Index: /trunk/MESOSCALE/MANUAL/SRC/advance.tex
===================================================================
--- /trunk/MESOSCALE/MANUAL/SRC/advance.tex	(revision 1706)
+++ /trunk/MESOSCALE/MANUAL/SRC/advance.tex	(revision 1707)
@@ -146,5 +146,5 @@
 \item in \ttt{namelist.input}, the 6th order small scale diffusion must be set to 0 (i.e. \ttt{diff\_6th\_opt = 0}) if the resolution is small ($<10$~km)
 \item additional \ttt{mars} modes can be accessed (e.g. for interactive dust or the radiative effect of clouds)
-\item if \ttt{init\_TI} is modified, \ttt{real.exe} must be run again (because of subsurface modeling)
+%\item if \ttt{init\_TI} is modified, \ttt{real.exe} must be run again (because of subsurface modeling)
 \item a varying map for surface roughness~$z_0$ can be used -- or a constant value can be set with \ttt{init\_Z0} in \ttt{namelist.input} (if there is a problem, the old reference of 1cm is chosen)
 \item (starting from version \ttt{r1038}) the model does not need to be recompiled if the number of tracers is changed
@@ -160,4 +160,42 @@
 %% run.def different if callphys different for nests
 
+%%% Here is how to output near-surface diagnostics
+%- Look for n_out in physiq.F this will lead you to a few lines of codes that will allow you to output near-surface diagnostics
+%- Change n_out to a value of 2
+%- A few lines below change z_out and make it equal to [1.6,0.5]
+%Now this is OK for physics, but you have to make this available in the dynamical outputs of WRF
+%Go to the mesoscale sources, then in Registry find Registry.EM
+%then following the example of this kind of line
+%state  real  ALBBARE   ij   misc  1  -  rhd   "ALBBARE"   "SOIL ALBEDO"                     ""        #SAVEMARS2 albedodat
+%add this
+%state  real  TVIK   ij   misc  1  -  rhd   "TVIK"   "temperature at 1.6m"     "K"       #SAVEMARS2 T_out1
+%Then proceed through a full recompile of the mesoscale model from scratch Here is how to output near-surface diagnostics
+%- Look for n_out in physiq.F this will lead you to a few lines of codes that will allow you to output near-surface diagnostics
+%- Change n_out to a value of 2
+%- A few lines below change z_out and make it equal to [1.6,0.5]
+%Now this is OK for physics, but you have to make this available in the dynamical outputs of WRF
+%Go to the mesoscale sources, then in Registry find Registry.EM
+%then following the example of this kind of line
+%state  real  ALBBARE   ij   misc  1  -  rhd   "ALBBARE"   "SOIL ALBEDO"                     ""        #SAVEMARS2 albedodat
+%add this
+%state  real  TVIK   ij   misc  1  -  rhd   "TVIK"   "temperature at 1.6m"     "K"       #SAVEMARS2 T_out1
+%Then proceed through a full recompile of the mesoscale model from scratch 
+
+\sk
+A fully functional modeling architecture with \ttt{LMD\_MM\_MARS} and the new physical parameterizations (as well as the \ttt{LMDZ\_MARS} Global Climate Model used to initialize the mesoscale simulations) can be downloaded and compiled using the \ttt{meso\_install.sh} script: \url{http://svn.lmd.jussieu.fr/Planeto/trunk/MESOSCALE/LMD_MM_MARS/SIMU/meso_install.sh}. The \ttt{NETCDF} environment variable shall be positioned. The \ttt{meso\_install.sh} script only works on the IPSL \ttt{ciclad} computing cluster with compiler ifort; it shall be used as a template for other environments (or manually installing the architecture step-by-step). Options in the \ttt{meso\_install.sh} script can be displayed with the \ttt{-h} option.
+
+%I think the main point is to change CICLAD for a name representative of your local cluster, and then creates a arch file analogous to what is done for arch_CICLADifort, but adapted to your local cluster
+
+%declare -x WHERE_MPI=/usr/lib64/openmpi/1.6.5-ifort/bin/
+%declare -x NETCDF=/opt/netcdf3/ifort
+%declare -x NCDFLIB=$NETCDF/lib
+%declare -x NCDFINC=$NETCDF/include
+%### pour fcm nouvelle version du GCM
+%declare -x PATH=~millour/FCM_V1.2/bin/:$PATH
+%## + mettre ./ dans PATH
+
+%r1613 (or slightly before) use of -p mars_lmd_new
+
+
 
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