From ee7b5a5324fc53d94a85a58f256e22b046d7b91c Mon Sep 17 00:00:00 2001
From: "Joachim Wuttke (l)" <j.wuttke@fz-juelich.de>
Date: Wed, 18 Feb 2015 10:09:04 +0100
Subject: [PATCH] Add ".jpg" to a few more includegraphic's; Insert copyright
header on top of each .tex source file.
---
Doc/UserManual/AppendixListings.tex | 16 +++++++
Doc/UserManual/AppendixPhysics.tex | 16 +++++++
Doc/UserManual/AppendixPythonEx.tex | 52 +++++++++++++++--------
Doc/UserManual/BackOfTitle.tex | 36 ++++++++++++++++
Doc/UserManual/BornAgainManual.tex | 24 +++++++++--
Doc/UserManual/Disclaimer.tex | 21 ---------
Doc/UserManual/Fitting.tex | 16 +++++++
Doc/UserManual/FittingAdvanced.tex | 16 +++++++
Doc/UserManual/FittingExamples.tex | 16 +++++++
Doc/UserManual/FittingImplementation.tex | 16 +++++++
Doc/UserManual/FittingRightAnswers.tex | 16 +++++++
Doc/UserManual/Installation.tex | 16 +++++++
Doc/UserManual/Introduction.tex | 16 +++++++
Doc/UserManual/QuickStart.tex | 16 +++++++
Doc/UserManual/Simulation.tex | 16 +++++++
Doc/UserManual/SimulationExamples.tex | 16 +++++++
Doc/UserManual/SoftwareArchitecture.tex | 16 +++++++
Doc/UserManual/SoftwareDesignOverview.tex | 16 +++++++
Doc/UserManual/Theory.tex | 16 +++++++
Doc/UserManual/UserAPI.tex | 16 +++++++
Doc/UserManual/UserManualVersion.tex | 7 ++-
Doc/UserManual/ff.tex | 16 +++++++
Doc/UserManual/interferences.tex | 16 +++++++
Doc/UserManual/theoryapp.tex | 16 +++++++
cmake/scripts/UserManualVersion.tex.in | 7 ++-
25 files changed, 404 insertions(+), 47 deletions(-)
create mode 100755 Doc/UserManual/BackOfTitle.tex
delete mode 100755 Doc/UserManual/Disclaimer.tex
diff --git a/Doc/UserManual/AppendixListings.tex b/Doc/UserManual/AppendixListings.tex
index 8b645fb5495..34f858c17f4 100755
--- a/Doc/UserManual/AppendixListings.tex
+++ b/Doc/UserManual/AppendixListings.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
%\newpage{\pagestyle{empty}\cleardoublepage}
diff --git a/Doc/UserManual/AppendixPhysics.tex b/Doc/UserManual/AppendixPhysics.tex
index b83e89582a2..cc78253b3ea 100755
--- a/Doc/UserManual/AppendixPhysics.tex
+++ b/Doc/UserManual/AppendixPhysics.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
%Appendix
\chapter{Implemented classes}
diff --git a/Doc/UserManual/AppendixPythonEx.tex b/Doc/UserManual/AppendixPythonEx.tex
index b3bb271315f..88c25bc9a34 100644
--- a/Doc/UserManual/AppendixPythonEx.tex
+++ b/Doc/UserManual/AppendixPythonEx.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
%\newpage
\chapter{\Python\ examples}
This appendix describes the samples and the simulated output intensity maps of the examples, whose \Python\ scripts are contained in the folder /Examples/python/simulation.
@@ -7,7 +23,7 @@ This appendix describes the samples and the simulated output intensity maps of t
\begin{figure}[H]
\begin{center}
-\includegraphics[width=0.6\textwidth]{Figures/py-ex/BAgeometry_wide}
+\includegraphics[width=0.6\textwidth]{Figures/py-ex/BAgeometry_wide.jpg}
\end{center}
\caption{The GISAS setup and the coordinate system used in
\BornAgain. The incoming beam propagates with incidence angles $\alpha_i$ and $\phi_i$ with respect to the sample axes as shown. A scattered (outgoing) beam, characterized by $\alpha_f$ and $\phi_f$ propagates toward the area detector.}
@@ -53,7 +69,7 @@ The simulation is performed using the Distorted Wave Born Approximation. The out
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex001}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex001.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex001.eps}}
\hfill
@@ -81,7 +97,7 @@ The result of the simulation is shown in fig.~\ref{fig:PythonEx2}(b).
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex002}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex002.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex002.eps}}
\hfill
@@ -100,7 +116,7 @@ The sample considered for this example and the output intensity generated using
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex003BA}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex003BA.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex003BA.eps}}
\hfill
@@ -113,7 +129,7 @@ This example considers a polydisperse distribution of cylinders (see fig.~\ref{f
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex003BASize}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex003BASize.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex003BASize.eps}}
\hfill
@@ -132,7 +148,7 @@ The distribution of cylinders is monodisperse with a height and a radius of 5~nm
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex003DWBA}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex003DWBA.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex003DWBA.eps}}
\hfill
@@ -185,7 +201,7 @@ The distribution function is a two-dimensional Cauchy function with correlation
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/g_r_2dparasq}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/g_r_2dparasq.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex0042DDLsq.eps}}
\hfill
@@ -211,7 +227,7 @@ The simulation is run using the DWBA.
% question: LMA with constant size of particles??
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex005Dis1}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex005Dis1.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex005Disorder1.eps}}
\hfill
@@ -224,7 +240,7 @@ This sample differs from the previous one by an overlap of two spatial distribut
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex005Dis2}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex005Dis2.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex005Disorder2.eps}}
\hfill
@@ -239,7 +255,7 @@ Compared to Section~\ref{sec:ex005Dis1}, the square lattice used in this example
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex005Dis3}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex005Dis3.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex005Disorder3.eps}}
\hfill
@@ -253,7 +269,7 @@ This sample is composed of identical cylinders. Their distribution is generated
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex005Dis4rand}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex005Dis4rand.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex005Disorder4.eps}}
\hfill
@@ -271,7 +287,7 @@ For the second example, shown in fig.~\ref{fig:PythonEx6RotatedPyramid}, the pyr
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex006Pyramids}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex006Pyramids.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex006Pyramids.eps}}
\hfill
@@ -281,7 +297,7 @@ For the second example, shown in fig.~\ref{fig:PythonEx6RotatedPyramid}, the pyr
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex006RotatedPyramids}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex006RotatedPyramids.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex006RotatedPyramids.eps}}
\hfill
@@ -301,7 +317,7 @@ The incident beam is characterized by a wavelength of 1~\AA, incident angles $\a
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex007Core}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex007Core.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex007CoreShell.eps}}
\hfill
@@ -336,7 +352,7 @@ There is no added particle. All layers present the same type of roughness on the
The incident beam is characterized by a wavelength of 1~\AA \ and incident angles $\alpha_i=0.2^{\circ}$ and $\phi_i=0^{\circ}$.
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex008Rough}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex008Rough.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex008CorrelatedRough.eps}}
\hfill
@@ -361,7 +377,7 @@ The interference considered is a two-dimensional orthogonal lattice with $L_1=20
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex009Cos}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex009Cos.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex009CosRipple2DLat.eps}}
\hfill
@@ -384,7 +400,7 @@ The influence of the interference function on the output pattern can be seen by
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex009Tri}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex009Tri.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex009TriRipple2DLat.eps}}
\hfill
@@ -415,7 +431,7 @@ The sample is made of cylinders (5~nm in radius and height) deposited on a subst
\begin{figure}[H]
\hfill
-\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex010BeamDiv}}
+\subfigure[Schematic of the sample]{\includegraphics[width=.49\textwidth]{Figures/py-ex/fig_ex010BeamDiv.jpg}}
\hfill
\subfigure[Simulated 2D pattern]{\includegraphics[width=.49\textwidth]{Figures/py-ex/figure_ex010BeamDiv.eps}}
\hfill
diff --git a/Doc/UserManual/BackOfTitle.tex b/Doc/UserManual/BackOfTitle.tex
new file mode 100755
index 00000000000..5c43b31b6fe
--- /dev/null
+++ b/Doc/UserManual/BackOfTitle.tex
@@ -0,0 +1,36 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+\newpage
+\thispagestyle{empty}
+
+\vfill
+
+\noindent
+\begin{tabular}{@{}p{7em}@{}l@{}}
+Homepage:& http://www.bornagainproject.org\\[2ex]
+Copyright:& Forschungszentrum Jülich GmbH 2015\\
+ &Software licence: GNU public licence version 3 or higher\\
+ &For documentation licence, contact the authors\\[2ex]
+Authors: &Scientific Computing Group at Heinz Maier-Leibnitz Zentrum (MLZ) Garching\\
+ &Céline Durniak, Marina Ganeva, Gennady Pospelov,
+ Walter Van Herck, Joachim Wuttke\\[2ex]
+Disclaimer: &Software and documentation are work in progress.\\
+ &We cannot guarantee that they are accurate and correct.\\
+ &Anyway, it is entirely in the responsibility of users
+ to check that their data interpretation is physically meaningful.\\
+ &If in doubt, contact us for assistance or scientific collaboration.
+\end{tabular}
diff --git a/Doc/UserManual/BornAgainManual.tex b/Doc/UserManual/BornAgainManual.tex
index b7bba0a838f..4618063f23d 100755
--- a/Doc/UserManual/BornAgainManual.tex
+++ b/Doc/UserManual/BornAgainManual.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\documentclass[a4paper,11pt,twoside,fleqn]{report}
%-------------------------------------------------------------------------------
@@ -234,14 +250,14 @@ Forschungszentrum J\"ulich GmbH \\ [40mm]
% DOCUMENT
%------------------------------------------------------------------------------
\begin{document}
+\pagenumbering{roman}
\maketitle
-\input{Disclaimer}
+\input{BackOfTitle}
\tableofcontents
-%\lstlistoflistings
-%\listoffigures
-%\listoftables
+\pagenumbering{arabic}
+\setcounter{page}{1}
\input{Introduction}
\input{QuickStart}
diff --git a/Doc/UserManual/Disclaimer.tex b/Doc/UserManual/Disclaimer.tex
deleted file mode 100755
index 24218791e31..00000000000
--- a/Doc/UserManual/Disclaimer.tex
+++ /dev/null
@@ -1,21 +0,0 @@
-\newpage
-
-{\Huge
-\vspace*{0.5cm}
-\noindent
-Disclaimer
-} \newline
-\vspace*{0.25cm}
-
-\noindent
-{\large
-This manual supplements BornAgain online documentation located at \url{http://www.bornagainproject.org}.
-Follow the link to get started.
-\vspace*{4mm}
-
-\noindent
-This manual is under development and does not yet constitute a comprehensive listing of
-all \BornAgain\ features and functionality.
-The included information and instructions are subject to substantial changes and
-are provided only as a preview.
-}
diff --git a/Doc/UserManual/Fitting.tex b/Doc/UserManual/Fitting.tex
index 23262a39c5e..6dd37f00860 100755
--- a/Doc/UserManual/Fitting.tex
+++ b/Doc/UserManual/Fitting.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\newpage
\chapter{Fitting} \SecLabel{Fitting}
diff --git a/Doc/UserManual/FittingAdvanced.tex b/Doc/UserManual/FittingAdvanced.tex
index 3664ce073c2..78b0c8d817a 100755
--- a/Doc/UserManual/FittingAdvanced.tex
+++ b/Doc/UserManual/FittingAdvanced.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\section {Advanced fitting} \SecLabel{FittingAdvanced}
\subsection{Affecting $\chi2$ calculations}
diff --git a/Doc/UserManual/FittingExamples.tex b/Doc/UserManual/FittingExamples.tex
index f6990b8a5b5..03705287bf2 100755
--- a/Doc/UserManual/FittingExamples.tex
+++ b/Doc/UserManual/FittingExamples.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\section{Basic Python fitting example} \SecLabel{FittingExamples}
In this section we are going to go through a complete example of
diff --git a/Doc/UserManual/FittingImplementation.tex b/Doc/UserManual/FittingImplementation.tex
index f1f37d18071..dfed33e0fca 100755
--- a/Doc/UserManual/FittingImplementation.tex
+++ b/Doc/UserManual/FittingImplementation.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/Doc/UserManual/FittingRightAnswers.tex b/Doc/UserManual/FittingRightAnswers.tex
index a7b7a4ff288..b1c62734e6f 100755
--- a/Doc/UserManual/FittingRightAnswers.tex
+++ b/Doc/UserManual/FittingRightAnswers.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\section {How to get the right answer from fitting}
\SecLabel{FittingRightAnswers}
diff --git a/Doc/UserManual/Installation.tex b/Doc/UserManual/Installation.tex
index a26cbe63fbf..6e4009bf89a 100755
--- a/Doc/UserManual/Installation.tex
+++ b/Doc/UserManual/Installation.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\newpage
\chapter{Installation} \SecLabel{Installation}
diff --git a/Doc/UserManual/Introduction.tex b/Doc/UserManual/Introduction.tex
index 325be8de54f..6c20d96390b 100755
--- a/Doc/UserManual/Introduction.tex
+++ b/Doc/UserManual/Introduction.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\newpage
\mychapter{0}{Introduction}
diff --git a/Doc/UserManual/QuickStart.tex b/Doc/UserManual/QuickStart.tex
index ff502dcf89a..28120f53c11 100755
--- a/Doc/UserManual/QuickStart.tex
+++ b/Doc/UserManual/QuickStart.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\newpage
\chapter{Quick start} \SecLabel{QuickStart}
diff --git a/Doc/UserManual/Simulation.tex b/Doc/UserManual/Simulation.tex
index 9e86b9760be..cc76db4b9e6 100755
--- a/Doc/UserManual/Simulation.tex
+++ b/Doc/UserManual/Simulation.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\newpage
\chapter{Simulation} \SecLabel{Simulation}
diff --git a/Doc/UserManual/SimulationExamples.tex b/Doc/UserManual/SimulationExamples.tex
index aa27a425072..aa60df255d7 100755
--- a/Doc/UserManual/SimulationExamples.tex
+++ b/Doc/UserManual/SimulationExamples.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\mysection{Example 1: two types of islands on a substrate without interference}{Example 1: two types of islands on top of
substrate without interference} \SecLabel{Example1Python}
diff --git a/Doc/UserManual/SoftwareArchitecture.tex b/Doc/UserManual/SoftwareArchitecture.tex
index 4c0c2c65303..7438f0df998 100755
--- a/Doc/UserManual/SoftwareArchitecture.tex
+++ b/Doc/UserManual/SoftwareArchitecture.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\newpage
\chapter{Software architecture}\SecLabel{SoftwareArchitecture}
diff --git a/Doc/UserManual/SoftwareDesignOverview.tex b/Doc/UserManual/SoftwareDesignOverview.tex
index 29e491bc1ea..13927350600 100755
--- a/Doc/UserManual/SoftwareDesignOverview.tex
+++ b/Doc/UserManual/SoftwareDesignOverview.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\section{Data classes for simulations and fits}
diff --git a/Doc/UserManual/Theory.tex b/Doc/UserManual/Theory.tex
index 024f1f20794..0375543ac6f 100755
--- a/Doc/UserManual/Theory.tex
+++ b/Doc/UserManual/Theory.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\chapter{Scattering cross--section} \SecLabel{ScatteringCrosssection}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/Doc/UserManual/UserAPI.tex b/Doc/UserManual/UserAPI.tex
index e5fd37f269c..c94c16e2938 100644
--- a/Doc/UserManual/UserAPI.tex
+++ b/Doc/UserManual/UserAPI.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\chapter{User API} \label{UserAPI}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/Doc/UserManual/UserManualVersion.tex b/Doc/UserManual/UserManualVersion.tex
index 699e6e1c9e9..7872c1d7872 100644
--- a/Doc/UserManual/UserManualVersion.tex
+++ b/Doc/UserManual/UserManualVersion.tex
@@ -1,4 +1,7 @@
% User Manual version number
-% this file is automatically generated by CMakeLists.txt using cmake/scripts/UserManualVersion.tex.in
-\newcommand{\UserManualVersionNumber}{1.0.0}
+% This file is automatically generated by CMakeLists.txt
+% using cmake/scripts/UserManualVersion.tex.in
+
+\newcommand{\UserManualVersionNumber}
+{1.0.0}
diff --git a/Doc/UserManual/ff.tex b/Doc/UserManual/ff.tex
index 44a7d78b6cf..3134e8ccb51 100755
--- a/Doc/UserManual/ff.tex
+++ b/Doc/UserManual/ff.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
%\newpage
\chapter{Form factors} \label{appendixff}
\hypertarget{formfactors}{}
diff --git a/Doc/UserManual/interferences.tex b/Doc/UserManual/interferences.tex
index 31d6364b995..cf3c6a9d127 100755
--- a/Doc/UserManual/interferences.tex
+++ b/Doc/UserManual/interferences.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\chapter{Collection of particles} \label{appendixinterf}
In the section we are going to describe how to simulate collections of particles using \BornAgain\ \textit{i.e.} the way their spatial distributions and the distribution of shapes and their correlations can influence the output scattered intensity. The samples generated with \BornAgain\ are made of different material layers characterized by their thicknesses, refractive indices, and possible surface roughnesses. Except for the thickness, the other dimensions of the layers are infinite.\\ Particles can be embedded in or deposited on the top of any layers. Those particles are characterized by their shapes, refractive indices, their spatial distribution and concentration in the sample. When the particles are densely packed, the distance relative to each other becomes of the same order as the particles' sizes. The radiation scattered from these various particles are going to interfere together. The influence of the particles' shapes has been described in the previous section about form factors.
diff --git a/Doc/UserManual/theoryapp.tex b/Doc/UserManual/theoryapp.tex
index 38806057961..55d6dc9b59e 100755
--- a/Doc/UserManual/theoryapp.tex
+++ b/Doc/UserManual/theoryapp.tex
@@ -1,3 +1,19 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%
+%% BornAgain: simulate and fit scattering at grazing incidence
+%%
+%% homepage: http://www.bornagainproject.org
+%%
+%% copyright: Forschungszentrum Jülich GmbH 2015
+%% Software licence does not cover this documentation
+%% For documentation licence, contact the authors
+%%
+%% authors: Scientific Computing Group at MLZ Garching
+%% C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
\chapter{Theory} \label{appendixtheory}
\section{Scattering on nanoparticles - Formal treatment} \label{sec:formal}
diff --git a/cmake/scripts/UserManualVersion.tex.in b/cmake/scripts/UserManualVersion.tex.in
index 17ea28579cc..6ab2fcfa066 100644
--- a/cmake/scripts/UserManualVersion.tex.in
+++ b/cmake/scripts/UserManualVersion.tex.in
@@ -1,4 +1,7 @@
% User Manual version number
-% this file is automatically generated by CMakeLists.txt using cmake/scripts/UserManualVersion.tex.in
-\newcommand{\UserManualVersionNumber}{@BornAgain_VERSION_MAJOR@.@BornAgain_VERSION_MINOR@.@BornAgain_VERSION_PATCH@}
+% This file is automatically generated by CMakeLists.txt
+% using cmake/scripts/UserManualVersion.tex.in
+
+\newcommand{\UserManualVersionNumber}
+{@BornAgain_VERSION_MAJOR@.@BornAgain_VERSION_MINOR@.@BornAgain_VERSION_PATCH@}
--
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