Corrections; start list of symbols ("nomenclature")

Doc/UserManual/BornAgainManual.tex

@@ -83,7 +83,9 @@
 %-------------------------------------------------------------------------------
 %	OTHER PACKAGES 
 %-------------------------------------------------------------------------------
+
 \usepackage{makeidx}\makeindex
+\usepackage{nomencl}\makenomenclature
 
 \usepackage{graphicx}
 \usepackage{subfigure}
@@ -343,6 +345,9 @@ Disclaimer: &Software and documentation are work in progress.\\
 \bibliographystyle{switch}
 \bibliography{jw7}
 
+\renewcommand{\nomname}{List of Symbols}
+\printnomenclature
+
 \printindex
 
 \end{document}

Doc/UserManual/Multilayers.tex

@@ -215,7 +215,6 @@ plane. }
   \label{fig:multil3d}
 \end{figure}
 
-
 The layers are defined by their thicknesses (parallel to the
 $z$-direction), their possible
 roughnesses (equal to 0 by default) and the
@@ -334,8 +333,8 @@ the in-plane component $\vect{r}_\parallel$ (\ref{Ewave3}):
 From the continuity conditions we infer that $\vect{k}_\parallel$
 is constant across layers.
 The wave equation~(\ref{Escalar_wave})
-reduces to a one-dimensional equation in~$z$,
-\begin{equation}\label{Ewavez}
+reduces to a one-dimensional equation in~$z$ [see (\ref{Ewavez})]
+\begin{equation}\label{Ewavezdup}
 \left(\partial_z^2 + K^2n_i^2 - k_\parallel^2 \right) \psi(z) = 0,
 \end{equation}
 which is solved by
@@ -348,7 +347,7 @@ introduced here as a constant offset for later convenience.
 In the case of the semi-infinite bottom layer~$N$,
 $z_N$ can be chosen arbitrarily.
 
-Inserting (\ref{Epsiz}) into (\ref{Ewavez}),
+Inserting (\ref{Epsiz}) into (\ref{Ewavezdup}),
 we obtain the dispersion relation
 \begin{equation}\label{Edisp}
   k_\parallel^2 + k_{\perp i}^2 = K^2 n_i^2.   

Doc/UserManual/PolarizedScattering.tex

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%%   BornAgain User Manual
+%%
+%%   homepage:   http://www.bornagainproject.org
+%%
+%%   copyright:  Forschungszentrum Jülich GmbH 2015
+%%
+%%   license:    Creative Commons CC-BY-SA
+%%   
+%%   authors:    Scientific Computing Group at MLZ Garching
+%%               C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\chapter{Polarized GISAS}  \SecLabel{polTheory}
+
+In this chapter,
+we extend the theory
+of grazing-incidence small-angle scattering (GISAS)
+to X-rays and polarized neutrons.
+We therefore need to study vectorial wave equations,
+in contrast to the scalar theory of the previous chapter.
+
+%===============================================================================
+\section{X-ray propagation}\label{Sxray}
+%===============================================================================
+\index{Wave propagation!X-rays}
+\index{X-rays!wave propagation}
+
+.... to come ....
+
+
+%===============================================================================
+\section{Polarized neutrons}\label{Snpol}
+%===============================================================================
+
+\index{Neutrons!polarized}
+\index{Polarization!neutrons}
+
+.... to come ....
+

Doc/UserManual/ScatteringTheory.tex

@@ -55,8 +55,11 @@ we refer to the excellent review \cite{ReLL09}.
 \index{Neutrons!wave propagation|(}%
 
 \index{Schrodinger@Schrödinger equation!microscopic}%
-The scalar wave function $\psi(\r,t)$ of a slow neutron
-is governed by the microscopic Schrödinger equation
+The scalar wave function $\psi(\r,t)$
+\nomenclature{$t$}{Time}
+\nomenclature{$\r$}{Position}
+\nomenclature{$\psi(\r,t)$}{Microscopic neutron wave function}
+of a slow neutron is governed by the microscopic Schrödinger equation
 \begin{equation}\label{ESchrodi}
   i\hbar\partial_t \psi(\r,t)
   = \left\{-\frac{\hbar^2}{2m}\Nabla^2+V(\r)\right\} \psi(\r,t).
@@ -65,6 +68,7 @@ By assuming a time-independent potential $V(\r)$,
 we have excluded inelastic scattering.
 Therefore we need only to consider monochromatic waves
 with given frequency~$\omega$.
+\nomenclature{$\omega$}{Frequency of incident radiation}
 In consequence, we have a stationary wave function
 \begin{equation}\label{Estationarywave}
   \psi(\r,t) = \psi(\r){\rm e}^{-i\omega t}.
@@ -419,7 +423,7 @@ of the scattering-length density.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 %===============================================================================
-\subsection{Wave propagation in $\v{2+1}$ dimensions}
+\subsection[Wave propagation in $2+1$ dimensions]{Wave propagation in $\v{2+1}$ dimensions}
 %===============================================================================
 
 Reflectometry and grazing-incidence scattering

Doc/UserManual/nomencl.ist

+%%
+%% This is file `nomencl.ist',
+%% generated with the docstrip utility.
+%%
+%% The original source files were:
+%%
+%% nomencl.dtx  (with options: `idxstyle')
+%% 
+%% Copyright 1996 Boris Veytsman
+%% Copyright 1999-2001 Bernd Schandl
+%% www http://sarovar.org/projects/nomencl
+%% 
+%% This file can be redistributed and/or modified under the terms
+%% of the LaTeX Project Public License distributed from CTAN
+%% archives in the directory macros/latex/base/lppl.txt; either
+%% version 1.2 of the license, or (at your option) any later version.
+%% 
+%% 
+%% Nomenclature style file for MAKEINDEX.
+%% For nomencl v2.5 (and later)
+%% 
+%% Formats glossary entries to show, e.g. nomenclature of equations.
+%% 
+%% Written by Boris Veytsman boris@plmsc.psu.edu
+%% Changed by Bernd Schandl schandl@gmx.net (starting 1999/02/20)
+%% Changed by Lee Netherton ltn100@users.sourceforge.net
+%% (starting 2005/03/31)
+%% 
+%% Changes:
+%%  2005/04/27. Updates to the documentation, including support for hyperref (LN)
+%%  2005/04/20. Improvements to Italian option, and minor documentation
+%%              changes (LN)
+%%  2005/03/31. Made more compatible with other glossary packages. (LN)
+%%              Added option to include nomenclature in TOC. (LN)
+%%  1996/11/25. Change quote character to % (BV)
+%%  1999/02/20. Removed setting of actual to its default value
+%%              Removed setting of quote to '%' to get its default '"' instead
+%%              Changed group_skip to do nothing; user should use \nomgroup
+%%              Changed spacing in gls file
+%% 
+%% \CharacterTable
+%%  {Upper-case    \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z
+%%   Lower-case    \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z
+%%   Digits        \0\1\2\3\4\5\6\7\8\9
+%%   Exclamation   \!     Double quote  \"     Hash (number) \#
+%%   Dollar        \$     Percent       \%     Ampersand     \&
+%%   Acute accent  \'     Left paren    \(     Right paren   \)
+%%   Asterisk      \*     Plus          \+     Comma         \,
+%%   Minus         \-     Point         \.     Solidus       \/
+%%   Colon         \:     Semicolon     \;     Less than     \<
+%%   Equals        \=     Greater than  \>     Question mark \?
+%%   Commercial at \@     Left bracket  \[     Backslash     \\
+%%   Right bracket \]     Circumflex    \^     Underscore    \_
+%%   Grave accent  \`     Left brace    \{     Vertical bar  \|
+%%   Right brace   \}     Tilde         \~}
+%%
+%% ---- for input file ----
+keyword    "\\nomenclatureentry"
+%% Germans might want to change this and delete the two %%
+%% quote '"'
+%% ---- for output file ----
+preamble   "\\begin{thenomenclature} \n"%
+postamble  "\n\n\\end{thenomenclature}\n" group_skip "\n"
+delim_0    ""
+delim_1    ""
+delim_2    ""
+%% The next lines will produce some warnings when
+%% running Makeindex as they try to cover two different
+%% versions of the program:
+lethead_prefix "\n \\nomgroup{"
+lethead_suffix "}\n"
+lethead_flag   1
+heading_prefix "\n \\nomgroup{"
+heading_suffix "}\n"
+headings_flag  1