Changeset 5313 for branches/2014/dev_r4650_UKMO11_restart_functionality/DOC

Timestamp:

2015-05-29T11:46:03+02:00 (9 years ago)

Author:

timgraham

Message:

Merged head of trunk (r5302) into branch

Location:

branches/2014/dev_r4650_UKMO11_restart_functionality/DOC/TexFiles

Files:

• Biblio/Biblio.bib (modified) (1 diff)
• Chapters/Chap_DOM.tex (modified) (1 diff)
• Chapters/Chap_DYN.tex (modified) (1 diff)
• Chapters/Chap_MISC.tex (modified) (1 diff)
• Chapters/Chap_SBC.tex (modified) (6 diffs)
• Chapters/Chap_ZDF.tex (modified) (2 diffs)
• Namelist/nambfr (modified) (1 diff)
• Namelist/namcfg_orca1 (copied) (copied from trunk/DOC/TexFiles/Namelist/namcfg_orca1)
• Namelist/namdyn_hpg (modified) (1 diff)
• Namelist/namsbc (modified) (1 diff)
• Namelist/namsbc_isf (copied) (copied from trunk/DOC/TexFiles/Namelist/namsbc_isf)
• Namelist/namzgr (modified) (1 diff)

branches/2014/dev_r4650_UKMO11_restart_functionality/DOC/TexFiles/Biblio/Biblio.bib

@@ -271 +271 @@
   volume = {326},
   pages = {677--684}
+}
+
+@ARTICLE{Beckmann2003,
+  author = {A. Beckmann and H. Goosse},
+  title = {A parameterization of ice shelf-ocean interaction for climate models},
+  journal = OM
+  year = {2003}
+  volume = {5}
+  pages = {157--170}
 }
 

branches/2014/dev_r4650_UKMO11_restart_functionality/DOC/TexFiles/Chapters/Chap_DOM.tex

@@ -493 +493 @@
 $z(i,j,k,t)$ (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). 
+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).
 
 Contrary to the horizontal grid, the vertical grid is computed in the code and no 

branches/2014/dev_r4650_UKMO11_restart_functionality/DOC/TexFiles/Chapters/Chap_DYN.tex

@@ -627 +627 @@
 \eqref{Eq_dynhpg_zco_surf} - \eqref{Eq_dynhpg_zco}, and $z_T$ is the depth of 
 the $T$-point evaluated from the sum of the vertical scale factors at the $w$-point 
-($e_{3w}$). 
+($e_{3w}$).
+ 
+$\bullet$ Traditional coding with adaptation for ice shelf cavities (\np{ln\_dynhpg\_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)

branches/2014/dev_r4650_UKMO11_restart_functionality/DOC/TexFiles/Chapters/Chap_MISC.tex

@@ -141 +141 @@
 computational domain is laid out on local processor memories following a 2D 
 horizontal splitting. % (see {\S}IV.2-c) ref to the section to be updated
+
+\subsection{Simple subsetting of input files via netCDF attributes}
+
+The extended grids for use with the under-shelf ice cavities will result in redundant rows
+around Antarctica if the ice cavities are not active. A simple mechanism for subsetting
+input files associated with the extended domains has been implemented to avoid the need to
+maintain different sets of input fields for use with or without active ice cavities. The
+existing 'zoom' options are overly complex for this task and marked for deletion anyway.
+This alternative subsetting operates for the j-direction only and works by optionally
+looking for and using a global file attribute (named: \np{open\_ocean\_jstart}) to
+determine the starting j-row for input. The use of this option is best explained with an
+example: Consider an ORCA1 configuration using the extended grid bathymetry and coordinate
+files:
+\vspace{-10pt}
+\begin{alltt}
+\tiny
+\begin{verbatim}
+eORCA1_bathymetry_v2.nc
+eORCA1_coordinates.nc
+\end{verbatim}
+\end{alltt}
+\noindent These files define a horizontal domain of 362x332. Assuming the first row with
+open ocean wet points in the non-isf bathymetry for this set is row 42 (Fortran indexing)
+then the formally correct setting for \np{open\_ocean\_jstart} is 41. Using this value as the
+first row to be read will result in a 362x292 domain which is the same size as the original
+ORCA1 domain. Thus the extended coordinates and bathymetry files can be used with all the
+original input files for ORCA1 if the ice cavities are not active (\np{ln\_isfcav =
+.false.}). Full instructions for achieving this are:
+
+\noindent Add the new attribute to any input files requiring a j-row offset, i.e:
+\vspace{-10pt}
+\begin{alltt}
+\tiny
+\begin{verbatim}
+ncatted  -a open_ocean_jstart,global,a,d,41 eORCA1_coordinates.nc 
+ncatted  -a open_ocean_jstart,global,a,d,41 eORCA1_bathymetry_v2.nc
+\end{verbatim}
+\end{alltt}
+ 
+\noindent Add the logical switch to \ngn{namcfg} in the configuration namelist and set true:
+%--------------------------------------------namcfg--------------------------------------------------------
+\namdisplay{namcfg_orca1}
+%--------------------------------------------------------------------------------------------------------------
+
+\noindent Note the j-size of the global domain is the (extended j-size minus
+\np{open\_ocean\_jstart} + 1 ) and this must match the size of all datasets other than
+bathymetry and coordinates currently. However the option can be extended to any global, 2D
+and 3D, netcdf, input field by adding the:
+\vspace{-10pt}
+\begin{alltt}
+\tiny
+\begin{verbatim}
+lrowattr=ln_use_jattr
+\end{verbatim}
+\end{alltt}
+optional argument to the appropriate \np{iom\_get} call and the \np{open\_ocean\_jstart} attribute to the corresponding input files. It remains the users responsibility to set \np{jpjdta} and \np{jpjglo} values in the \np{namelist\_cfg} file according to their needs.
 
 %>>>>>>>>>>>>>>>>>>>>>>>>>>>>

branches/2014/dev_r4650_UKMO11_restart_functionality/DOC/TexFiles/Chapters/Chap_SBC.tex

@@ -1 +1 @@
 % ================================================================
-% Chapter � Surface Boundary Condition (SBC, ICB) 
-% ================================================================
-\chapter{Surface Boundary Condition (SBC, ICB) }
+% Chapter � Surface Boundary Condition (SBC, ISF, ICB) 
+% ================================================================
+\chapter{Surface Boundary Condition (SBC, ISF, ICB) }
 \label{SBC}
 \minitoc
@@ -48 +48 @@
 below ice-covered areas (using observed ice-cover or a sea-ice model) 
 (\np{nn\_ice}~=~0,1, 2 or 3); the addition of river runoffs as surface freshwater 
-fluxes or lateral inflow (\np{ln\_rnf}~=~true); the addition of a freshwater flux adjustment 
-in order to avoid a mean sea-level drift (\np{nn\_fwb}~=~0,~1~or~2); the 
+fluxes or lateral inflow (\np{ln\_rnf}~=~true); the addition of isf melting as lateral inflow (parameterisation) 
+(\np{nn\_isf}~=~2 or 3 and \np{ln\_isfcav}~=~false) or as surface flux at the land-ice ocean interface
+(\np{nn\_isf}~=~1 or 4 and \np{ln\_isfcav}~=~true); 
+the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift (\np{nn\_fwb}~=~0,~1~or~2); the 
 transformation of the solar radiation (if provided as daily mean) into a diurnal 
 cycle (\np{ln\_dm2dc}~=~true); and a neutral drag coefficient can be read from an external wave 
@@ -60 +62 @@
 Finally, the different options that further modify the fluxes applied to the ocean are discussed.
 One of these is modification by icebergs (see \S\ref{ICB_icebergs}), which act as drifting sources of fresh water.
+Another example of modification is that due to the ice shelf melting/freezing (see \S\ref{SBC_isf}), 
+which provides additional sources of fresh water.
 
 
@@ -686 +690 @@
 air temperature, sea-surface temperature, cloud cover and relative humidity.
 Sensible heat and latent heat fluxes are computed by classical
-bulk formulae parameterized according to \citet{Kondo1975}.
+bulk formulae parameterised according to \citet{Kondo1975}.
 Details on the bulk formulae used can be found in \citet{Maggiore_al_PCE98} and \citet{Castellari_al_JMS1998}.
 
@@ -826 +830 @@
 \Pi-g\delta = (1+k-h) \Pi_{A}(\lambda,\phi)
 \end{equation}
-with $k$ a number of Love estimated to 0.6 which parametrized the astronomical tidal land,
-and $h$ a number of Love to 0.3 which parametrized the parametrization due to the astronomical tidal land.
+with $k$ a number of Love estimated to 0.6 which parameterised the astronomical tidal land,
+and $h$ a number of Love to 0.3 which parameterised the parameterisation due to the astronomical tidal land.
 
 % ================================================================
@@ -945 +949 @@
 
 %}
-
-
+% ================================================================
+%        Ice shelf melting
+% ================================================================
+\section   [Ice shelf melting (\textit{sbcisf})]
+                        {Ice shelf melting (\mdl{sbcisf})}
+\label{SBC_isf}
+%------------------------------------------namsbc_isf----------------------------------------------------
+\namdisplay{namsbc_isf}
+%--------------------------------------------------------------------------------------------------------
+Namelist variable in \ngn{namsbc}, \np{nn\_isf},  control the kind of 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. 
+
+\item[\np{nn\_isf}~=~2]
+A parameterisation of isf is used. The ice shelf cavity is not represented. 
+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. 
+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.
+
+\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. 
+\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.
+
+ 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}). 
+%
 % ================================================================
 %        Handling of icebergs

branches/2014/dev_r4650_UKMO11_restart_functionality/DOC/TexFiles/Chapters/Chap_ZDF.tex

@@ -830 +830 @@
 % Bottom Friction
 % ================================================================
-\section  [Bottom Friction (\textit{zdfbfr})]   {Bottom Friction (\mdl{zdfbfr} module)}
+\section  [Bottom and top Friction (\textit{zdfbfr})]   {Bottom Friction (\mdl{zdfbfr} module)}
 \label{ZDF_bfr}
 
@@ -837 +837 @@
 %--------------------------------------------------------------------------------------------------------------
 
-Options are defined through the  \ngn{nambfr} namelist variables.
+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.
+
 Both the surface momentum flux (wind stress) and the bottom momentum 
 flux (bottom friction) enter the equations as a condition on the vertical 

branches/2014/dev_r4650_UKMO11_restart_functionality/DOC/TexFiles/Namelist/nambfr

@@ -5 +5 @@
                            !                              = 2 : nonlinear friction
    rn_bfri1    =    4.e-4  !  bottom drag coefficient (linear case)
-   rn_bfri2    =    1.e-3  !  bottom drag coefficient (non linear case)
+   rn_bfri2    =    1.e-3  !  bottom drag coefficient (non linear case). Minimum coeft if ln_loglayer=T
+   rn_bfri2_max =   1.e-1  !  max. bottom drag coefficient (non linear case and ln_loglayer=T)
    rn_bfeb2    =    2.5e-3 !  bottom turbulent kinetic energy background  (m2/s2)
-   rn_bfrz0    =    3.e-3  ! bottom roughness for loglayer bfr coeff 
+   rn_bfrz0    =    3.e-3  !  bottom roughness [m] if ln_loglayer=T
    ln_bfr2d    = .false.   !  horizontal variation of the bottom friction coef (read a 2D mask file )
    rn_bfrien   =    50.    !  local multiplying factor of bfr (ln_bfr2d=T)
+   rn_tfri1    =    4.e-4  !  top drag coefficient (linear case)
+   rn_tfri2    =    2.5e-3 !  top drag coefficient (non linear case). Minimum coeft if ln_loglayer=T
+   rn_tfri2_max =   1.e-1  !  max. top drag coefficient (non linear case and ln_loglayer=T)
+   rn_tfeb2    =    0.0    !  top turbulent kinetic energy background  (m2/s2)
+   rn_tfrz0    =    3.e-3  !  top roughness [m] if ln_loglayer=T
+   ln_tfr2d    = .false.   !  horizontal variation of the top friction coef (read a 2D mask file )
+   rn_tfrien   =    50.    !  local multiplying factor of tfr (ln_tfr2d=T)
+
    ln_bfrimp   = .true.    !  implicit bottom friction (requires ln_zdfexp = .false. if true)
+   ln_loglayer = .false.   !  logarithmic formulation (non linear case)
 /

branches/2014/dev_r4650_UKMO11_restart_functionality/DOC/TexFiles/Namelist/namdyn_hpg

@@ -5 +5 @@
    ln_hpg_zps  = .true.    !  z-coordinate - partial steps (interpolation)
    ln_hpg_sco  = .false.   !  s-coordinate (standard jacobian formulation)
+   ln_hpg_isf  = .false.   !  s-coordinate (sco ) adapted to ice shelf cavity
    ln_hpg_djc  = .false.   !  s-coordinate (Density Jacobian with Cubic polynomial)
    ln_hpg_prj  = .false.   !  s-coordinate (Pressure Jacobian scheme)

branches/2014/dev_r4650_UKMO11_restart_functionality/DOC/TexFiles/Namelist/namsbc

@@ -19 +19 @@
    ln_dm2dc    = .false.   !  daily mean to diurnal cycle on short wave
    ln_rnf      = .true.    !  runoffs                                   (T => fill namsbc_rnf)
+   nn_isf      = 0         !  ice shelf melting/freezing                (/=0 => fill namsbc_isf)
+                           !  0 =no isf                  1 = presence of ISF
+                           !  2 = bg03 parametrisation   3 = rnf file for isf
+                           !  4 = ISF fwf specified
+                           !  option 1 and 4 need ln_isfcav = .true. (domzgr)
    ln_ssr      = .true.    !  Sea Surface Restoring on T and/or S       (T => fill namsbc_ssr)
    nn_fwb      = 3         !  FreshWater Budget: =0 unchecked

branches/2014/dev_r4650_UKMO11_restart_functionality/DOC/TexFiles/Namelist/namzgr

@@ -5 +5 @@
    ln_zps      = .true.    !  z-coordinate - partial steps   (T/F)
    ln_sco      = .false.   !  s- or hybrid z-s-coordinate    (T/F)
+   ln_isfcav   = .false.   !  ice shelf cavity               (T/F)
 /