\documentclass{article}
\usepackage[english]{babel}
\usepackage[latin1]{inputenc}

\usepackage{a4wide}
\begin{document}

\def\afaire#1{{\bf Afaire : #1}}
\title{Hands on tutorial session 1: First steps with the model \date{\today}}
\author{The LMDZ team}

\maketitle

This first tutorial essentially focuses on installing and making basic first
runs using the LMDZ model.

This document can be downloaded as a pdf file:
\begin{verbatim}
wget http://www.lmd.jussieu.fr/~lmdz/Distrib/TD1_en.pdf
\end{verbatim}
which should ease any copy/paste of command lines to issue.

%\def\infol#1{#1}
%\def\infol#1{\verb+ #1 +}
\def\infol#1{{\bf #1}}
%\newcommand{\infol}[1]{\verb\+ #1 \+}

\def\resol#1#2#3{#1$\times$#2-L#3} %


If you are working on a machine which is part of the LMD local network, then you have to log in as "tdlmdz" or something similar (the associated password will be given during the training session).
Log in and go to the local machine a directory where you will work:
\begin{verbatim}
cd /home/tdlmdz
\end{verbatim}
If on the local LMD machines, it is important to work in the \infol{/home} directory (and not the \infol{/home/users/tdlmdz} login directory) as it is physically present on the machine you logged on (and thus minimizes disk access latencies).

\section{Running the install.sh script}

The first step consits in downloading the install.sh script from the LMD website
and {\em blindly} running it (after having first set the access permissions to make it executable):
\begin{verbatim}
wget http://www.lmd.jussieu.fr/~lmdz/Distrib/install.sh
chmod +x install.sh
./install.sh
\end{verbatim}
The default behavior of the \verb+ install.sh + script is to install the model
using the \verb+ gfortran + compiler.
On some local machines only an old version is available, 
so the script stops with a messge that invites you to switch to another
compiler.
Set \verb+ compilo=ifort + in the script and then run \verb+ ./install.sh + again.


The script should then run smoothly without errors. If it isn't the case, immediately ask for some assistance.
The script will end with messages of the likes of:
\begin{verbatim}
##########################################################
Simulation finished in ...
You may re-run it with : cd  ...
or ./bench.sh
##########################################################
\end{verbatim}

As the script runs, which takes a dozen minutes\footnote{Compilation LMDZ will be faster if one uses the {\bf makelmdz\_fcm} script rather than the default {\bf makelmdz} script.
To change this behaviour in the {\bf install.sh} script find the instruction line {\bf compile\_with\_fcm=0} and change it to {\bf compile\_with\_fcm=1}. }, you will see messages
corresponding to the download of various elements via \infol{wget} or
informational messages from the compiler. The script ends by running a 5 days long test simulation on a regular \resol{48}{36}{19} grid.


As the automated installation proceeds, you can open a different terminal window and explore the downloaded directories and files.
When install.sh runs, it creates a \infol{LMDZtesting} directory in which
you will find subdirectories \infol{modipsl}, which contains the model, and
\infol{netcdf-4.0.1}, which contains the NetCDF library installed by
\infol{install.sh}.
In \infol{modipsl}, you will find directory \infol{modeles}, which contains the 
\infol{LMDZ5} directory.
Go to this directory.
Once the test bench simulation has been launched (the final step of the \infol{install.sh} script), you will find a 
\infol{BENCH48x36x19/} directory in which you can visualize the outputs of the
run (even if the simulation is still running).
Check out the contents of the directory and use your favorite software (Grads,
Ferret,...) to browse the contents of the \infol{histday.nc} file.


\section{Switching to a different version of the model}

The bench run that has been made used the latest {\em testing} version of the model, dated December 3rd 2014, which corresponds to {\em svn release} 2168. This information can moreover be obtained by checking at the last line of file
\begin{verbatim}
http://www.lmd.jussieu.fr/~lmdz/Distrib/LISMOI.testing
\end{verbatim}
or on the web page about the testing versions
\begin{verbatim}
http://lmdz.lmd.jussieu.fr/utilisateurs/distribution-du-modele/versions-intermediaires-en
\end{verbatim}
or directly from within the LMDZ directory
\begin{verbatim}
cd LMDZtesting/modipsl/modeles/LMDZ5
svn info
\end{verbatim}

With svn, one can change the model version by seting it to a more recent or
older {\em svn release}, which we will now do here as an exercice since using
the latest testing (the one you just installed) is the recommended way to
proceed.
To change version, go to directory \infol{LMDZ5} and issue command:
\begin{verbatim}
svn update --revision 2116
\end{verbatim}
to revert to {\em svn release} 2116 (a previous {\em testing}).
%Important: as you change svn revision, a conflict on some files will occur,
%answer {\em mf} ('mf' for mine-full) to tell svn you want to keep your personal
%modifications\footnote{This conflict comes from the fact that the installation %script
%{\em install.sh} modifies some lines of the now obsolete \infol{makegcm} script and that
%there have also been some (harmless) changes of these very same lines between
%svn revisions of that script. Thus svn cannot know which modifications should
%overrule and thus asks you.}
%of the files.


Still from the \infol{LMDZ5} directory, run command \infol{./makelmdz\_fcm -arch local -d 48x36x19 -v true -j 8 gcm} (or alternatively \infol{./makelmdz -arch local -d 48x36x19 -v true gcm}.
Option \infol{-v true} is not mandatory. It only indicates that we compile with
Orchidee, but in fact it won't be used for the runs in this tutorial.
Only some routines (those modified by the svn update and routines which depend thereupon) will be recompiled.
%If using the \infol{makelmdz} script, it might be necessary to re-issue the command a second time\footnote{Having to sometimes run the \infol{makelmdz} command to create gcm.e comes from an (yet unresolved) issue in the script which fails to see some of the dependencies between source files} to generate the \infol{gcm.e} program.


Once the model has been successfully recompiled, run a new simulation.
To do so, create a new subdirectory in \infol{LMDZ5} and copy boundary
conditions, initial conditions and parameter files (\infol{limit.nc, star*nc, *.def}) over from
directory \infol{BENCH48x36x19}, along with the newly created \infol{gcm.e} (
if using \infol{makelmdz}, the executable will be called \infol{gcm.e} and created in the LMDZ5 directory; if using \infol{makelmdz\_fcm} it will be called gcm\_48x36x19\_phylmd\_seq\_orch.e and will be found in the LMDZ5/bin directory).

Then run \infol{./gcm.e $>$ listing 2$>$\&1} (the redirection of the model outputs in a text file is usually the best way to keep a trace of the run).
Once the simulation is finished, you can compare, using the \infol{diff}
command, the simulation results (compare files \infol{listing}, \infol{hist*.nc}
\infol{restart.nc} and \infol{restartphy.nc} from the two simulations).
At the time of this tutorial, the changes between the latest {\em testing}
versions impact on the results; fields will be numerically different from one case to the next.


Once this test finished, revert to the latest {\em testing} version of the model
by going to directory \infol{LMDZ5} and using:
\begin{verbatim}
svn update
\end{verbatim}
Note that using \infol{svn update} without any specific revision number implies
updating to the latest version on the branch (which is something you should do
regularly if you want to keep up with model updates!). And don't forget to
recompile the model after any svn update!


\section{Making some sensitivity test runs}

You can now move on to changing parameters in a .def file.
One may for instance deactivate the subgrid orography parametrizations by
changing the \infol{ok\_orodr} and \infol{ok\_orolf} flags in
\infol{physiq.def}.
One could also choose to change the value of the cloud water to rain conversion
factor \infol{cld\_tau\_lsc} (in \infol{physiq.def}), or the atmospheric CO$_2$
concentration, etc. (check the LMDZ documentation and/or ask around
to find out the meaning of the various available parameters).

Just run the simulation (in a different directory to avoid overwritting output
files) and investigate the differences between simulations.


\section{Changing the outputs}

The model outputs are controled in file \infol{config.def} by the following
lines:
\begin{verbatim}
phys_out_filekeys=       y       y       n       y       n
phys_out_filenames=      histmth histday histhf  histins histLES
phys_out_filetimesteps=  5day    1day    1hr     6hr     6hr
phys_out_filelevels=     10      5       0       4       4
phys_out_filetypes=      ave(X)  ave(X)  ave(X) inst(X) inst(X)
\end{verbatim}
With these settings, you have outputs in a \verb+ histmth.nc + file, which
contains the average over the 5 days of the run and a \verb+ histday.nc + file
which contains the daily averages (a 5 elements long time series).


You can find out which variables have been outputed by running the command
\begin{verbatim}
ncdump -h histmth.nc | grep long_name
\end{verbatim}
in the directory where the simulation was run.


You may also rerun the simulation but with a higher frequency of outputs for
given variables (e.g. atmospheric temperature at 2m above the surface: \infol{t2m}, surface pressure: \infol{psol}, precipitation: \infol{precip}, etc.), for instance by using the following settings in \infol{config.def}:
\begin{verbatim}
phys_out_filekeys=       y       y       y       y       y
phys_out_filenames=      histmth histday histhf  histts histhfm
phys_out_filetimesteps=  10day   1day    1hr     1ts     1hr
phys_out_filelevels=     10      5       0       0       0
phys_out_filetypes=      ave(X)  ave(X)  inst(X) inst(X)  ave(X)
flag_t2m=                10      10       1       1       1
flag_psol=               10      10       1       1       0
flag_precip=             10      10       0       1       1
\end{verbatim}


\section{Running an aquaplanet configuration}

The simulations run in the previous example included initial and
boundary conditions (\infol{start*.nc} and \infol{limit.nc} files).
It is also possible to run the model in "aquaplanet"
configuration, where idealized initial and boundary conditions are used
(no topography and imposed surface temperatures).


Make an \infol{AQUAPLANET} directory where you will run the model.
Copy over the \infol{gcm.e} and \infol{*.def} files from another simulation
to this directory. Edit the \infol{gcm.def} file to set 
\begin{verbatim}
read_start=n
\end{verbatim}
and
\begin{verbatim}
iflag_phys=101
\end{verbatim}
Note that there are various possibilities for flag \infol{iflag\_phys},
values between 101 and 114 correspond to different choices
of imposed SSTs (see routines \infol{iniaqua} and \infol{profil\_sst} in
file \infol{phyaqua\_mod.F} in the \infol{libf/phylmd}
directory).


Then run the model: \infol{./gcm.e $>$ listing 2$>$\&1}, inspect the
various outputs (e.g. zonal averages and deviations of meteorological quantities such as surface pressure $psol$) and their temporal evolution,
and compare to previously obtained simulations.
Experiment changing the length of the run (variable \infol{nday} in the
\infol{run.def} file to investigate the evolution of the system from
initial settings to a "converged" state.


If time permits, experiment running at a different resolution (e.g.
\resol{96}{95}{19} ; which means you will have to recompile the model).
Note that if you keep the same settings as for the \resol{48}{36}{19},
case, your run will crash (try it!); at such resolution, one needs to
use more time steps per day (set \infol{day\_step=480} and \infol{iphysiq=10}
in gcm.def), as can be seen in the sample \infol{gcm.def} file in the
\infol{DefLists} directory.


\end{document}



\begin{verbatim}
		lon: Longitude ;
		lat: Latitude ;
		presnivs: Vertical levels ;
		Ahyb: Ahyb comp of Hyb Cord ;
		Bhyb: Bhyb comp of Hyb Cord ;
		Alt: Height approx for scale heigh of 8km at levels ;
		t_ave_00864000: Time axis ;
		t_t_min_00864000: Time axis ;
		t_t_max_00864000: Time axis ;
		t_inst_00864000: Time axis ;
		aire: Grid area ;
		contfracATM: % sfce ter+lic ;
		phis: Surface geop.height ;
		contfracOR: % sfce terre OR ;
		aireTER: Grid area CONT ;
		flat: Latent heat flux ;
		slp: Sea Level Pressure ;
		tsol: Surface Temperature ;
		t2m: Temperature 2m ;
		t2m_min: Temp 2m min ;
		t2m_max: Temp 2m max ;
		wind10m: 10-m wind speed ;
		wind10max: 10m wind speed max ;
		sicf: Sea-ice fraction ;
		q2m: Specific humidity 2m ;
		u10m: Vent zonal 10m ;
		v10m: Vent meridien 10m ;
		psol: Surface Pressure ;
		qsurf: Surface Air humidity ;
		qsol: Soil watter content ;
		ndayrain: Number of dayrain(liq+sol) ;
		precip: Precip Totale liq+sol ;
		plul: Large-scale Precip. ;
		pluc: Convective Precip. ;
		snow: Snow fall ;
		msnow: Surface snow amount ;
		fsnow: Surface snow area fraction ;
		evap: Evaporat ;
		tops: Solar rad. at TOA ;
		tops0: CS Solar rad. at TOA ;
		topl: IR rad. at TOA ;
		topl0: IR rad. at TOA ;
		SWupTOA: SWup at TOA ;
		SWupTOAclr: SWup clear sky at TOA ;
		SWdnTOA: SWdn at TOA ;
		SWdnTOAclr: SWdn clear sky at TOA ;
		nettop: Net dn radiatif flux at TOA ;
		SWup200: SWup at 200mb ;
		SWup200clr: SWup clear sky at 200mb ;
		SWdn200: SWdn at 200mb ;
		SWdn200clr: SWdn clear sky at 200mb ;
		LWup200: LWup at 200mb ;
		LWup200clr: LWup clear sky at 200mb ;
		LWdn200: LWdn at 200mb ;
		LWdn200clr: LWdn clear sky at 200mb ;
		sols: Solar rad. at surf. ;
		sols0: Solar rad. at surf. ;
		soll: IR rad. at surface ;
		radsol: Rayonnement au sol ;
		soll0: IR rad. at surface ;
		SWupSFC: SWup at surface ;
		SWupSFCclr: SWup clear sky at surface ;
		SWdnSFC: SWdn at surface ;
		SWdnSFCclr: SWdn clear sky at surface ;
		LWupSFC: Upwd. IR rad. at surface ;
		LWdnSFC: Down. IR rad. at surface ;
		LWupSFCclr: CS Upwd. IR rad. at surface ;
		LWdnSFCclr: Down. CS IR rad. at surface ;
		bils: Surf. total heat flux ;
		sens: Sensible heat flux ;
		fder: Heat flux derivation ;
		ffonte: Thermal flux for snow melting ;
		fqcalving: Ice Calving ;
		fqfonte: Land ice melt ;
		taux: Zonal wind stress ;
		tauy: Meridional wind stress ;
		pourc_ter: % ter ;
		fract_ter: Fraction ter ;
		taux_ter: Zonal wind stresster ;
		tauy_ter: Meridional wind stress ter ;
		tsol_ter: Temperature ter ;
		u10m_ter: Vent Zonal 10m ter ;
		evap_ter: evaporation at surface ter ;
		v10m_ter: Vent meredien 10m ter ;
		t2m_ter: Temp 2m ter ;
		sens_ter: Sensible heat flux ter ;
		lat_ter: Latent heat flux ter ;
		flw_ter: LW ter ;
		fsw_ter: SW ter ;
		wbils_ter: Bilan sol ter ;
		wbilo_ter: Bilan eau ter ;
		albe_ter: Albedo VIS surf. ter ;
		rugs_ter: Surface roughness ter ;
		ages_ter: Snow age ;
		pourc_lic: % lic ;
		fract_lic: Fraction lic ;
		taux_lic: Zonal wind stresslic ;
		tauy_lic: Meridional wind stress lic ;
		tsol_lic: Temperature lic ;
		u10m_lic: Vent Zonal 10m lic ;
		evap_lic: evaporation at surface lic ;
		v10m_lic: Vent meredien 10m lic ;
		t2m_lic: Temp 2m lic ;
		sens_lic: Sensible heat flux lic ;
		lat_lic: Latent heat flux lic ;
		flw_lic: LW lic ;
		fsw_lic: SW lic ;
		wbils_lic: Bilan sol lic ;
		wbilo_lic: Bilan eau lic ;
		albe_lic: Albedo VIS surf. lic ;
		rugs_lic: Surface roughness lic ;
		ages_lic: Snow age ;
		pourc_oce: % oce ;
		fract_oce: Fraction oce ;
		taux_oce: Zonal wind stressoce ;
		tauy_oce: Meridional wind stress oce ;
		tsol_oce: Temperature oce ;
		u10m_oce: Vent Zonal 10m oce ;
		evap_oce: evaporation at surface oce ;
		v10m_oce: Vent meredien 10m oce ;
		t2m_oce: Temp 2m oce ;
		sens_oce: Sensible heat flux oce ;
		lat_oce: Latent heat flux oce ;
		flw_oce: LW oce ;
		fsw_oce: SW oce ;
		wbils_oce: Bilan sol oce ;
		wbilo_oce: Bilan eau oce ;
		albe_oce: Albedo VIS surf. oce ;
		rugs_oce: Surface roughness oce ;
		ages_oce: Snow age ;
		pourc_sic: % sic ;
		fract_sic: Fraction sic ;
		taux_sic: Zonal wind stresssic ;
		tauy_sic: Meridional wind stress sic ;
		tsol_sic: Temperature sic ;
		u10m_sic: Vent Zonal 10m sic ;
		evap_sic: evaporation at surface sic ;
		v10m_sic: Vent meredien 10m sic ;
		t2m_sic: Temp 2m sic ;
		sens_sic: Sensible heat flux sic ;
		lat_sic: Latent heat flux sic ;
		flw_sic: LW sic ;
		fsw_sic: SW sic ;
		wbils_sic: Bilan sol sic ;
		wbilo_sic: Bilan eau sic ;
		albe_sic: Albedo VIS surf. sic ;
		rugs_sic: Surface roughness sic ;
		ages_sic: Snow age ;
		alb1: Surface VIS albedo ;
		alb2: Surface Near IR albedo ;
		cdrm: Momentum drag coef. ;
		cdrh: Heat drag coef. ;
		cldl: Low-level cloudiness ;
		cldm: Mid-level cloudiness ;
		cldh: High-level cloudiness ;
		cldt: Total cloudiness ;
		cldq: Cloud liquid water path ;
		lwp: Cloud water path ;
		iwp: Cloud ice water path ;
		ue: Zonal energy transport ;
		ve: Merid energy transport ;
		uq: Zonal humidity transport ;
		vq: Merid humidity transport ;
		cape: Conv avlbl pot ener ;
		pbase: Cld base pressure ;
		ptop: Cld top pressure ;
		fbase: Cld base mass flux ;
		prw: Precipitable water ;
		cape_max: CAPE max. ;
		upwd: saturated updraft ;
		Ma: undilute adiab updraft ;
		dnwd: saturated downdraft ;
		dnwd0: unsat. downdraft ;
		mc: Convective mass flux ;
		ftime_con: Fraction of time convection Occurs ;
		s_pblh: Boundary Layer Height ;
		s_pblt: t at Boundary Layer Height ;
		s_lcl: Condensation level ;
		s_therm: Exces du thermique ;
		u850: Zonal wind 850 hPa ;
		v850: Meridional wind 850 hPa ;
		w850: Vertical wind 850 hPa ;
		z850: Geopotential height 850 hPa ;
		q850: Specific humidity 850 hPa ;
		t850: Temperature 850 hPa ;
		u700: Zonal wind 700 hPa ;
		v700: Meridional wind 700 hPa ;
		w700: Vertical wind 700 hPa ;
		z700: Geopotential height 700 hPa ;
		q700: Specific humidity 700 hPa ;
		t700: Temperature 700 hPa ;
		u500: Zonal wind 500 hPa ;
		v500: Meridional wind 500 hPa ;
		w500: Vertical wind 500 hPa ;
		z500: Geopotential height 500 hPa ;
		q500: Specific humidity 500 hPa ;
		t500: Temperature 500 hPa ;
		u200: Zonal wind 200 hPa ;
		v200: Meridional wind 200 hPa ;
		w200: Vertical wind 200 hPa ;
		z200: Geopotential height 200 hPa ;
		q200: Specific humidity 200 hPa ;
		t200: Temperature 200 hPa ;
		u100: Zonal wind 100 hPa ;
		v100: Meridional wind 100 hPa ;
		w100: Vertical wind 100 hPa ;
		z100: Geopotential height 100 hPa ;
		q100: Specific humidity 100 hPa ;
		t100: Temperature 100 hPa ;
		u50: Zonal wind 50  hPa ;
		v50: Meridional wind 50  hPa ;
		w50: Vertical wind 50  hPa ;
		z50: Geopotential height 50  hPa ;
		q50: Specific humidity 50  hPa ;
		t50: Temperature 50  hPa ;
		u10: Zonal wind 10  hPa ;
		v10: Meridional wind 10  hPa ;
		w10: Vertical wind 10  hPa ;
		z10: Geopotential height 10  hPa ;
		q10: Specific humidity 10  hPa ;
		t10: Temperature 10  hPa ;
		t_oce_sic: Temp mixte oce-sic ;
		weakinv: Weak inversion ;
		dthmin: dTheta mini ;
		rh2m: Relative humidity at 2m ;
		rh2m_min: Min Relative humidity at 2m ;
		rh2m_max: Max Relative humidity at 2m ;
		qsat2m: Saturant humidity at 2m ;
		tpot: Surface air potential temperature ;
		tpote: Surface air equivalent potential temperature ;
		SWnetOR: Sfce net SW radiation OR ;
		SWdownOR: Sfce incident SW radiation OR ;
		LWdownOR: Sfce incident LW radiation OR ;
		snowl: Solid Large-scale Precip. ;
		solldown: Down. IR rad. at surface ;
		dtsvdfo: Boundary-layer dTs(o) ;
		dtsvdft: Boundary-layer dTs(t) ;
		dtsvdfg: Boundary-layer dTs(g) ;
		dtsvdfi: Boundary-layer dTs(g) ;
		rugs: rugosity ;
		ec550aer: Extinction at 550nm ;
		lwcon: Cloud liquid water content ;
		iwcon: Cloud ice water content ;
		temp: Air temperature ;
		theta: Potential air temperature ;
		ovap: Specific humidity ;
		ovapinit: Specific humidity (begin of timestep) ;
		geop: Geopotential height ;
		vitu: Zonal wind ;
		vitv: Meridional wind ;
		vitw: Vertical wind ;
		pres: Air pressure ;
		paprs: Air pressure Inter-Couches ;
		mass: Masse Couches ;
		zfull: Altitude of full pressure levels ;
		zhalf: Altitude of half pressure levels ;
		rneb: Cloud fraction ;
		rnebcon: Convective Cloud Fraction ;
		rhum: Relative humidity ;
		ozone: Ozone mole fraction ;
		dtphy: Physics dT ;
		dqphy: Physics dQ ;
		cldtau: Cloud optical thickness ;
		cldemi: Cloud optical emissivity ;
		pr_con_l: Convective precipitation lic ;
		pr_con_i: Convective precipitation ice ;
		pr_lsc_l: Large scale precipitation lic ;
		pr_lsc_i: Large scale precipitation ice ;
		re: Cloud droplet effective radius ;
		fl: Denominator of Cloud droplet effective radius ;
		kz: Kz melange ;
		kz_max: Kz melange max ;
		clwcon: Convective Cloud Liquid water content ;
		dtdyn: Dynamics dT ;
		dqdyn: Dynamics dQ ;
		dudyn: Dynamics dU ;
		dvdyn: Dynamics dV ;
		dtcon: Convection dT ;
		ducon: Convection du ;
		dqcon: Convection dQ ;
		dtlsc: Condensation dT ;
		dtlschr: Large-scale condensational heating rate ;
		dqlsc: Condensation dQ ;
		dtvdf: Boundary-layer dT ;
		dqvdf: Boundary-layer dQ ;
		dteva: Reevaporation dT ;
		dqeva: Reevaporation dQ ;
		ptconv: POINTS CONVECTIFS ;
		ratqs: RATQS ;
		dtthe: Thermal dT ;
		dtajs: Dry adjust. dT ;
		dqajs: Dry adjust. dQ ;
		dtswr: SW radiation dT ;
		dtsw0: CS SW radiation dT ;
		dtlwr: LW radiation dT ;
		dtlw0: CS LW radiation dT ;
		dtec: Cinetic dissip dT ;
		duvdf: Boundary-layer dU ;
		dvvdf: Boundary-layer dV ;
		rsu: SW upward radiation ;
		rsd: SW downward radiation ;
		rlu: LW upward radiation ;
		rld: LW downward radiation ;
		rsucs: SW CS upward radiation ;
		rsdcs: SW CS downward radiation ;
		rlucs: LW CS upward radiation ;
		rldcs: LW CS downward radiation ;
		tnt: Tendency of air temperature ;
		tntc: Tendency of air temperature due to Moist Convection ;
		tntr: Air temperature tendency due to Radiative heating ;
		tntscpbl: Air temperature tendency due to St cloud and
precipitation and BL mixing ;
		tnhus: Tendency of specific humidity ;
		tnhusc: Tendency of specific humidity due to convection ;
		tnhusscpbl: Tendency of Specific humidity due to ST cl, precip
and BL mixing ;
		evu: Eddy viscosity coefficient for Momentum Variables ;
		h2o: Mass Fraction of Water ;
		mcd: Downdraft COnvective Mass Flux ;
		dmc: Deep COnvective Mass Flux ;
		ref_liq: Effective radius of convective cloud liquid water
particle ;
		ref_ice: Effective radius of startiform cloud ice particle ;
		RN: Tracer RNVL1 ;
		PB: Tracer PBVL1 ;

\end{verbatim}

