Changeset 10442 for NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

Timestamp:

2018-12-21T15:18:38+01:00 (5 years ago)

Author:

nicolasmartin

Message:

Front page edition, cleaning in custom LaTeX commands and add index for single subfile compilation

• Use \thanks storing cmd to refer to the ST members list for 2018 in an footnote on the cover page
• NEMO and Fortran in small capitals
• Removing of unused or underused custom cmds, move local cmds to their respective .tex file
• Addition of new ones (\zstar, \ztilde, \sstar, \stilde, \ie, \eg, \fortran, \fninety)
• Fonts for indexed items: italic font for files (modules and .nc files), preformat for code (CPP keys, routines names and namelists content)

File:

• NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex (modified) (15 diffs)

NEMO/trunk/doc/latex/NEMO/subfiles/chap_DIA.tex

@@ -83 +83 @@
   The possibility to extract a vertical or an horizontal subdomain.
 \item
-  The choice of the temporal operation to perform, $e.g.$: average, accumulate, instantaneous, min, max and once.
+  The choice of the temporal operation to perform, \eg: average, accumulate, instantaneous, min, max and once.
 \item
   Control over metadata via a large XML "database" of possible output fields.
@@ -106 +106 @@
 create a single output file and therefore to bypass the rebuilding phase.
 Note that writing in parallel into the same NetCDF files requires that your NetCDF4 library is linked to
-an HDF5 library that has been correctly compiled ($i.e.$ with the configure option $--$enable-parallel).
+an HDF5 library that has been correctly compiled (\ie with the configure option $--$enable-parallel).
 Note that the files created by iomput through XIOS are incompatible with NetCDF3.
 All post-processsing and visualization tools must therefore be compatible with NetCDF4 and not only NetCDF3.
@@ -222 +222 @@
 
 It is very easy to add your own outputs with iomput.
-Many standard fields and diagnostics are already prepared ($i.e.$, steps 1 to 3 below have been done) and
+Many standard fields and diagnostics are already prepared (\ie, steps 1 to 3 below have been done) and
 simply need to be activated by including the required output in a file definition in iodef.xml (step 4).
 To add new output variables, all 4 of the following steps must be taken.
@@ -251 +251 @@
 reference grids and axes either defined in the code
 (iom\_set\_domain\_attr and iom\_set\_axis\_attr in \mdl{iom}) or defined in the domain\_def.xml file.
-$e.g.$:
+\eg:
 
 \begin{xmllines}
@@ -1349 +1349 @@
 
 \noindent for a standard ORCA2\_LIM configuration gives chunksizes of {\small\tt 46x38x1} respectively in
-the mono-processor case (i.e. global domain of {\small\tt 182x149x31}).
+the mono-processor case (\ie global domain of {\small\tt 182x149x31}).
 An illustration of the potential space savings that NetCDF4 chunking and compression provides is given in 
 table \autoref{tab:NC4} which compares the results of two short runs of the ORCA2\_LIM reference configuration with
@@ -1419 +1419 @@
 Each trend of the dynamics and/or temperature and salinity time evolution equations can be send to
 \mdl{trddyn} and/or \mdl{trdtra} modules (see TRD directory) just after their computation
-($i.e.$ at the end of each $dyn\cdots.F90$ and/or $tra\cdots.F90$ routines).
+(\ie at the end of each $dyn\cdots.F90$ and/or $tra\cdots.F90$ routines).
 This capability is controlled by options offered in \ngn{namtrd} namelist.
 Note that the output are done with xIOS, and therefore the \key{IOM} is required.
@@ -1451 +1451 @@
 \textbf{Note that} in the current version (v3.6), many changes has been introduced but not fully tested.
 In particular, options associated with \np{ln\_dyn\_mxl}, \np{ln\_vor\_trd}, and \np{ln\_tra\_mxl} are not working,
-and none of the options have been tested with variable volume ($i.e.$ \key{vvl} defined).
+and none of the options have been tested with variable volume (\ie \key{vvl} defined).
 
 % -------------------------------------------------------------------------------------------------------------
@@ -1657 +1657 @@
  - \texttt{long2 lat2}, coordinates of the second extremity of the section;
 
- - \texttt{nclass}    the number of bounds of your classes (e.g. 3 bounds for 2 classes);
+ - \texttt{nclass}    the number of bounds of your classes (\eg bounds for 2 classes);
 
  - \texttt{okstrpond} to compute    heat and       salt transports, \texttt{nostrpond} if no;
@@ -1824 +1824 @@
 
 The first term in equation \autoref{eq:ssh_nBq} alters sea level by adding or subtracting mass from the ocean. 
-The second term arises from temporal changes in the global mean density; $i.e.$ from steric effects.
+The second term arises from temporal changes in the global mean density; \ie from steric effects.
 
 In a Boussinesq fluid, $\rho$ is replaced by $\rho_o$ in all the equation except when $\rho$ appears multiplied by
-the gravity ($i.e.$ in the hydrostatic balance of the primitive Equations).
+the gravity (\ie in the hydrostatic balance of the primitive Equations).
 In particular, the mass conservation equation, \autoref{eq:Co_nBq}, degenerates into the incompressibility equation:
 
@@ -1874 +1874 @@
 The above formulation of the steric height of a Boussinesq ocean requires four remarks.
 First, one can be tempted to define $\rho_o$ as the initial value of $\mathcal{M}/\mathcal{V}$,
-$i.e.$ set $\mathcal{D}_{t=0}=0$, so that the initial steric height is zero.
+\ie set $\mathcal{D}_{t=0}=0$, so that the initial steric height is zero.
 We do not recommend that.
 Indeed, in this case $\rho_o$ depends on the initial state of the ocean.
@@ -1890 +1890 @@
   
 Third, the discretisation of \autoref{eq:steric_Bq} depends on the type of free surface which is considered.
-In the non linear free surface case, $i.e.$ \key{vvl} defined, it is given by
+In the non linear free surface case, \ie \key{vvl} defined, it is given by
 
 \[
@@ -1913 +1913 @@
 so that there are no associated ocean currents.
 Hence, the dynamically relevant sea level is the effective sea level,
-$i.e.$ the sea level as if sea ice (and snow) were converted to liquid seawater \citep{Campin_al_OM08}.
+\ie the sea level as if sea ice (and snow) were converted to liquid seawater \citep{Campin_al_OM08}.
 However, in the current version of \NEMO the sea-ice is levitating above the ocean without mass exchanges between
 ice and ocean.
@@ -1949 +1949 @@
 - the turbocline depth (based on a turbulent mixing coefficient criterion) (\mdl{diahth})
 
-- the depth of the 20\deg C isotherm (\mdl{diahth})
+- the depth of the 20\deg{C} isotherm (\mdl{diahth})
 
 - the depth of the thermocline (maximum of the vertical temperature gradient) (\mdl{diahth})
@@ -1968 +1968 @@
 (see the \textit{\ngn{namptr} } namelist below).
 When \np{ln\_subbas}\forcode{ = .true.}, transports and stream function are computed for the Atlantic, Indian,
-Pacific and Indo-Pacific Oceans (defined north of 30\deg S) as well as for the World Ocean.
+Pacific and Indo-Pacific Oceans (defined north of 30\deg{S}) as well as for the World Ocean.
 The sub-basin decomposition requires an input file (\ifile{subbasins}) which contains three 2D mask arrays,
 the Indo-Pacific mask been deduced from the sum of the Indian and Pacific mask (\autoref{fig:mask_subasins}).
@@ -2060 +2060 @@
 \biblio
 
+\pindex
+
 \end{document}