Changeset 6225 for branches/2014/dev_r4704_NOC5_MPP_BDY_UPDATE/DOC/TexFiles/Chapters/Chap_DOM.tex

Timestamp:

2016-01-08T10:35:19+01:00 (8 years ago)

Author:

jamesharle

Message:

Update MPP_BDY_UPDATE branch to be consistent with head of trunk

File:

• branches/2014/dev_r4704_NOC5_MPP_BDY_UPDATE/DOC/TexFiles/Chapters/Chap_DOM.tex (modified) (6 diffs)

branches/2014/dev_r4704_NOC5_MPP_BDY_UPDATE/DOC/TexFiles/Chapters/Chap_DOM.tex

@@ -1 +1 @@
 % ================================================================
-% Chapter 2 � Space and Time Domain (DOM)
+% Chapter 2 ——— Space and Time Domain (DOM)
 % ================================================================
 \chapter{Space Domain (DOM) }
@@ -364 +364 @@
 For both grids here,  the same $w$-point depth has been chosen but in (a) the 
 $t$-points are set half way between $w$-points while in (b) they are defined from 
-an analytical function: $z(k)=5\,(i-1/2)^3 - 45\,(i-1/2)^2 + 140\,(i-1/2) - 150$. 
+an analytical function: $z(k)=5\,(k-1/2)^3 - 45\,(k-1/2)^2 + 140\,(k-1/2) - 150$. 
 Note the resulting difference between the value of the grid-size $\Delta_k$ and 
 those of the scale factor $e_k$. }
@@ -475 +475 @@
 (d) hybrid $s-z$ coordinate, 
 (e) hybrid $s-z$ coordinate with partial step, and 
-(f) same as (e) but with variable volume associated with the non-linear free surface. 
-Note that the variable volume option (\key{vvl}) can be used with any of the 
+(f) same as (e) but in the non-linear free surface (\np{ln\_linssh}=false). 
+Note that the non-linear free surface can be used with any of the 
 5 coordinates (a) to (e).}
 \end{center}   \end{figure}
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
-The choice of a vertical coordinate, even if it is made through a namelist parameter, 
+The choice of a vertical coordinate, even if it is made through \ngn{namzgr} namelist parameters, 
 must be done once of all at the beginning of an experiment. It is not intended as an 
 option which can be enabled or disabled in the middle of an experiment. Three main 
@@ -488 +488 @@
 (\np{ln\_zps}~=~true), or generalized, $s$-coordinate (\np{ln\_sco}~=~true). 
 Hybridation of the three main coordinates are available: $s-z$ or $s-zps$ coordinate 
-(Fig.~\ref{Fig_z_zps_s_sps}d and \ref{Fig_z_zps_s_sps}e). When using the variable 
-volume option \key{vvl} ($i.e.$ non-linear free surface), the coordinate follow the 
-time-variation of the free surface so that the transformation is time dependent: 
-$z(i,j,k,t)$ (Fig.~\ref{Fig_z_zps_s_sps}f). This option can be used with full step 
-bathymetry or $s$-coordinate (hybrid and partial step coordinates have not 
-yet been tested in NEMO v2.3). 
+(Fig.~\ref{Fig_z_zps_s_sps}d and \ref{Fig_z_zps_s_sps}e). By default a non-linear free surface is used:
+the coordinate follow the time-variation of the free surface so that the transformation is time dependent: 
+$z(i,j,k,t)$ (Fig.~\ref{Fig_z_zps_s_sps}f). When a linear free surface is assumed (\np{ln\_linssh}=true), 
+the vertical coordinate are fixed in time, but the seawater can move up and down across the z=0 surface 
+(in other words, the top of the ocean in not a rigid-lid). 
+The last choice in terms of vertical coordinate concerns the presence (or not) in the model domain 
+of ocean cavities beneath ice shelves. Setting \np{ln\_isfcav} to true allows to manage ocean cavities, 
+otherwise they are filled in.
 
 Contrary to the horizontal grid, the vertical grid is computed in the code and no 
 provision is made for reading it from a file. The only input file is the bathymetry 
-(in meters) (\ifile{bathy\_meter}) 
+(in meters) (\ifile{bathy\_meter}). 
 \footnote{N.B. in full step $z$-coordinate, a \ifile{bathy\_level} file can replace the 
 \ifile{bathy\_meter} file, so that the computation of the number of wet ocean point 
 in each water column is by-passed}. 
+If \np{ln\_isfcav}~=~true, an extra file input file describing the ice shelf draft 
+(in meters) (\ifile{isf\_draft\_meter}) is needed and all the location where the isf cavity thinnest
+ than \np{rn\_isfhmin} meters are grounded (ie masked). 
+
 After reading the bathymetry, the algorithm for vertical grid definition differs 
 between the different options:
@@ -518 +524 @@
 %%%
 
-The arrays describing the grid point depths and vertical scale factors 
-are three dimensional arrays $(i,j,k)$ even in the case of $z$-coordinate with 
-full step bottom topography. In non-linear free surface (\key{vvl}), their knowledge
-is required at \textit{before}, \textit{now} and \textit{after} time step, while they 
-do not vary in time in linear free surface case. 
-To improve the code readability while providing this flexibility, the vertical coordinate 
-and scale factors are defined as functions of 
-$(i,j,k)$ with "fs" as prefix (examples: \textit{fse3t\_b, fse3t\_n, fse3t\_a,} 
-for the  \textit{before}, \textit{now} and \textit{after} scale factors at $t$-point) 
-that can be either three different arrays when \key{vvl} is defined, or a single fixed arrays. 
-These functions are defined in the file \hf{domzgr\_substitute} of the DOM directory. 
-They are used throughout the code, and replaced by the corresponding arrays at 
-the time of pre-processing (CPP capability).
+Unless a linear free surface is used (\np{ln\_linssh}=false), the arrays describing 
+the grid point depths and vertical scale factors are three set of three dimensional arrays $(i,j,k)$ 
+defined at \textit{before}, \textit{now} and \textit{after} time step. The time at which they are
+defined is indicated by a suffix:$\_b$, $\_n$, or $\_a$, respectively. They are updated at each model time step
+using a fixed reference coordinate system which computer names have a $\_0$ suffix. 
+When the linear free surface option is used (\np{ln\_linssh}=true), \textit{before}, \textit{now} 
+and \textit{after} arrays are simply set one for all to their reference counterpart. 
+
 
 % -------------------------------------------------------------------------------------------------------------
@@ -839 +840 @@
 %        z*- or s*-coordinate
 % -------------------------------------------------------------------------------------------------------------
-\subsection{$z^*$- or $s^*$-coordinate (add \key{vvl}) }
-\label{DOM_zgr_vvl}
+\subsection{$z^*$- or $s^*$-coordinate (\np{ln\_linssh}=false) }
+\label{DOM_zgr_star}
 
 This option is described in the Report by Levier \textit{et al.} (2007), available on