Merge branch 'tilted_particles' into develop

Conflicts:
	Core/Samples/inc/Layer.h
	Core/Samples/inc/LayerDecorator.h
	Core/Samples/src/Layer.cpp
	Doc/UserManual/UserManual.pdf
	Doc/UserManual/UserManual.tex

Doc/UserManual/Appendix.tex

+%Appendix
+\chapter{Implemented classes}
+
+\begin{itemize}
+\item Particle decoration
+\item Layer
+\item MultiLayer
+\item Simulation
+\end{itemize}
+
+\chapter{Form factors}
+% plots of particles + orientation of the axes
+% plots of the form factors
+
+\begin{itemize}
+\item Parallelepiped (\texttt{FormFactorParallelepiped})
+
+\begin{equation}
+F() = 4H R^2\exp(i q_z H/2) \frac{sin(q_xR)}{q_x R}\frac{ \sin(q_yR)}{q_y R}\frac{\sin(q_z H/2)}{q_z H/2}
+\end{equation}
+\item Pyramid (\texttt{FormFactorPyramid})
+
+\begin{align*}
+        q_1 &=(H/2)((q_x-q_y)/\tan(\alpha) + q_z)\\
+        q_2 &=(H/2)((q_x-q_y)/\tan(\alpha) - q_z)\\
+        q_3 &=(H/2)((q_x+q_y)/\tan(\alpha) + q_z) \\
+        q_4 &=(H/2)((q_x+q_y)/\tan(\alpha) - q_z)\\
+        K_1 &= \frac{\sin(q_1)}{q_1} \exp(i q_1)  + i \frac{\sin(q_2)}{q_2} \exp(-i q_2)\\
+        K_2 &= -i \frac{sin(q_1)}{q_1} exp(i q_1) +i \frac{\sin(q_2)}{q_2} \exp(-i q_2)\\
+        K_3 &= \frac{\sin(q_3)}{q_3}\exp(i q_3)    + \frac{\sin(q_4)}{q_4} \exp(-i q_4)\\
+        K_4 &= -i \frac{\sin(q_3)}{q_3} \exp(i q_3) + i \frac{\sin(q_4)}{q_4} \exp(-i q_4)\\     
+  F() &= \frac{H}{q_x q_y} [ K_1 \cos( (q_x-q_y)R ) + K_2 \sin( (q_x-q_y)R ) - K_3 \cos( (q_x+q_y) R ) - K_4 \sin( (q_x+q_y) R )]
+   \end{align*}
+	
+\item Cylinder (\texttt{FormFactorCylinder})
+
+  \begin{equation}
+ F()=   H  \frac{\sin(q_ z H/2)}{q_z H/2} \exp(i q_ z H/2) 2\pi R^2 \frac{J_1(|q_{\parallel} R |)}{|q_{\parallel} R| }
+ \end{equation}
+ 
+
+\item Prism3 (\texttt{FormFactorPrism3})
+
+\begin{equation}
+    F()= 2 \sqrt{3}\frac{\exp(-i q_y R/\sqrt{3})}{q_x^2-3q_y^2}[\exp(i \sqrt{3} q_y R ) -\cos(q_x R)-i \sqrt{3} q_y R \frac{\sin(q_x R)}{q_x R}]   H \frac{\sin(q_z H/2 )}{q_z H/2} \exp(i q_z H/2)
+\end{equation}
+
+\item Sphere (\texttt{FormFactorSphere})
+
+\begin{equation}    
+return 2\pi \exp(i q_z (H-R))\int_{R-H} ^{R} R_z^2 \frac{J_1(|q_p*R_z|) }{|q_p*R_z|}
+        \exp(i q_z*Z)
+\end{equation}
+
+
+\item Full sphere (\texttt{FormFactorFullSphere})
+
+\begin{equation}
+radial = 4\pi R^3*\frac{\sin(q R) - q R*\cos(q R)}{(qR)^3}
+\end{equation}
+
+\item Box (\texttt{FormFactorBox})
+
+\begin{equation}
+F()= 4H R W\exp(i q_z H/2) \frac{\sin(q_x R)}{q_x R} \frac{  \sin(q_y W) }{q_y W}\frac{\sin(q_z H/2)}{q_z H/2}
+\end{equation}
+    
+	
+\end{itemize}
+
+\chapter{Interference functions}
+
+\begin{itemize}
+\item	No interference 
+\item	decoupling approximation 	
+\item 	local mono disperse approximation 
+\item 	size spacing approximation 
+\end{itemize}
+
+
+\chapter{Pair correlation functions}
+\begin{itemize}
+\item The Debye hard core 
+\item The gaussian
+\item The Lennard-Jonnes  	
+\item The gate pair correlation 	
+\item The Debye hard core with power-law decrease  	
+\item The Zhu pair correlation function 	
+\item The Venables pair correlation function 	
+\item The bidimensional hard core pair function.
+\end{itemize}	
\ No newline at end of file

Doc/UserManual/UserManual.tex

-\documentclass[a4paper,10pt]{article}
-
+\documentclass[a4paper,10pt]{report}
+\usepackage{cite}
+%----------------------------------------------------------------------------------------
+%	FONT
+%----------------------------------------------------------------------------------------
 \usepackage[utf8]{inputenc}
 \usepackage[T1]{fontenc}
+
+\usepackage[scaled=0.8]{beramono} % beramono or luximono give very nice ttfamily fonts
+
+%----------------------------------------------------------------------------------------
+%	PAGE LAYOUT
+%----------------------------------------------------------------------------------------
+\usepackage[toc,page]{appendix}
+
+\textwidth = 410pt
+
+\usepackage{fancyhdr}
+\pagestyle{fancy}
+
+
+\fancyhf{}
+
+%\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}}
+
+%\nouppercase{\rightmark}
+
+\lhead{\bfseries \nouppercase{\leftmark}}
+\rhead{\bfseries \nouppercase{\rightmark}}
+\lfoot{}
+\rfoot{\bfseries Page \thepage}
+
+\headwidth=1.1\textwidth
+\renewcommand{\headrulewidth}{1.5pt}
+\renewcommand{\footrulewidth}{1.5pt}
+\fancyhfoffset[L]{24pt}
+\fancyhfoffset[R]{24pt}
+
+\fancypagestyle{plain}{%
+\fancyhf{} % clear all header and footer fields
+\headwidth=1.1\textwidth
+\renewcommand{\headrulewidth}{1.5pt}
+\renewcommand{\footrulewidth}{1.5pt}
+\lhead{\bfseries \nouppercase{\leftmark}}
+\rhead{\bfseries \nouppercase{\rightmark}}
+%\lhead{\leftmark}
+%\rhead{\rightmark}
+\lfoot{}
+\rfoot{\bfseries Page \thepage}
+%\rfoot{Page \thepage}
+\headwidth=1.1\textwidth
+\fancyhfoffset[L]{24pt}
+\fancyhfoffset[R]{24pt}
+}
+
+\newcommand{\mysection}[2]{%
+                         \sectionmark{#1}%
+                         \section{#2}%
+                         \sectionmark{#1}%
+                       }
+
+%%%%%%%%%
+%\renewcommand{\chaptermark}[1]{\markboth{\uppercase{\thechapter.\ #1}}{}}
+%\renewcommand{\sectionmark}[1]{\markright{\uppercase{\thesection.\ #1}}}
+%\newcommand{\helv}{\fontfamily{phv}\fontseries{b}\fontsize{9}{11}\selectfont}
+%\lhead[\helv \thepage]{\helv \rightmark}
+%\rhead[\helv \leftmark]{\helv \thepage}
+%\cfoot{}
+%----------------------------------------------------------------------------------------
+%	OTHER PACKAGES and COMMANDS
+%----------------------------------------------------------------------------------------
+\usepackage{graphicx}
+\usepackage{epstopdf}
+
+
 \usepackage{float}
 \usepackage{tikz}
 \usepackage{tikz-uml} 
 \usepackage{amsmath}
 
+\usepackage{pifont}
+\usepackage{fourier}
+\usepackage{dingbat}
+
+\usepackage{hyperref}
+
+\newcommand{\reffig}[1]{figure \ref{fig:#1}}
 
-% custom listing settings
+\newcommand{\myparagraph}[1]{\paragraph{#1}\mbox{}\\}
+%----------------------------------------------------------------------------------------
+%	CUSTON LISTING SETTINGS
+%----------------------------------------------------------------------------------------
 \usepackage{listings}
 \usepackage{lstcustom}
-\usepackage[utf8]{inputenc}
-\usepackage[T1]{fontenc}
-\usepackage[scaled=0.8]{beramono} % beramono or luximono give very nice ttfamily fonts
 \renewcommand{\lstfontfamily}{\ttfamily}
+%----------------------------------------------------------------------------------------
+%	COLORS
+%----------------------------------------------------------------------------------------
 
-\newcommand{\reffig}[1]{figure \ref{fig:#1}}
+\definecolor{Lightgray}{gray}{.80}
+\definecolor{lightgrey}{rgb}{0.9,0.9,0.9}
+%----------------------------------------------------------------------------------------
+%	TITLE PAGE
+%----------------------------------------------------------------------------------------
 
-%\usepackage{minted}
+% Front page: logo?
 
+\title{BornAgain. }
+\author{}
+
+\usepackage{eso-pic}
+\newcommand\BackgroundPic{%
+\put(0,0){%
+\parbox[b][\paperheight]{\paperwidth}{%
+\vfill
+\centering
+\includegraphics[width=\paperwidth,height=\paperheight,%
+keepaspectratio]{results2_2.png}%
+\vfill
+}}}
+
+%----------------------------------------------------------------------------------------
+%	DOCUMENT
+%----------------------------------------------------------------------------------------
+
+\begin{document}
+
+%\AddToShipoutPicture*{\BackgroundPic} % add bakcground image to the
+%first page
+\maketitle
 
-%\maketitle
 
 %\begin{abstract}
 %This document describes the general architecture of the BornAgain project.
 %\end{abstract}
 
+\tableofcontents
+\lstlistoflistings
+\listoffigures
+\listoftables
 
-\title{BornAgain. }
-\author{}
+\newpage
 
+BornAgain is a  software to simulate and fit neutron and X-ray
+scattering at grazing incidence. It is a multi–platform open–source project that aims at supporting scientists in the analysis and fitting
+of their GISAS data, both for synchrotron (GISAXS) and neutron (GISANS) facilities. The name of the software,
+BornAgain, indicates the central role of the distorted-wave Born
+approximation (DWBA) in the physical description of the
+scattering process. The software provides a generic framework for modeling multilayer samples with smooth or
+rough interfaces and with various types of embedded nanoparticles. In this way, it reproduces and enhances the
+functionality of the present reference software, IsGISAXS by
+R. Lazzari \cite{Lazzari:vi0158}, and lays a solid base for future
+extensions in response to specific user needs. 
 
+To meet the growing demand for GISAS simulation of more
+complex structured materials, BornAgain has extended the IsGISAXS program’s functionality by removing the
+restrictions on the number of layers and particles, by providing diffuse reflection from rough layer interfaces and
+by adding particles with inner structure. \\
 
-\begin{document}
-A software to simulate and fit neutron and x-ray scattering at grazing incidence
-Some software
+
+For details about the theory (DWBA,\ldots), please refer to IsGISAXS manual (\url{http://ln-www.insp.upmc.fr/axe4/Oxydes/IsGISAXS/figures/doc/manual.html}).\\
+
+
+\colorbox{Lightgray}{\parbox{\linewidth-8\fboxsep}
+{\noindent \underline{Icons used in this manual:}
+\begin{itemize}
+\item[] \smallpencil: this sign highlights further references.
+%\item[] {\huge\ding{45}} - \smallpencil \textbf{\smallpencil}: this sign highlights further references.
+\item[] {\huge\danger}: this sign highlights essential points.
+\end{itemize}}}
 
 
-\input{QuickStart}
-\input{Introduction}
-\input{Installation}
-\input{Architecture}
-\input{Fitting}
+
+%\input{Introduction}
+%\input{Installation}
+%\input{Architecture}
+%\input{Fitting}
 \input{Examples}
 
+Bugs\\ License agreement\\ Directory layout \\ FAQ \\ Future development.
+%\appendix
+%\input{Appendix}
+
+
+%\printindex
+%generate an index - hyperref
+
+\bibliography{ref}
+\bibliographystyle{unsrt}
+
+
+
+
 \end{document}
 

Doc/UserManual/lstcustom.sty

@@ -2,10 +2,8 @@
 % this is customisation of 'listings' package
 % TODO: cleanup
 
-
-
-\usepackage{color}
-
+%\usepackage{color}
+\usepackage{xcolor}
 \lstdefinelanguage{pseudo}{
   keywords={procedure,end,return,integer,real,foreach,for,each,
   do,if,then,else,while,until,true,false,algorithm}, 
@@ -211,22 +209,27 @@ height, collapsed, true, false%
 \definecolor{darkblue}{rgb}{0.1,0.1,0.9}
 \definecolor{darkgrey}{rgb}{0.5,0.5,0.5}
 \definecolor{lightblue}{rgb}{0.4,0.4,1}
+\definecolor{lightblue1}{rgb}{0 0.25 1}
+\definecolor{darkpink}{rgb}{1 0 0.75}
 
 \lstdefinestyle{eclipse}{
-	basicstyle=\small\lstfontfamily,
+    basicstyle=\small\lstfontfamily,
     emphstyle=\color{red}\bfseries, 
     keywordstyle=\color{darkviolet}\bfseries,
     commentstyle=\color{darkgreen},
     stringstyle=\color{darkblue},
     numberstyle=\color{darkgrey}\lstfontfamily,
-    emphstyle=\color{red},
+    emph={Simulation,MaterialManager,MultiLayer}, 
+    emphstyle=\color{cyan}, %darkpink}, %red},
     % get also javadoc style comments
     morecomment=[s][\color{lightblue}]{/**}{*/},
    %columns=fullflexible, %spaceflexible, %flexible, fullflexible             
 %  escapeinside=`',
 %  escapechar=@,
   showstringspaces=false,
-  numbers=left
+  numbers=left,
+escapeinside={@}{@}, %reference to line number in text
+breaklines = true
 }
 
 \lstdefinestyle{black}{
@@ -241,6 +244,31 @@ height, collapsed, true, false%
   showstringspaces=false
 }
 
+\definecolor{lightgrey}{rgb}{0.9,0.9,0.9}
+
+\lstdefinestyle{eclipseboxed}{
+   escapeinside={@}{@},
+    basicstyle=\small\lstfontfamily,
+    emphstyle=\color{red}\bfseries, 
+    keywordstyle=\color{darkviolet}\bfseries,
+    commentstyle=\color{darkgreen},
+    stringstyle=\color{darkblue},
+    numberstyle=\color{darkgrey}\lstfontfamily,
+    emphstyle=\color{red},
+    backgroundcolor=\color{lightgrey},
+    morecomment=[s][\color{lightblue}]{/**}{*/},
+  showstringspaces=false,
+  numbers=left,%none,
+ emphstyle={[2]\color{blue}},
+ frame=shadowbox,
+firstnumber=auto,
+ rulesepcolor=\color{darkgrey},
+breaklines = true
+%showspaces=true,
+%showtabs=true,
+%tabsize=1
+}
+
 % use proper tt font that supports bold printing, e.g. by
 % \usepackage{courier}
 \lstdefinestyle{seminar}{

Doc/UserManual/ref.bib

+@article{Lazzari:vi0158,
+author = "Lazzari, R{\'{e}}mi",
+title = "{{\it IsGISAXS}: a program for grazing-incidence small-angle X-ray scattering analysis of supported islands}",
+journal = "Journal of Applied Crystallography",
+year = "2002",
+volume = "35",
+number = "4",
+pages = "406--421",
+month = "Aug",
+doi = {10.1107/S0021889802006088},
+url = {http://dx.doi.org/10.1107/S0021889802006088}
+}
+
+
+@article{PhysRevB.76.125411,
+  title = {Grazing-incidence small-angle x-ray scattering from dense packing of islands on surfaces: Development of distorted wave Born approximation and correlation between particle sizes and spacing},
+  author = {Lazzari, R\'emi and Leroy, Fr\'ed\'eric and Renaud, Gilles},
+  journal = {Phys. Rev. B},
+  volume = {76},
+  issue = {12},
+  pages = {125411},
+  numpages = {14},
+  year = {2007},
+  month = {Sep},
+  doi = {10.1103/PhysRevB.76.125411},
+  url = {http://link.aps.org/doi/10.1103/PhysRevB.76.125411},
+  publisher = {American Physical Society}
+}
+
+@Book{Pythonref,
+ author    = "Mark {Lutz}",
+ title     = "Python pocket reference",
+ publisher = "O'Reilly media",
+ year      =  2009,
+ edition   = "fourth edition"
+}
+
+@Book{Cppref,
+ author    = "Kyle {Loudon}",
+ title     = "C++ pocket reference",
+ publisher = "O'Reilly media",
+ year      =  2008
+}
+
+