restore UserAPI.tex (was accidentally moved to unused/)

Doc/UserManual/BornAgainManual.tex

@@ -308,7 +308,6 @@ Disclaimer:\index{Disclaimer}\index{BornAgain@\BornAgain!disclaimer}
 
 \appendix
 \addtocontents{toc}{\protect\setcounter{tocdepth}{1}}
-%\addtocontents{lof}{\protect\setcounter{tocdepth}{2}}
 %\input{AppendixListings}
 \input{theoryapp}
 \input{FormFactors}

Doc/UserManual/Theory.tex

@@ -213,8 +213,10 @@ For the LMA, its implementation is automatically done when using more than one l
 \end{lstlisting}
 
 %%ADD EXPLANATION ABOUT LMA
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%-------------------------------------------------------------------------------
 \subsubsection{Probability distribution functions}\label{baftd}
+%-------------------------------------------------------------------------------
 
 The probability distribution functions have been implemented in the reciprocal space in \BornAgain. Their expressions are given in Table~\ref{table:pdf}.
 
@@ -590,6 +592,7 @@ Function  & Parameters & Comments\\
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Particles - Form factors} \SecLabel{sect:ff}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\index{Form factors}
 
 %===============================================================================
 \subsection{Born approximation}
@@ -652,6 +655,7 @@ Ripple1, \SecRef{Ripple1} &  & Ripple2, \SecRef{Ripple2}& &   & &  \\
 \includegraphics[width=1in]{fig/blue/Ripple23d.png} & &  & & \\
 \hline 
 \end{tabulary}
+\index{Form factors!table of implemented}
 \end{table}
 
 
@@ -659,6 +663,7 @@ Ripple1, \SecRef{Ripple1} &  & Ripple2, \SecRef{Ripple2}& &   & &  \\
 %===============================================================================
 \subsection{Distorted Wave Born Approximation} \SecLabel{sect:dwba}
 %===============================================================================
+\index{Distorted wave Born approximation}
 
 The Born approximation fails when multiple reflections and refractions have to be taken into account at interfaces because of the presence of underlying layers of materials and the closeness of  the incident angle $\alpha_i$ to the critical angle of total external reflection $\alpha_c$. The first order correction to the scattering theory is the Distorted Wave Born Approximation (DWBA), whereas the Born approximation is the zeroth order. \\
 The collective effects between the particles are not considered in this section. They have been described in~\SecRef{sect:interf}.  We also do not take any polarization effects into account. \\
@@ -803,7 +808,6 @@ where index $n$ is related to the layers, $z$ to the vertical component, and $j$
 \end{figure}
 
 
-
 Figure~\ref{fig:dwbaburied} shows a typical example of the output intensity scattered from a sample made of 3 layers: air, substrate, and in between, spherical particles embedded in the middle of a 30~nm-thick layer. This figure had been generated using listing~\ref{lst:dwbaburied}.
 
 \begin{lstlisting}[language=python, style=eclipseboxed,numbers=none,nolol,caption={\Code{Python} script to generate a sample where spherical particles are embedded in the middle of a layer on a substrate.},label={lst:dwbaburied}]
@@ -871,6 +875,7 @@ def get_sample():
 %===============================================================================
 \subsection{Core-shell particles} \label{subsec:CoreShell}
 %===============================================================================
+\index{Core-shell particles}
 
 To generate a core-shell particle, the combination is performed using the following command:\\
 \Code{ParticleCoreShell(shell\_particle, core\_particle, relative\_core\_position)},\\
@@ -890,7 +895,6 @@ Figure~\ref{fig:FFCoreShellBA} displays the output intensity scattered in the Bo
 
 \newpage
 
-
 \begin{lstlisting}[language=python,
   style=eclipseboxed,numbers=none,nolol,caption={\Code{Python} script
     to create a core-shell particle made of a box with a pyramidal shifted inset.},label={lst:cshellsample}]
@@ -914,6 +918,8 @@ Figure~\ref{fig:FFCoreShellBA} displays the output intensity scattered in the Bo
 %===============================================================================
 \subsection{Rotation of particles}
 %===============================================================================
+\index{Rotation of particles}
+\index{Orientation of particles}
 
 The particles can be rotated in a different direction by using one of
 the following transformations: \Code{CreateRotateX($\theta$),