Changeset 6317 for branches/2015

Timestamp:

2016-02-15T16:21:15+01:00 (8 years ago)

Author:

mathiot

Message:

ISF: update documentation and biblio

Location:

branches/2015/nemo_v3_6_STABLE/DOC/TexFiles

Files:

• Biblio/Biblio.bib (modified) (2 diffs)
• Chapters/Chap_DOM.tex (modified) (4 diffs)
• Chapters/Chap_DYN.tex (modified) (2 diffs)
• Chapters/Chap_SBC.tex (modified) (2 diffs)
• Chapters/Chap_TRA.tex (modified) (3 diffs)
• Chapters/Chap_ZDF.tex (modified) (2 diffs)

branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Biblio/Biblio.bib

@@ -1514 +1514 @@
 }
 
+@TechReport{Hunter2006,
+  Title                    = {Specification for Test Models of Ice Shelf Cavities},
+  Author                   = {J. R. Hunter},
+  Institution              = {Antarctic Climate \& Ecosystems Cooperative Research Centre Private Bag 80, Hobart, Tasmania 7001},
+  Year                     = {2006},
+}
+
 @TECHREPORT{TEOS10,
   author = {IOC and SCOR and IAPSO},
@@ -1594 +1601 @@
   volume = {96},  number = {C11},
   pages = {2298--2312}
+}
+
+@ARTICLE{Jenkins2001,
+  author = {A. Jenkins},
+  title = {The Role of Meltwater Advection in the Formulation of Conservative Boundary Conditions at an Ice-Ocean Interface},
+  journal = JPO,
+  year = {2001},
+  volume = {31},
+  pages = {285--296}
 }
 

branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_DOM.tex

@@ -494 +494 @@
 bathymetry or $s$-coordinate (hybrid and partial step coordinates have not 
 yet been tested in NEMO v2.3). If using $z$-coordinate with partial step bathymetry
-(\np{ln\_zps}~=~true), ocean cavity beneath ice shelves can be open (\np{ln\_isfcav}~=~true).
+(\np{ln\_zps}~=~true), ocean cavity beneath ice shelves can be open (\np{ln\_isfcav}~=~true) 
+and partial step are also applied at the ocean/ice shelf interface. 
 
 Contrary to the horizontal grid, the vertical grid is computed in the code and no 
@@ -548 +549 @@
 domain width at the central latitude. This is meant for the "EEL-R5" configuration, 
 a periodic or open boundary channel with a seamount. 
-\item[\np{nn\_bathy} = 1] read a bathymetry. The \ifile{bathy\_meter} file (Netcdf format) 
-provides the ocean depth (positive, in meters) at each grid point of the model grid. 
-The bathymetry is usually built by interpolating a standard bathymetry product 
+\item[\np{nn\_bathy} = 1] read a bathymetry and ice shelf draft (if needed).
+ The \ifile{bathy\_meter} file (Netcdf format) provides the ocean depth (positive, in meters)
+ at each grid point of the model grid. The bathymetry is usually built by interpolating a standard bathymetry product 
 ($e.g.$ ETOPO2) onto the horizontal ocean mesh. Defining the bathymetry also 
 defines the coastline: where the bathymetry is zero, no model levels are defined 
 (all levels are masked).
+
+The \ifile{isfdraft\_meter} file (Netcdf format) provides the ice shelf draft (positive, in meters)
+ at each grid point of the model grid. This file is only needed if \np{ln\_isfcav}~=~true. 
+Defining the ice shelf draft will also define the ice shelf edge and the grounding line position.
 \end{description}
 
@@ -610 +615 @@
 (Fig.~\ref{Fig_zgr}).
 
+If the ice shelf cavities are opened (\np{ln\_isfcav}=~true~}), the definition of $z_0$ is the same. 
+However, definition of $e_3^0$ at $t$- and $w$-points is respectively changed to:
+\begin{equation} \label{DOM_zgr_ana}
+\begin{split}
+ e_3^T(k) &= z_W (k+1) - z_W (k)   \\
+ e_3^W(k) &= z_T (k)   - z_T (k-1) \\
+\end{split}
+\end{equation}
+This formulation decrease the self-generated circulation into the ice shelf cavity 
+(which can, in extreme case, leads to blow up).\\
+
+ 
 The most used vertical grid for ORCA2 has $10~m$ ($500~m)$ resolution in the 
 surface (bottom) layers and a depth which varies from 0 at the sea surface to a 
@@ -860 +877 @@
 gives the number of ocean levels ($i.e.$ those that are not masked) at each 
 $t$-point. mbathy is computed from the meter bathymetry using the definiton of 
-gdept as the number of $t$-points which gdept $\leq$ bathy. 
+gdept as the number of $t$-points which gdept $\leq$ bathy.
 
 Modifications of the model bathymetry are performed in the \textit{bat\_ctl} 
 routine (see \mdl{domzgr} module) after mbathy is computed. Isolated grid points 
-that do not communicate with another ocean point at the same level are eliminated.
+that do not communicate with another ocean point at the same level are eliminated.\\
+
+As for the representation of bathymetry, a 2D integer array, misfdep, is created. 
+misfdep defines the level of the first wet $t$-point. All the cells between $k=1$ and $misfdep(i,j)-1$ are masked. 
+By default, misfdep(:,:)=1 and no cells are masked.
+
+In case of ice shelf cavities, modifications of the model bathymetry and ice shelf draft into 
+the cavities are performed in the \textit{zgr\_isf} routine. The compatibility between ice shelf draft and bathymetry is checked. 
+If only one cell on the water column is opened at $t$-, $u$- or $v$-points, the bathymetry or the ice shelf draft is dug to fit this constrain.
+If the incompatibility is too strong (need to dig more than 1 cell), the cell is masked.\\ 
 
 From the \textit{mbathy} array, the mask fields are defined as follows:
 \begin{align*}
-tmask(i,j,k) &= \begin{cases}   \; 1&   \text{ if $k\leq mbathy(i,j)$  }    \\
-                                                \; 0&   \text{ if $k\leq mbathy(i,j)$  }    \end{cases}     \\
+tmask(i,j,k) &= \begin{cases}   \; 0&   \text{ if $k < misfdep(i,j) $ } \\
+                                \; 1&   \text{ if $misfdep(i,j) \leq k\leq mbathy(i,j)$  }    \\
+                                \; 0&   \text{ if $k > mbathy(i,j)$  }    \end{cases}     \\
 umask(i,j,k) &=         \; tmask(i,j,k) \ * \ tmask(i+1,j,k)   \\
 vmask(i,j,k) &=         \; tmask(i,j,k) \ * \ tmask(i,j+1,k)   \\
 fmask(i,j,k) &=         \; tmask(i,j,k) \ * \ tmask(i+1,j,k)   \\
-                   & \ \ \, * tmask(i,j,k) \ * \ tmask(i+1,j,k)
+                   & \ \ \, * tmask(i,j,k) \ * \ tmask(i+1,j,k) \\
+wmask(i,j,k) &=         \; tmask(i,j,k) \ * \ tmask(i,j,k-1) \text{ with } wmask(i,j,1) = tmask(i,j,1) 
 \end{align*}
 
-Note that \textit{wmask} is not defined as it is exactly equal to \textit{tmask} with 
-the numerical indexing used (\S~\ref{DOM_Num_Index}). Moreover, the 
-specification of closed lateral boundaries requires that at least the first and last 
+Note, wmask is now defined. It allows, in case of ice shelves, 
+to deal with the top boundary (ice shelf/ocean interface) exactly in the same way as for the bottom boundary. 
+
+The specification of closed lateral boundaries requires that at least the first and last 
 rows and columns of the \textit{mbathy} array are set to zero. In the particular 
 case of an east-west cyclical boundary condition, \textit{mbathy} has its last 

branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_DYN.tex

@@ -637 +637 @@
 ($e_{3w}$).
  
-$\bullet$ Traditional coding with adaptation for ice shelf cavities (\np{ln\_hpg\_isf}=true).
-This scheme need the activation of ice shelf cavities (\np{ln\_isfcav}=true).
-
 $\bullet$ Pressure Jacobian scheme (prj) (a research paper in preparation) (\np{ln\_dynhpg\_prj}=true)
 
@@ -654 +651 @@
 pressure Jacobian method is used to solve the horizontal pressure gradient. This method can provide
 a more accurate calculation of the horizontal pressure gradient than the standard scheme.
+
+\subsection{Ice shelf cavity}
+\label{DYN_hpg_isf}
+Beneath an ice shelf, the total pressure gradient is the sum of the pressure gradient due to the ice shelf load and
+ the pressure gradient due to the ocean load. If cavity opened (\np{ln\_isfcav}~=~true) these 2 terms can be
+ calculated by setting \np{ln\_dynhpg\_isf}~=~true. No other scheme are working with the ice shelf.\\
+
+$\bullet$ The main hypothesis to compute the ice shelf load is that the ice shelf is in an isostatic equilibrium.
+ The top pressure is computed integrating from surface to the base of the ice shelf a reference density profile 
+(prescribed as density of a water at 34.4 PSU and -1.9$\degres C$) and corresponds to the water replaced by the ice shelf. 
+This top pressure is constant over time. A detailed description of this method is described in \citet{Losch2008}.\\
+
+$\bullet$ The ocean load is computed using the expression \eqref{Eq_dynhpg_sco} described in \ref{DYN_hpg_sco}. 
+A treatment of the partial cell for top and bottom similar to the one described in \ref{DYN_hpg_zps} is done 
+to reduce the residual circulation generated by the top partial cell. 
 
 %--------------------------------------------------------------------------------------------------------------

branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_SBC.tex

@@ -924 +924 @@
 \namdisplay{namsbc_isf}
 %--------------------------------------------------------------------------------------------------------
-Namelist variable in \ngn{namsbc}, \np{nn\_isf}, control the kind of ice shelf representation used. 
+Namelist variable in \ngn{namsbc}, \np{nn\_isf}, controls the ice shelf representation used. 
 \begin{description}
 \item[\np{nn\_isf}~=~1]
-The ice shelf cavity is represented. The fwf and heat flux are computed. 
-Full description, sensitivity and validation in preparation. 
+The ice shelf cavity is represented. The fwf and heat flux are computed. Two different bulk formula are available:
+   \begin{description}
+   \item[\np{nn\_isfblk}~=~1]
+   The bulk formula used to compute the melt is based the one described in \citet{Hunter2006}.
+        This formulation is based on a balance between the upward ocean heat flux and the latent heat flux at the ice shelf base.
+
+   \item[\np{nn\_isfblk}~=~2] 
+   The bulk formula used to compute the melt is based the one described in \citet{Jenkins1991}.
+        This formulation is based on a 3 equations formulation (a heat flux budget, a salt flux budget and a linearised freezing point temperature equation).
+   \end{description}
+
+For this 2 bulk formulations, there are 3 different ways to compute the exchange coeficient:
+   \begin{description}
+        \item[\np{nn\_gammablk~=~0~}]
+   The salt and heat exchange coefficients are constant and defined by \np{rn\_gammas0} and \np{rn\_gammat0}
+
+   \item[\np{nn\_gammablk~=~1~}]
+   The salt and heat exchange coefficients are velocity dependent and defined as $\np{rn\_gammas0} \times u_{*}$ and $\np{rn\_gammat0} \times u_{*}$
+        where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters).
+        See \citet{Jenkins2010} for all the details on this formulation.
+   
+   \item[\np{nn\_gammablk~=~2~}]
+   The salt and heat exchange coefficients are velocity and stability dependent and defined as 
+        $\gamma_{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}$
+        where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters), 
+        $\Gamma_{Turb}$ the contribution of the ocean stability and 
+        $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion.
+        See \citet{Holland1999} for all the details on this formulation.
+        \end{description}
 
 \item[\np{nn\_isf}~=~2]
@@ -934 +961 @@
 The fwf is distributed along the ice shelf edge between the depth of the average grounding line (GL)
 (\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}) as in (\np{nn\_isf}~=~3). 
-Furthermore the fwf is computed using the \citet{Beckmann2003} parameterisation of isf melting. 
+Furthermore the fwf and heat flux are computed using the \citet{Beckmann2003} parameterisation of isf melting. 
 The effective melting length (\np{sn\_Leff\_isf}) is read from a file.
 
 \item[\np{nn\_isf}~=~3]
 A simple parameterisation of isf is used. The ice shelf cavity is not represented. 
-The fwf (\np{sn\_rnfisf}) is distributed along the ice shelf edge between the depth of the average grounding line (GL)
-(\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}).
-Full description, sensitivity and validation in preparation.
+The fwf (\np{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between the depth of the average grounding line (GL)
+(\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}). 
+The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
 
 \item[\np{nn\_isf}~=~4]
-The ice shelf cavity is represented. However, the fwf (\np{sn\_fwfisf}) and heat flux (\np{sn\_qisf}) are 
-not computed but specified from file. 
+The ice shelf cavity is opened. However, the fwf is not computed but specified from file \np{sn\_fwfisf}). 
+The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.\\
 \end{description}
 
-\np{nn\_isf}~=~1 and \np{nn\_isf}~=~2 compute a melt rate based on the water masse properties, ocean velocities and depth.
- This flux is thus highly dependent of the model resolution (horizontal and vertical), realism of the water masse onto the shelf ...
-
-\np{nn\_isf}~=~3 and \np{nn\_isf}~=~4 read the melt rate and heat flux from a file. You have total control of the fwf scenario.
-
+
+$\bullet$ \np{nn\_isf}~=~1 and \np{nn\_isf}~=~2 compute a melt rate based on the water mass properties, ocean velocities and depth.
+ This flux is thus highly dependent of the model resolution (horizontal and vertical), realism of the water masses onto the shelf ...\\
+
+
+$\bullet$ \np{nn\_isf}~=~3 and \np{nn\_isf}~=~4 read the melt rate from a file. You have total control of the fwf forcing.
 This can be usefull if the water masses on the shelf are not realistic or the resolution (horizontal/vertical) are too 
-coarse to have realistic melting or for sensitivity studies where you want to control your input. 
-Full description, sensitivity and validation in preparation. 
-
-There is 2 ways to apply the fwf to NEMO. The first possibility (\np{ln\_divisf}~=~false) applied the fwf
- and heat flux directly on the salinity and temperature tendancy. The second possibility (\np{ln\_divisf}~=~true)
- apply the fwf as for the runoff fwf (see \S\ref{SBC_rnf}). The mass/volume addition due to the ice shelf melting is,
- at each relevant depth level, added to the horizontal divergence (\textit{hdivn}) in the subroutine \rou{sbc\_isf\_div} 
-(called from \mdl{divcur}). 
+coarse to have realistic melting or for studies where you need to control your heat and fw input.\\ 
+
+Two namelist parameters control how the heat and fw fluxes are passed to NEMO: \np{rn\_hisf\_tbl} and \np{ln\_divisf}
+\begin{description}
+\item[\np{rn\_hisf\_tbl}] is the top boundary layer thickness as defined in \citet{Losch2008}. 
+This parameter is only used if \np{nn\_isf}~=~1 or \np{nn\_isf}~=~4
+It allows you to control over which depth you want to spread the heat and fw fluxes. 
+
+If \np{rn\_hisf\_tbl} = 0.0, the fluxes are put in the top level whatever is its tickness. 
+
+If \np{rn\_hisf\_tbl} $>$ 0.0, the fluxes are spread over the first \np{rn\_hisf\_tbl} m (ie over one or several cells).
+
+\item[\np{ln\_divisf}] is a flag to apply the fw flux as a volume flux or as a salt flux. 
+
+\np{ln\_divisf}~=~true applies the fwf as a volume flux. This volume flux is implemented with in the same way as for the runoff.
+The fw addition due to the ice shelf melting is, at each relevant depth level, added to the horizontal divergence 
+(\textit{hdivn}) in the subroutine \rou{sbc\_isf\_div}, called from \mdl{divcur}. 
+See the runoff section \ref{SBC_rnf} for all the details about the divergence correction. 
+
+\np{ln\_divisf}~=~false applies the fwf and heat flux directly on the salinity and temperature tendancy.
+
+\item[\np{ln\_conserve}] is a flag for \np{nn\_isf}~=~1. A conservative boundary layer scheme as described in \citet{Jenkins2001} 
+is used if \np{ln\_conserve}=true. It takes into account the fact that the melt water is at freezing T and needs to be warm up to ocean temperature. 
+It is only relevant for \np{ln\_divisf}~=~false. 
+If \np{ln\_divisf}~=~true, \np{ln\_conserve} has to be set to false to avoid a double counting of the contribution. 
+ 
+\end{description}
 %
 % ================================================================

branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_TRA.tex

@@ -641 +641 @@
 $\bullet$ \textit{rnf}, the mass flux associated with runoff 
 (see \S\ref{SBC_rnf} for further detail of how it acts on temperature and salinity tendencies)
+
+$\bullet$ \textit{fwfisf}, the mass flux associated with ice shelf melt, (see \S\ref{SBC_isf} for further details 
+on how the ice shelf melt is computed and applied).\\
 
 In the non-linear free surface case (\key{vvl} is defined), the surface boundary condition 
@@ -1280 +1283 @@
                    I've changed "derivative" to "difference" and "mean" to "average"}
 
-With partial bottom cells (\np{ln\_zps}=true), in general, tracers in horizontally 
+With partial cells (\np{ln\_zps}=true) at bottom and top (\np{ln\_isfcav}=true), in general, tracers in horizontally 
 adjacent cells live at different depths. Horizontal gradients of tracers are needed 
 for horizontal diffusion (\mdl{traldf} module) and for the hydrostatic pressure 
 gradient (\mdl{dynhpg} module) to be active. 
 \gmcomment{STEVEN from gm : question: not sure of  what -to be active- means}
+
 Before taking horizontal gradients between the tracers next to the bottom, a linear 
 interpolation in the vertical is used to approximate the deeper tracer as if it actually 
@@ -1360 +1364 @@
 \gmcomment{gm :   this last remark has to be done}
 %%%
+
+If under ice shelf seas opened (\np{ln\_isfcav}=true), the partial cell properties 
+at the top are computed in the same way as for the bottom. Some extra variables are, 
+however, computed to reduce the flow generated at the top and bottom if $z*$ coordinates activated.
+The extra variables calculated and used by \S\ref{DYN_hpg_isf} are:
+
+$\bullet$ $\overline{T}_k^{\,i+1/2}$ as described in \eqref{Eq_zps_hde}
+
+$\bullet$ $\delta _{i+1/2} Z_{T_k} = \widetilde {Z}^{\,i}_{T_k}-Z^{\,i}_{T_k}$ to compute 
+the pressure gradient correction term used by \eqref{Eq_dynhpg_sco} in \S\ref{DYN_hpg_isf},
+ with $\widetilde {Z}_{T_k}$ the depth of the point $\widetilde {T}_{k}$ in case of $z^*$ coordinates 
+(this term = 0 in z-coordinates)

branches/2015/nemo_v3_6_STABLE/DOC/TexFiles/Chapters/Chap_ZDF.tex

@@ -857 +857 @@
 % Bottom Friction
 % ================================================================
-\section  [Bottom and top Friction (\textit{zdfbfr})]   {Bottom Friction (\mdl{zdfbfr} module)}
+\section  [Bottom and Top Friction (\textit{zdfbfr})]   {Bottom and Top Friction (\mdl{zdfbfr} module)}
 \label{ZDF_bfr}
 
@@ -865 +865 @@
 
 Options to define the top and bottom friction are defined through the  \ngn{nambfr} namelist variables.
-The top friction is activated only if the ice shelf cavities are opened (\np{ln\_isfcav}~=~true).
-As the friction processes at the top and bottom are the represented similarly, only the bottom friction is described in detail.
+The bottom friction represents the friction generated by the bathymetry. 
+The top friction represents the friction generated by the ice shelf/ocean interface. 
+As the friction processes at the top and bottom are represented similarly, only the bottom friction is described in detail below.\\
+
 
 Both the surface momentum flux (wind stress) and the bottom momentum