
    39  
    40 The 1D model option simulates a stand alone water column within the 3D \NEMO system. 
     39The 1D model option simulates a stand alone water column within the 3D NEMO system. 
    4140It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers or a biogeochemical model. 
    4241It is set up by defining the position of the 1D water column in the grid 
    43 (see \textit{CONFIG/SHARED/namelist\_ref} ).  
     42(see \textit{cfgs/SHARED/namelist\_ref}).  
    4443The 1D model is a very useful tool 
    4544\textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes; 
     
    5049\textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model. 
    5150 
    52 The methodology is based on the use of the zoom functionality over the smallest possible domain: 
    53 a 3x3 domain centered on the grid point of interest, with some extra routines. 
    54 There is no need to define a new mesh, bathymetry, initial state or forcing, 
    55 since the 1D model will use those of the configuration it is a zoom of. 
    56 The chosen grid point is set in \textit{\ngn{namcfg}} namelist by 
    57 setting the \np{jpizoom} and \np{jpjzoom} parameters to the indices of the location of the chosen grid point. 
     51The methodology is based on the configuration of the smallest possible domain: 
     52a 3x3 domain with 75 vertical levels. 
    5853 
    5954The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero, 
    6055and second, the two components of the velocity are moved on a $T$-point.  
    61 Therefore, defining \key{c1d} changes five main things in the code behaviour:  
     56Therefore, defining \key{c1d} changes some things in the code behaviour:  
    6257\begin{description} 
    6358\item[(1)] 
    64   the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column of 
    65   the 3x3 domain is imposed over the whole domain; 
    66 \item[(3)] 
    67   a call to \rou{lbc\_lnk} is systematically done when reading input data (\ie in \mdl{iom}); 
    68 \item[(3)] 
    6959  a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which 
    7060  both lateral tendancy terms and lateral physics are not called; 
    71 \item[(4)] 
     61\item[(2)] 
    7262  the vertical velocity is zero 
    7363  (so far, no attempt at introducing a Ekman pumping velocity has been made); 
    74 \item[(5)] 
     64\item[(3)] 
    7565  a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same 
    7666  (see \mdl{dyncor\_c1d}). 
    7767\end{description} 
    78 All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of 
    79 the \NEMO distribution. 
     68All the relevant \textit{\_c1d} modules can be found in the src/OCE/C1D directory of 
     69the NEMO distribution. 
    8070 
    8171% to be added:  a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985) 
     
    8878 
    8979The ORCA family is a series of global ocean configurations that are run together with 
    90 the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model (ORCA-LIM-PISCES), 
    91 using various resolutions. 
    92 An appropriate namelist is available in \path{CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_cfg} for ORCA2. 
     80the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE-PISCES). 
     81An appropriate namelist is available in \path{cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2. 
    9382The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file, 
    94 this file is available in tar file in the wiki of NEMO: \\ 
    95 https://forge.ipsl.jussieu.fr/nemo/wiki/Users/ReferenceConfigurations/ORCA2\_LIM3\_PISCES \\ 
     83this file is available in tar file on the NEMO community zenodo platform: \\ 
     84https://doi.org/10.5281/zenodo.2640723 
     85 
    9686In this namelist\_cfg the name of domain input file is set in \ngn{namcfg} block of namelist.  
    9787 
     
    119109\label{subsec:CFG_orca_grid} 
    120110 
    121 The ORCA grid is a tripolar is based on the semi-analytical method of \citet{Madec_Imbard_CD96}. 
     111The ORCA grid is a tripolar grid based on the semi-analytical method of \citet{Madec_Imbard_CD96}. 
    122112It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside 
    123113the computational domain since two north mesh poles are introduced and placed on lands. 
     
    158148 
    159149% ------------------------------------------------------------------------------------------------------------- 
    160 %       ORCA-LIM(-PISCES) configurations 
     150%       ORCA-ICE(-PISCES) configurations 
    161151% ------------------------------------------------------------------------------------------------------------- 
    162152\subsection{ORCA pre-defined resolution} 
     
    199189The ORCA\_R2 configuration has the following specificity: starting from a 2\deg~ORCA mesh, 
    200190local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas, 
    201 so that the resolution is 1\deg \time 1\deg there. 
     191so that the resolution is 1\deg~ there. 
    202192A local transformation were also applied with in the Tropics in order to refine the meridional resolution up to 
    203 0.5\deg at the Equator. 
     1930.5\deg~ at the Equator. 
    204194 
    205195The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional resolution up to 
     
    211201For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, otherwise 46 are used. 
    212202In the other ORCA configurations, 31 levels are used 
    213 (see \autoref{tab:orca_zgr} %\sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:zgr}). 
    214  
    215 Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution. 
    216 It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of 
    217 climate change (Marti et al., 2009). 
    218 It is also the basis for the \NEMO contribution to the Coordinate Ocean-ice Reference Experiments (COREs) 
    219 documented in \citet{Griffies_al_OM09}.  
     203(see \autoref{tab:orca_zgr}). %\sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:zgr}). 
     204 
     205Only the ORCA\_R2 is provided with all its input files in the NEMO distribution. 
     206%It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of 
     207%climate change (Marti et al., 2009). 
     208%It is also the basis for the \NEMO contribution to the Coordinate Ocean-ice Reference Experiments (COREs) 
     209%documented in \citet{Griffies_al_OM09}.  
    220210 
    221211This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) in the upper 150m 
     
    227217This \citet{Large_Yeager_Rep04} dataset is available through 
    228218the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}. 
    229 The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution since release v3.3.  
     219The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the NEMO distribution since release v3.3.  
    230220 
    231221ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas current area 
    232 (\key{agrif} defined) and, by setting the appropriate variables, see \path{CONFIG/SHARED/namelist_ref}. 
     222(\key{agrif} defined) and, by setting the appropriate variables, see \path{cfgs/SHARED/namelist_ref}. 
    233223A regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations using 
    234224sponge layers at open boundaries.  
     
    248238and their contribution to the large scale circulation.  
    249239 
     240The GYRE configuration run together with the PISCES biogeochemical model (GYRE-PISCES). 
    250241The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\deg{N} and 
    251242rotated by 45\deg, 3180~km long, 2120~km wide and 4~km deep (\autoref{fig:MISC_strait_hand}). 
     
    266257The GYRE configuration is set like an analytical configuration. 
    267258Through \np{ln\_read\_cfg}\forcode{ = .false.} in \textit{namcfg} namelist defined in 
    268 the reference configuration \path{CONFIG/GYRE/EXP00/namelist_cfg} 
     259the reference configuration \path{cfgs/GYRE_PISCES/EXPREF/namelist_cfg} 
    269260analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines. 
    270261Its horizontal resolution (and thus the size of the domain) is determined by 
    271262setting \np{nn\_GYRE} in \ngn{namusr\_def}: \\ 
     263 
    272264\np{jpiglo} $= 30 \times$ \np{nn\_GYRE} + 2   \\ 
     265 
    273266\np{jpjglo} $= 20 \times$ \np{nn\_GYRE} + 2   \\ 
     267 
    274268Obviously, the namelist parameters have to be adjusted to the chosen resolution, 
    275 see the Configurations pages on the NEMO web site (Using NEMO\/Configurations). 
     269see the Configurations pages on the NEMO web site (NEMO Configurations). 
    276270In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:zgr}). 
    277271 
     
    281275even though the physical integrity of the solution can be compromised. 
    282276Benchmark is activate via \np{ln\_bench}\forcode{ = .true.} in \ngn{namusr\_def} in 
    283 namelist \path{CONFIG/GYRE/EXP00/namelist_cfg}. 
     277namelist \path{cfgs/GYRE_PISCES/EXPREF/namelist_cfg}. 
    284278 
    285279%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     
    304298The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on 
    305299a regular lat-lon grid at approximately 12km horizontal resolution. 
    306 The appropriate \textit{\&namcfg} namelist  is available in \textit{CONFIG/AMM12/EXP00/namelist\_cfg}. 
     300The appropriate \textit{\&namcfg} namelist  is available in \textit{cfgs/AMM12/EXPREF/namelist\_cfg}. 
    307301It is used to build the correct dimensions of the AMM domain. 
    308302 
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