Changeset 11112

Timestamp:

2019-06-14T15:57:28+02:00 (5 years ago)

Author:

mocavero

Message:

Update the chapter on reference configurations for 4.0 release, see #2216

File:

• NEMO/trunk/doc/latex/NEMO/subfiles/chap_CONFIG.tex (modified) (14 diffs)

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

@@ -18 +18 @@
 \label{sec:CFG_intro}
 
-The purpose of this part of the manual is to introduce the \NEMO reference configurations.
+The purpose of this part of the manual is to introduce the NEMO reference configurations.
 These configurations are offered as means to explore various numerical and physical options,
 thus allowing the user to verify that the code is performing in a manner consistent with that we are running.
@@ -24 +24 @@
 The reference configurations also provide a sense for some of the options available in the code,
 though by no means are all options exercised in the reference configurations.
+Configuration is defined manually through the \textit{namcfg} namelist variables.
 
 %------------------------------------------namcfg----------------------------------------------------
@@ -36 +37 @@
 \label{sec:CFG_c1d}
 
-BE careful: to be re-written according to suppression of jpizoom and jpjzoom !!!!
-
-The 1D model option simulates a stand alone water column within the 3D \NEMO system.
+The 1D model option simulates a stand alone water column within the 3D NEMO system.
 It can be applied to the ocean alone or to the ocean-ice system and can include passive tracers or a biogeochemical model.
 It is set up by defining the position of the 1D water column in the grid
-(see \textit{CONFIG/SHARED/namelist\_ref} ). 
+(see \textit{cfgs/SHARED/namelist\_ref}). 
 The 1D model is a very useful tool
 \textit{(a)} to learn about the physics and numerical treatment of vertical mixing processes;
@@ -50 +49 @@
 \textit{(d)} to produce extra diagnostics, without the large memory requirement of the full 3D model.
 
-The methodology is based on the use of the zoom functionality over the smallest possible domain:
-a 3x3 domain centered on the grid point of interest, with some extra routines.
-There is no need to define a new mesh, bathymetry, initial state or forcing,
-since the 1D model will use those of the configuration it is a zoom of.
-The chosen grid point is set in \textit{\ngn{namcfg}} namelist by
-setting the \np{jpizoom} and \np{jpjzoom} parameters to the indices of the location of the chosen grid point.
+The methodology is based on the configuration of the smallest possible domain:
+a 3x3 domain with 75 vertical levels.
 
 The 1D model has some specifies. First, all the horizontal derivatives are assumed to be zero,
 and second, the two components of the velocity are moved on a $T$-point. 
-Therefore, defining \key{c1d} changes five main things in the code behaviour: 
+Therefore, defining \key{c1d} changes some things in the code behaviour: 
 \begin{description}
 \item[(1)]
-  the lateral boundary condition routine (\rou{lbc\_lnk}) set the value of the central column of
-  the 3x3 domain is imposed over the whole domain;
-\item[(3)]
-  a call to \rou{lbc\_lnk} is systematically done when reading input data (\ie in \mdl{iom});
-\item[(3)]
   a simplified \rou{stp} routine is used (\rou{stp\_c1d}, see \mdl{step\_c1d} module) in which
   both lateral tendancy terms and lateral physics are not called;
-\item[(4)]
+\item[(2)]
   the vertical velocity is zero
   (so far, no attempt at introducing a Ekman pumping velocity has been made);
-\item[(5)]
+\item[(3)]
   a simplified treatment of the Coriolis term is performed as $U$- and $V$-points are the same
   (see \mdl{dyncor\_c1d}).
 \end{description}
-All the relevant \textit{\_c1d} modules can be found in the NEMOGCM/NEMO/OPA\_SRC/C1D directory of
-the \NEMO distribution.
+All the relevant \textit{\_c1d} modules can be found in the src/OCE/C1D directory of
+the NEMO distribution.
 
 % to be added:  a test case on the yearlong Ocean Weather Station (OWS) Papa dataset of Martin (1985)
@@ -88 +78 @@
 
 The ORCA family is a series of global ocean configurations that are run together with
-the LIM sea-ice model (ORCA-LIM) and possibly with PISCES biogeochemical model (ORCA-LIM-PISCES),
-using various resolutions.
-An appropriate namelist is available in \path{CONFIG/ORCA2_LIM3_PISCES/EXP00/namelist_cfg} for ORCA2.
+the SI3 model (ORCA-ICE) and possibly with PISCES biogeochemical model (ORCA-ICE-PISCES).
+An appropriate namelist is available in \path{cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg} for ORCA2.
 The domain of ORCA2 configuration is defined in \ifile{ORCA\_R2\_zps\_domcfg} file,
-this file is available in tar file in the wiki of NEMO: \\
-https://forge.ipsl.jussieu.fr/nemo/wiki/Users/ReferenceConfigurations/ORCA2\_LIM3\_PISCES \\
+this file is available in tar file on the NEMO community zenodo platform: \\
+https://doi.org/10.5281/zenodo.2640723
+
 In this namelist\_cfg the name of domain input file is set in \ngn{namcfg} block of namelist. 
 
@@ -119 +109 @@
 \label{subsec:CFG_orca_grid}
 
-The ORCA grid is a tripolar is based on the semi-analytical method of \citet{Madec_Imbard_CD96}.
+The ORCA grid is a tripolar grid based on the semi-analytical method of \citet{Madec_Imbard_CD96}.
 It allows to construct a global orthogonal curvilinear ocean mesh which has no singularity point inside
 the computational domain since two north mesh poles are introduced and placed on lands.
@@ -158 +148 @@
 
 % -------------------------------------------------------------------------------------------------------------
-%       ORCA-LIM(-PISCES) configurations
+%       ORCA-ICE(-PISCES) configurations
 % -------------------------------------------------------------------------------------------------------------
 \subsection{ORCA pre-defined resolution}
@@ -199 +189 @@
 The ORCA\_R2 configuration has the following specificity: starting from a 2\deg~ORCA mesh,
 local mesh refinements were applied to the Mediterranean, Red, Black and Caspian Seas,
-so that the resolution is 1\deg \time 1\deg there.
+so that the resolution is 1\deg~ there.
 A local transformation were also applied with in the Tropics in order to refine the meridional resolution up to
-0.5\deg at the Equator.
+0.5\deg~ at the Equator.
 
 The ORCA\_R1 configuration has only a local tropical transformation to refine the meridional resolution up to
@@ -211 +201 @@
 For ORCA\_R1 and R025, setting the configuration key to 75 allows to use 75 vertical levels, otherwise 46 are used.
 In the other ORCA configurations, 31 levels are used
-(see \autoref{tab:orca_zgr} %\sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:zgr}).
-
-Only the ORCA\_R2 is provided with all its input files in the \NEMO distribution.
-It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of
-climate change (Marti et al., 2009).
-It is also the basis for the \NEMO contribution to the Coordinate Ocean-ice Reference Experiments (COREs)
-documented in \citet{Griffies_al_OM09}. 
+(see \autoref{tab:orca_zgr}). %\sfcomment{HERE I need to put new table for ORCA2 values} and \autoref{fig:zgr}).
+
+Only the ORCA\_R2 is provided with all its input files in the NEMO distribution.
+%It is very similar to that used as part of the climate model developed at IPSL for the 4th IPCC assessment of
+%climate change (Marti et al., 2009).
+%It is also the basis for the \NEMO contribution to the Coordinate Ocean-ice Reference Experiments (COREs)
+%documented in \citet{Griffies_al_OM09}. 
 
 This version of ORCA\_R2 has 31 levels in the vertical, with the highest resolution (10m) in the upper 150m
@@ -227 +217 @@
 This \citet{Large_Yeager_Rep04} dataset is available through
 the \href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
-The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the \NEMO distribution since release v3.3. 
+The "normal year" of \citet{Large_Yeager_Rep04} has been chosen of the NEMO distribution since release v3.3. 
 
 ORCA\_R2 pre-defined configuration can also be run with an AGRIF zoom over the Agulhas current area
-(\key{agrif} defined) and, by setting the appropriate variables, see \path{CONFIG/SHARED/namelist_ref}.
+(\key{agrif} defined) and, by setting the appropriate variables, see \path{cfgs/SHARED/namelist_ref}.
 A regional Arctic or peri-Antarctic configuration is extracted from an ORCA\_R2 or R05 configurations using
 sponge layers at open boundaries. 
@@ -248 +238 @@
 and their contribution to the large scale circulation. 
 
+The GYRE configuration run together with the PISCES biogeochemical model (GYRE-PISCES).
 The domain geometry is a closed rectangular basin on the $\beta$-plane centred at $\sim$ 30\deg{N} and
 rotated by 45\deg, 3180~km long, 2120~km wide and 4~km deep (\autoref{fig:MISC_strait_hand}).
@@ -266 +257 @@
 The GYRE configuration is set like an analytical configuration.
 Through \np{ln\_read\_cfg}\forcode{ = .false.} in \textit{namcfg} namelist defined in
-the reference configuration \path{CONFIG/GYRE/EXP00/namelist_cfg}
+the reference configuration \path{cfgs/GYRE_PISCES/EXPREF/namelist_cfg}
 analytical definition of grid in GYRE is done in usrdef\_hrg, usrdef\_zgr routines.
 Its horizontal resolution (and thus the size of the domain) is determined by
 setting \np{nn\_GYRE} in \ngn{namusr\_def}: \\
+
 \np{jpiglo} $= 30 \times$ \np{nn\_GYRE} + 2   \\
+
 \np{jpjglo} $= 20 \times$ \np{nn\_GYRE} + 2   \\
+
 Obviously, the namelist parameters have to be adjusted to the chosen resolution,
-see the Configurations pages on the NEMO web site (Using NEMO\/Configurations).
+see the Configurations pages on the NEMO web site (NEMO Configurations).
 In the vertical, GYRE uses the default 30 ocean levels (\jp{jpk}\forcode{ = 31}) (\autoref{fig:zgr}).
 
@@ -281 +275 @@
 even though the physical integrity of the solution can be compromised.
 Benchmark is activate via \np{ln\_bench}\forcode{ = .true.} in \ngn{namusr\_def} in
-namelist \path{CONFIG/GYRE/EXP00/namelist_cfg}.
+namelist \path{cfgs/GYRE_PISCES/EXPREF/namelist_cfg}.
 
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
@@ -304 +298 @@
 The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on
 a regular lat-lon grid at approximately 12km horizontal resolution.
-The appropriate \textit{\&namcfg} namelist  is available in \textit{CONFIG/AMM12/EXP00/namelist\_cfg}.
+The appropriate \textit{\&namcfg} namelist  is available in \textit{cfgs/AMM12/EXPREF/namelist\_cfg}.
 It is used to build the correct dimensions of the AMM domain.