Index: trunk/LMDZ.GENERIC/DOC/main.aux
===================================================================
--- trunk/LMDZ.GENERIC/DOC/main.aux	(revision 1424)
+++ trunk/LMDZ.GENERIC/DOC/main.aux	(revision 1746)
@@ -28,57 +28,57 @@
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-\@writefile{toc}{\contentsline {subsection}{\numberline {2.4.2}Physical variables}{9}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {2.4.3}Tracers}{10}}
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+\@writefile{toc}{\contentsline {section}{\numberline {2.4}Variables used in the model}{6}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.4.1}Dynamical variables}{6}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.4}{\ignorespaces Vertical grid description of the {\tt  llm (or nlayer)} atmospheric layers in the programming code ({\tt  llm} is the variable used in the dynamical part, and {\tt  nlayer} is used in the physical part). Variables {\tt  ap, bp} and {\tt  aps, bps} indicate the hybrid levels at the interlayer levels and at middle of the layers respectively. Pressure at the interlayer is $Plev(l)=ap(l)+bp(l) \times Ps$ and pressure in the middle of the layer is defined by $Play(l)=aps(l)+bps(l) \times Ps$, (where $Ps$ is surface pressure). Sigma coordinates are merely a specific case of hybrid coordinates such that $aps=0$ and $bps=P/Ps$. Note that for the hybrid coordinates, $bps=0$ above $\sim 50$~km, leading to purely pressure levels. The user can choose whether to run the model using hybrid coordinates or not by setting variable {\tt  hybrid} in run.def to True or False.}}{7}}
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+\@writefile{toc}{\contentsline {subsection}{\numberline {2.4.2}Physical variables}{8}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.4.3}Tracers}{8}}
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 \citation{Arak:77}
-\@writefile{toc}{\contentsline {chapter}{\numberline {3}3D Dynamical Code}{11}}
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-\@writefile{toc}{\contentsline {paragraph}{la pression extensive:}{11}}
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-\@writefile{toc}{\contentsline {paragraph}{le facteur de Coriolis multipli\'e par l'aire de la maille:}{13}}
-\@writefile{toc}{\contentsline {paragraph}{la vorticit\'e potentielle absolue:}{13}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {3.2}{\ignorespaces Disposition des variables dans la grille du LMD}}{10}}
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+\@writefile{toc}{\contentsline {paragraph}{les trois composantes du flux de masse:}{10}}
+\@writefile{toc}{\contentsline {paragraph}{le facteur de Coriolis multipli\'e par l'aire de la maille:}{10}}
+\@writefile{toc}{\contentsline {paragraph}{la vorticit\'e potentielle absolue:}{10}}
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+\@writefile{toc}{\contentsline {paragraph}{\'equation thermodynamique:}{10}}
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 \citation{Lewi:99}
-\@writefile{toc}{\contentsline {chapter}{\numberline {4}Physical parameterizations of the generic model: some references}{16}}
+\@writefile{toc}{\contentsline {chapter}{\numberline {4}Physical parameterizations of the generic model: some references}{13}}
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-\@writefile{toc}{\contentsline {paragraph}{General references:}{16}}
-\@writefile{toc}{\contentsline {section}{\numberline {4.2}Radiative transfer}{16}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.2.1}\bf  Absorption/emission and diffusion by dust:}{16}}
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+\@writefile{toc}{\contentsline {section}{\numberline {4.1}General}{13}}
+\@writefile{toc}{\contentsline {paragraph}{General references:}{13}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.2}Radiative transfer}{13}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.2.1}\bf  Absorption/emission and diffusion by dust:}{13}}
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-\@writefile{toc}{\contentsline {section}{\numberline {4.5}CO$_2$ Condensation}{17}}
-\@writefile{toc}{\contentsline {section}{\numberline {4.6}Tracer transport and sources}{17}}
-\@writefile{toc}{\contentsline {chapter}{\numberline {5}Running the model: a practice simulation}{19}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.3}Subgrid atmospheric dynamical processes}{14}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.3.1}Turbulent diffusion in the upper layer}{14}}
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+\@writefile{toc}{\contentsline {section}{\numberline {4.6}Tracer transport and sources}{14}}
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+\@writefile{toc}{\contentsline {section}{\numberline {5.4}Compiling the LMDZ.COMMON model (sequential or parallel)}{19}}
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+\@writefile{toc}{\contentsline {section}{\numberline {5.5}Input files (initial states and def files)}{20}}
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-\@writefile{toc}{\contentsline {paragraph}{Help manual for the makegcm script}{31}}
-\@writefile{toc}{\contentsline {chapter}{\numberline {7}Input/Output}{33}}
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-\@writefile{toc}{\contentsline {subsection}{\numberline {7.3.3}Stats files}{47}}
-\@writefile{toc}{\contentsline {chapter}{\numberline {8}Water Cycle Simulation}{51}}
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+\@writefile{toc}{\contentsline {section}{\numberline {7.1}NetCDF format}{32}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {7.1.1}NetCDF file editor: ncdump}{32}}
+\@writefile{toc}{\contentsline {paragraph}{Main commands for ncdump}{32}}
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+\@writefile{toc}{\contentsline {subsection}{\numberline {7.1.2}Graphic visualization of the NetCDF files using GrAds}{33}}
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+\@writefile{toc}{\contentsline {subsection}{\numberline {7.3.3}Stats files}{46}}
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-\@writefile{toc}{\contentsline {chapter}{\numberline {9}1D version of the generic model}{54}}
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