diff --git a/Doc/UserManual/CMakeLists.txt b/Doc/UserManual/CMakeLists.txt
index 9139781e1a8bf56c192c09fb13e1c4639331f815..eebb2e9c002c32ab5193d732ce5f8709ba9ae43f 100644
--- a/Doc/UserManual/CMakeLists.txt
+++ b/Doc/UserManual/CMakeLists.txt
@@ -134,6 +134,43 @@ set(UM_IMAGES
     Figures/drawingDA.eps
     Figures/drawing2Dparacrystal.eps
     Figures/S_q_1Dparacrystal.eps
+    Figures/figure_ex001.eps
+    Figures/figure_ex002.eps
+    Figures/figure_ex003BA.eps
+    Figures/figure_ex003BASize.eps
+    Figures/figure_ex003DWBA.eps
+    Figures/figure_ex0041DDL.eps
+    Figures/figure_ex0042DDL.eps
+    Figures/figure_ex005Disorder1.eps
+    Figures/figure_ex005Disorder2.eps
+    Figures/figure_ex005Disorder3.eps
+    Figures/figure_ex005Disorder4.eps
+    Figures/figure_ex006Pyramids.eps
+    Figures/figure_ex006RotatedPyramids.eps
+    Figures/figure_ex007CoreShell.eps
+    Figures/figure_ex008CorrelatedRough.eps
+    Figures/figure_ex009CosRipple2DLat.eps
+    Figures/figure_ex009CosRippleNoInterf.eps
+    Figures/figure_ex009TriRipple2DLat.eps
+    Figures/figure_ex009TriRippleNoInterf.eps
+    Figures/figure_ex010Beamdiv.eps
+    Figures/BAgeometry_wide.jpg
+    Figures/fig_ex001.jpg	
+    Figures/fig_ex002.jpg		
+    Figures/fig_ex003BA.jpg	
+    Figures/fig_ex003BASize.jpg
+    Figures/fig_ex003DWBA.jpg
+    Figures/fig_ex005Dis1.jpg
+    Figures/fig_ex005Dis2.jpg
+    Figures/fig_ex005Dis3.jpg
+    Figures/fig_ex005Dis4.jpg
+    Figures/fig_ex006Pyramids.jpg
+    Figures/fig_ex006RotatedPyramids.jpg
+    Figures/fig_ex007Core.jpg
+    Figures/fig_ex008Rough.jpg
+    Figures/fig_ex009Cos.jpg
+    Figures/fig_ex009Tri.jpg
+    Figures/fig_ex010BeamDiv.jpg
 )
 
 
diff --git a/Doc/UserManual/Simulation.tex b/Doc/UserManual/Simulation.tex
index d42e5f5e8b6b62566c08dc82cbaf1b788596e6ce..6a2c8a196c8ecd38919f4f1ebf378407eb6c27c6 100755
--- a/Doc/UserManual/Simulation.tex
+++ b/Doc/UserManual/Simulation.tex
@@ -1,97 +1,97 @@
-\newpage
-\chapter{Simulation}  \SecLabel{Simulation}
-
-\section{General methodology}
-A simulation of GISAXS using \BornAgain\ consists of following steps:
-\begin{itemize}
-\item define materials by specifying name and refractive index,
-\item define embedded particles by specifying shape, size,
-   constituting material, interference function,
-\item define layers by specifying thickness, roughness, material,
-\item include particles in layers, specifying density, position, orientation, 
-\item assemble a multilayered sample,
-\item specify input beam and detector characteristics,
-\item run the simulation,
-\item save the simulated detector image.
-\end{itemize}
-
-\noindent
-We are planing to organize all these steps in a graphical user interface (GUI).
-For the time being, however, \BornAgain\ must be used via a \Code{C++} program or
-\Code{Python} scripts. In the following, we describe how to write a 
-\Code{Python} script which runs a \BornAgain\ simulation. For tutorials about this programming language, the users are referred to \cite{Lut09}.
-
-
-More information about the general software architecture and \BornAgain\ internal design are given in \SecRef{SoftwareArchitecture}.
-
-
-\section{Geometry of the sample}
-
-\noindent The geometry used to describe the sample is shown in \reffig{multil3d}. The $z$-axis is perpendicular to the sample's
-surface and pointing upwards. The $x$-axis  is perpendicular to the
-detector plane. The input and the
-scattered output beams are each characterized by two angles
-$\alpha_i$, $\phi_i$ and $\alpha_f$, $\phi_f$, respectively. Our choice of orientation for the
-angles $\alpha_i$ and $\alpha_f$ is so that they are positive as shown in \reffig{multil3d}. \\
-
-\begin{figure}[h]
-  \centering
-    \includegraphics[clip=, width=120mm]{Figures/multilayer3d3.eps}
-  \caption[Representation of the scattering geometry.]{Representation of the scattering geometry. $n_j$ is
-    the refractive index of layer $j$ and $\alpha_i$ and $\phi_i$ are the incident
-    angles of the wave propagating. $\alpha_f$ is the exit angle with respect to the sample's surface and
-$\phi_f$ is the scattering angle with respect to the scattering
-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
-materials they are made of. They have an infinite extension in the $x$ and $y$
-directions. And, except for roughness, their interfaces are plane and
-perpendicular to the $z$-axis. There is also no limitation to the
-number of layers that could be defined in \BornAgain. Note that the
-top and bottom layers are semi-infinite and they thicknesses are not defined.
-
-%\ImportantPoint{Remark:}{Order of layers: \\
-%When assembling the sample, the layers are defined from top to
-%bottom. So in most cases the first layer will be the air layer.}\\
-
-The nanoparticles are characterized by their form factors
-(\textit{i.e.} the Fourier transform of the shape function - see Appendix~\ref{appendixff} for a list of form factors implemented in \BornAgain) and the composing material. The number of input parameters for the form factor depends on the particle symmetry; it ranges from one parameter for a sphere (its radius) to three for an ellipsoid (its three main axis lengths).
-  
-By placing the particles
-inside or on top of a layer, we impose their vertical positions, whose
-values correspond to the bottoms of the particles. The in-plane distribution of particles is linked with the way the
-particles interfere with each other. It is therefore implemented
-when dealing with the interference function.
-
-%\ImportantPoint{Remark:}{Depth of particles\\
-%The vertical positions of particles in a layer are given in relative
-%coordinates. For the top layer, the bottom corresponds to
-%\texttt{depth}=0. But for all the other layers, it is the top of the
-%layer which corresponds to \texttt{depth}=0.}\\
-
-The complex refractive index associated with a layer or a particle is written as $n=1-\delta +i\beta$, with
-$\delta, \beta \in \mathbb{R}$. In our program, we input $\delta$ and
-$\beta$ directly.
-
-
-\noindent The input beam is assumed to be monochromatic without any
-spatial divergence.%\textbf{polarization term?}
-
-\paragraph{Units:} 
-
-By default the angles are expressed in radians and the lengths are given in
-nanometers.  But it is possible to use other units by
-specifying them right after the value of the corresponding
-parameter like, for example, \Code{20.0*micrometer}.
-
-
-
-
-\input{SimulationExamples}
-
-
+\newpage
+\chapter{Simulation}  \SecLabel{Simulation}
+
+\section{General methodology}
+A simulation of GISAXS using \BornAgain\ consists of following steps:
+\begin{itemize}
+\item define materials by specifying name and refractive index,
+\item define embedded particles by specifying shape, size,
+   constituting material, interference function,
+\item define layers by specifying thickness, roughness, material,
+\item include particles in layers, specifying density, position, orientation, 
+\item assemble a multilayered sample,
+\item specify input beam and detector characteristics,
+\item run the simulation,
+\item save the simulated detector image.
+\end{itemize}
+
+\noindent
+We are planing to organize all these steps in a graphical user interface (GUI).
+For the time being, however, \BornAgain\ must be used via a \Code{C++} program or
+\Code{Python} scripts. In the following, we describe how to write a 
+\Code{Python} script which runs a \BornAgain\ simulation. For tutorials about this programming language, the users are referred to \cite{Lut09}.
+
+
+More information about the general software architecture and \BornAgain\ internal design are given in \SecRef{SoftwareArchitecture}.
+
+
+\section{Geometry of the sample}
+
+\noindent The geometry used to describe the sample is shown in \reffig{multil3d}. The $z$-axis is perpendicular to the sample's
+surface and pointing upwards. The $x$-axis  is perpendicular to the
+detector plane. The input and the
+scattered output beams are each characterized by two angles
+$\alpha_i$, $\phi_i$ and $\alpha_f$, $\phi_f$, respectively. Our choice of orientation for the
+angles $\alpha_i$ and $\alpha_f$ is so that they are positive as shown in \reffig{multil3d}. \\
+
+\begin{figure}[h]
+  \centering
+    \includegraphics[clip=, width=120mm]{Figures/multilayer3d3.eps}
+  \caption[Representation of the scattering geometry.]{Representation of the scattering geometry. $n_j$ is
+    the refractive index of layer $j$ and $\alpha_i$ and $\phi_i$ are the incident
+    angles of the wave propagating. $\alpha_f$ is the exit angle with respect to the sample's surface and
+$\phi_f$ is the scattering angle with respect to the scattering
+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
+materials they are made of. They have an infinite extension in the $x$ and $y$
+directions. And, except for roughness, their interfaces are plane and
+perpendicular to the $z$-axis. There is also no limitation to the
+number of layers that could be defined in \BornAgain. Note that the
+thickness of the top and bottom layer are not defined.
+
+%\ImportantPoint{Remark:}{Order of layers: \\
+%When assembling the sample, the layers are defined from top to
+%bottom. So in most cases the first layer will be the air layer.}\\
+
+The nanoparticles are characterized by their form factors
+(\textit{i.e.} the Fourier transform of the shape function - see Appendix~\ref{appendixff} for a list of form factors implemented in \BornAgain) and the composing material. The number of input parameters for the form factor depends on the particle symmetry; it ranges from one parameter for a sphere (its radius) to three for an ellipsoid (its three main axis lengths).
+  
+By placing the particles
+inside or on top of a layer, we impose their vertical positions, whose
+values correspond to the bottoms of the particles. The in-plane distribution of particles is linked with the way the
+particles interfere with each other. It is therefore implemented
+when dealing with the interference function.
+
+%\ImportantPoint{Remark:}{Depth of particles\\
+%The vertical positions of particles in a layer are given in relative
+%coordinates. For the top layer, the bottom corresponds to
+%\texttt{depth}=0. But for all the other layers, it is the top of the
+%layer which corresponds to \texttt{depth}=0.}\\
+
+The complex refractive index associated with a layer or a particle is written as $n=1-\delta +i\beta$, with
+$\delta, \beta \in \mathbb{R}$. In our program, we input $\delta$ and
+$\beta$ directly.
+
+
+\noindent The input beam is assumed to be monochromatic without any
+spatial divergence.\\ %\textbf{polarization term?}
+
+\paragraph{Units:} 
+
+By default the angles are expressed in radians and the lengths are given in
+nanometers.  But it is possible to use other units by
+specifying them right after the value of the corresponding
+parameter like, for example, \Code{20.0*micrometer}.
+
+
+
+
+\input{SimulationExamples}
+
+
diff --git a/Doc/UserManual/Theory.tex b/Doc/UserManual/Theory.tex
index 2425239911c042bf7b333765a34969fb8bc964a9..d13ea23a81f37655372b30119f1a89177882d188 100755
--- a/Doc/UserManual/Theory.tex
+++ b/Doc/UserManual/Theory.tex
@@ -298,11 +298,11 @@ def get_sample():
     |interference = InterferenceFunction1DLattice(lattice_params)|
     |pdf = FTDistribution1DCauchy(200./2./M_PI*nanometer)|
     |interference.setProbabilityDistribution(pdf)|
-    |particle_decoration.addInterferenceFunction(interference)|
+    |particle_layout.addInterferenceFunction(interference)|
 
     # air layer with particles and substrate form multi layer
     air_layer = Layer(m_air)
-    air_layer.setDecoration(particle_decoration)
+    air_layer.setLayout(particle_layout)
     substrate_layer = Layer(m_substrate, 0)
 
     multi_layer = MultiLayer()
@@ -430,7 +430,7 @@ def get_simulation():
     Create and return GISAXS simulation with beam and detector
     """
     simulation = Simulation()
-    simulation.setDetectorParameters(100, 0.0*degree, 2.0*degree, 100, 0.0*degree, 2.0*degree)
+    simulation.setDetectorParameters(100, 0.0*degree, 2.0*degree, 100, 0.0*degree, 2.0*degree, True)
     simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree)
     |sim_params= SimulationParameters()|
     |sim_params.me_if_approx = SimulationParameters.LMA|
@@ -487,7 +487,7 @@ Probability distribution functions have to be defined. As the two-dimensional pa
     interference = InterferenceFunction2DParaCrystal.createHexagonal(30.0*nanometer,0.0, 40.0*micrometer, 40.0*micrometer)|
     pdf = FTDistribution2DCauchy(1.0*nanometer, 1.0*nanometer)
     interference.setProbabilityDistributions(pdf, pdf)
-    particle_decoration.addInterferenceFunction(interference)
+    particle_layout.addInterferenceFunction(interference)
 \end{lstlisting}
 
 \begin{figure}[h]
@@ -635,7 +635,7 @@ In this configuration, the particles are sitting on top of a substrate layer, in
 F_{\rm{DWBA}}(q_{\parallel}, k_{i,z}, k_{f,z}) &= F_{\rm{BA}}(q_{\parallel}, k_{i,z}-k_{f,z})+ R_i F_{\rm{BA}}(q_{\parallel}, -k_{i,z}-k_{f,z}) \nonumber \\
 &+ R_f F_{\rm{BA}}(q_{\parallel}, k_{i,z}+k_{f,z}) + R_i R_f F_{\rm{BA}}(q_{\parallel},-k_{i,z}+k_{f,z}), \label{eq:dwbaair}
 \end{align}
-where $q_{\parallel}$ is the component of the scattering beam in the plane of the interface ($\vect{q}=\vect{k}_i-\vect{k}_f$), $k_{i,z}$ and $k_{f,z}$ are the z-component of the incident and scattered beam, respectively. $R_i$, $R_f$ are the reflection coefficients in incidence and reflection. They are defined as\\ $R=\dfrac{k_z+\sqrt{n_s^2k_0^2-|k_{\parallel}|^2}}{k_z-\sqrt{n_s^2 k_0^2-|k_{\parallel}|^2}}$, where $n_s=1-\delta_s -i \beta_s$ is the refractive index of the substrate, $k_0$ is the wavelength in vacuum ($2\pi /\lambda$), $k_z$ and $k_{\parallel}$ are the $z$-component and the in-plane component of $\vect{k}_i$ or $\vect{k}_f$. \\
+where $q_{\parallel}$ is the component of the scattering beam in the plane of the interface ($\vect{q}=\vect{k}_i-\vect{k}_f$), $k_{i,z}$ and $k_{f,z}$ are the z-component of the incident and scattered beam, respectively. $R_i$, $R_f$ are the reflection coefficients in incidence and reflection. They are defined as\\ $R=\dfrac{k_z+\sqrt{n_s^2k_0^2-|k_{\parallel}|^2}}{k_z-\sqrt{n_s^2 k_0^2-|k_{\parallel}|^2}}$, where $n_s=1-\delta_s +i \beta_s$ is the refractive index of the substrate, $k_0$ is the wavelength in vacuum ($2\pi /\lambda$), $k_z$ and $k_{\parallel}$ are the $z$-component and the in-plane component of $\vect{k}_i$ or $\vect{k}_f$. \\
 
 \ImportantPoint{Remark:}{If the particles are sitting on a multilayered system, the expression of the form factor in the DWBA is obtained by replacing the Fresnel coefficient by the corresponding coefficients of the underlying layers \cite{Parr54,BoWo99}.}
 
@@ -817,7 +817,7 @@ def get_sample():
 \section{More complicated particles' shapes} 
 \BornAgain\ also offers the possibility to simulate more complicated shapes of particles by combining those listed in Table~\ref{tab:formfactors}. 
 
-\subsection{Core-shell particles}
+\subsection{Core-shell particles} \label{subsec:CoreShell}
  To generate a core-shell particle, the combination is performed using the following command:\\
 \Code{ParticleCoreShell(shell\_particle, core\_particle, relative\_core\_position)},\\
 where \Code{shell\_particle} and \Code{core\_particle} are the outer and inner parts of the core-shell particle, respectively. They refer to one of the form factors defined previously and to an associated material. For example, for the outer part,\\ \Code{shell\_particle=Particle(material\_shell, outer\_form\_factor)},\\ where \Code{material\_shell} is the material of the shell and \Code{outer\_form\_factor} is the shape of the outer part (cf. listing~\ref{lst:cshellsample}). \\ \Code{relative\_core\_position} defines the position of the inner shape with respect to the outer one; it is defined with respect to the centre of the base of the particular form factor. An example in fig.~\ref{fig:coreshell} shows a core shell particle made of a box for the outer part and of a shifted pyramidal shape for the inner one.\\
diff --git a/Doc/UserManual/UserManual.pdf b/Doc/UserManual/UserManual.pdf
index 8f956bd665ecd619c1786a63907c693f256530d3..04739c4c62576e4de7115dafffe5c094fb69f776 100644
Binary files a/Doc/UserManual/UserManual.pdf and b/Doc/UserManual/UserManual.pdf differ
diff --git a/Doc/UserManual/UserManual.tex b/Doc/UserManual/UserManual.tex
index 30b3abde5f7b7f6e9d7ec2a2fa25f02cf20b9a8e..5bdc8b14ac216bddc853ccfc581283b234f35329 100755
--- a/Doc/UserManual/UserManual.tex
+++ b/Doc/UserManual/UserManual.tex
@@ -79,6 +79,22 @@
 \usepackage{longtable,tabulary,tabularx}
 \usepackage{pdflscape}
 
+\usepackage{multirow}
+
+
+\usetikzlibrary{matrix,positioning,decorations.pathreplacing,calc}
+
+\newcommand{\ntikzmark}[2]{#2\thinspace\tikz[overlay,remember picture,baseline=(#1.base)]{\node[inner sep=0pt] (#1) {};}}
+
+\newcommand{\makebrace}[3]{%
+    \begin{tikzpicture}[overlay, remember picture]
+        \draw [decoration={brace,amplitude=0.6em},decorate]
+        let \p1=(#1), \p2=(#2) in
+        ({max(\x1,\x2)}, {\y1+1.5em}) -- node[right=0.6em] {#3} ({max(\x1,\x2)}, {\y2});
+    \end{tikzpicture}
+}
+
+
 %-------------------------------------------------------------------------------
 %	TABULARY AND LONGTABLE http://tex.stackexchange.com/questions/78075/multi-page-with-tabulary
 %-------------------------------------------------------------------------------
@@ -241,9 +257,8 @@ Forschungszentrum J\"ulich GmbH
 \input{AppendixListings}
 \input{theoryapp}
 \input{ff}
-%\input{interferences}
-%benchmarking - comparison with Isgisaxs
-%\input{AppendixPhysics}
+%\input{AppendixPythonEx}
+
 
 \bibliographystyle{switch}
 \bibliography{jw7}
diff --git a/Doc/UserManual/ff.tex b/Doc/UserManual/ff.tex
index 062b852f50b0812438433946f3f80b5e799ce373..a98c074b03e5a24c3aeeaec84a074366f368aef1 100755
--- a/Doc/UserManual/ff.tex
+++ b/Doc/UserManual/ff.tex
@@ -1,1421 +1,1421 @@
-%\newpage
-\chapter{Form factors} \label{appendixff}
-In \BornAgain\ the expression of the form factor has been implemented in the Born approximation. Each of them is defined as
-\begin{equation*}
-F(\mathbf{q})=\int_V \exp (i\mathbf{q}.\mathbf{r}) d^3 \mathbf{r},
-\end{equation*}
-where $V$ is the volume of the particle's shape,
-$\mathbf{q}=\mathbf{k}_i - \mathbf{k}_f$ is the scattering vector with
-$\mathbf{k}_f$ and $\mathbf{k}_i$ the scattered and incident wave
-vector, respectively. The Distorted Wave Born Approximation can be taken into account as it has been explained in \SecRef{sect:dwba}.\\
-
-The particle's shape is parametrized in a cartesian frame, with its
-$z$-axis pointing upwards and its origin at the center of the bottom
-of the particle: $\mathbf{r}=(x,y,z)$. In the followings, a schematic view will depict this layout for each
-form factor.\\
-
-
-All form factors have been implemented with complex scattering vectors
-in order to take any material absorption into account.\\
-
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Box} \SecLabel{Box} 
-
-\paragraph{Real-space geometry}\mbox{}\\
-This shape is a rectangular cuboid as
-shown in fig.~\ref{fig:box}. 
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Box2dxz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Box2dxy}}
-\hfill
-\caption{Sketch of a Box.}
-\label{fig:box}
-\end{figure}
-
-\FloatBarrier
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item length of the base $L$,
-\item width of the base $W$,
-\item height  $H$.
-\end{itemize}
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V= LWH$,
-\item particle surface seen from above $S = LW$.
-%\item radius of gyration
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-\begin{equation*}
-F(\mathbf{q},L,W,H)= L W H\exp\left(i q_z \frac{H}{2}\right) \sinc\left(q_x \frac{L}{2}\right)
-\sinc\left(q_y \frac{W}{2}\right) \sinc\left(q_z \frac{H}{2}\right),
-\end{equation*}
-   
-where $\sinc(x)=\sin(x)/x$ is the cardinal sine.
-
-\paragraph{Syntax:} \Code{FormFactorBox(length, width, height)}
-
-\newpage
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:FFBoxEx} shows the normalized intensity
-$|F|^2/V^2$, computed with $L=20$~nm, $W=16$~nm, and $H=13$~nm:
-
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffbox}
-\end{center}
-\caption{Normalized intensity for the form factor of a Box plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$) and computed with \Code{FormFactorBox(20.*nanometer, 16.*nanometer, 13.*nanometer)}.}
-\label{fig:FFBoxEx}
-\end{figure}
-
-\FloatBarrier
-%\subsection{References}
-%\BornAgain\ uses a different convention for the parameters in comparison with \Code{IsGISAXS}, where the half length
-%values are used (see fig.~\ref{box}).
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Prism3} \SecLabel{Prism3}
-
-\paragraph{Real-space geometry}\mbox{}\\
-This shape is a triangular prism, whose base is an equilateral
-triangle as shown in fig.~\ref{fig:prism3}.
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Prism32dxz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Prism32dxy}}
-\hfill
-\caption{Sketch of a Prism3.}
-\label{fig:prism3}
-\end{figure}
-
-\FloatBarrier
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item length $L$ of one side of the base, 
-\item height $H$.
-\end{itemize}
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V= \dfrac{\sqrt{3}}{4} H L^2$,
-\item particle surface seen from above $S =\dfrac{\sqrt{3}}{4}L^2$.
-
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-\begin{align*}
-F(\mathbf{q},L, H) &= \frac{2 \sqrt{3}}{q_x^2-3q_y^2}  \exp\left(-i q_y\frac{L}{2\sqrt{3}}\right)\left[\exp\left(i \sqrt{3} q_y \frac{L}{2} \right)-\cos\left(q_x \frac{L}{2}\right)-i \sqrt{3} q_y \frac{L}{2} \sinc\left(q_x \frac{L}{2}\right) \right] \\
-  &
-\times  H \sinc\left(q_z \frac{H}{2} \right) \exp\left(i q_z \frac{H}{2}\right),
-\end{align*}
-where $\sinc(x)=\sin(x)/x$ is the cardinal sine.
-
-\paragraph{Syntax:} \Code{FormFactorPrism3(length, height)}
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:FFprism3Ex} shows the normalized intensity
-$|F|^2/V^2$, computed with $L=10$~nm and \mbox{$H=13$~nm.}
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffprism3}
-\end{center}
-\caption{Normalized intensity for the form factor of a Prism3
- plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$) and
-  computed with \Code{FormFactorPrism3(10.*nanometer, 13.*nanometer)}.}
-\label{fig:FFprism3Ex}
-\end{figure}
-
-%\subsection{References}
-%In the $x,y$ plane , we use the full side length of the triangular
-%base instead of  half as implemented in \Code{IsGISAXS}: $L= 2
-%R_{\rm{\Code{IsGISAXS}}}$.
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Tetrahedron}  \SecLabel{Tetrahedron} 
- 
-\paragraph{Real-space geometry}\mbox{}\\
-This shape is a truncated tetrahedron as shown in fig.~\ref{fig:tetrahedron}.
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Tetrahedron2dxz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Tetrahedron2dxy}}
-\hfill
-\caption{Sketch of a Tetrahedron. The implementation of this shape uses angle
-  $\alpha$, which is linked to $\beta$ via $\tan \alpha = 2 \tan 
-  \beta$. $\alpha$ is measured along one of the base lines and $\beta$
-  at one of the base vertices.}
-\label{fig:tetrahedron}
-\end{figure}
-
-\FloatBarrier
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item length of one side of the equilateral triangular base $L$,
-\item height $H$,
-\item angle $\alpha$ is the angle between the base and the
-  side faces, taken in the middle of the base lines.
-\end{itemize}
-
-\paragraph{Restrictions on the parameters:} 
-$\dfrac{H}{L}< \dfrac{\tan{\alpha}}{2\sqrt{3}}$.
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V= \dfrac{\tan(\alpha) L^3}{24} \left[1- \left(1 -
-  \dfrac{2\sqrt{3} H}{L \tan(\alpha)} \right)^3\right]$,
-\item particle surface seen from above $S =\dfrac{\sqrt{3}}{4}L^2$.
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-
-\begin{align*}
-&F(\mathbf{q}, L, H, \alpha)=\frac{\sqrt{3}H}{q_x (q_x^2-3q_y^2)}
-\exp\left(i\frac{q_z L}{2\tan (\alpha)\sqrt{3}}\right) \times \\
-&\Big\{2q_x \exp(iq_3 D)\sinc(q_3 H) - (q_x +\sqrt{3}q_y)
-\exp(iq_1 D)\sinc(q_1 D) -(q_x-\sqrt{3}q_y)\exp(-iq_2
-D)\sinc(q_2 H) \Big\}, 
-\end{align*}
-with $\sinc(x)=\sin(x)/x$,
-\begin{equation*}
-q_1  =\frac{1}{2}\left[\frac{q_x\sqrt{3} -q_y}{\tan \alpha}-q_z \right],
-\quad q_2 = \frac{1}{2}\left[\frac{q_x\sqrt{3} +q_y}{\tan \alpha}+q_z
-\right], \quad 
-q_3 = \frac{q_y}{\tan \alpha} -\frac{q_z}{2}, \quad D = \frac{L \tan \alpha}{\sqrt{3}} -H.
-\end{equation*}
-
-\paragraph{Syntax:} \Code{FormFactorTetrahedron(length, height, alpha)}
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:FFtetrahEx} shows the normalized intensity
-$|F|^2/V^2$, computed with $L=15$~nm, $H=6$~nm and $\alpha =60
-^{\circ}$.
-
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figfftetrahedron}
-\end{center}
-\caption{Normalized intensity for the form factor of a Tetrahedron
-  plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$) and
-  computed with \Code{FormFactorTetrahedron(15.*nanometer, 6.*nanometer, 60.*degree)}.}
-\label{fig:FFtetrahEx}
-\end{figure}
-
-%\FloatBarrier
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Prism6} \SecLabel{Prism6}
-
-\paragraph{Real-space geometry}\mbox{}\\
-This shape is an hexagonal prism (see fig.~\ref{fig:prism6}).
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Prism62dxz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Prism62dxy}}
-\hfill
-\caption{Sketch of a Prism6.}
-\label{fig:prism6}
-\end{figure}
-
-\FloatBarrier
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item radius of the hexagonal base $R$,
-\item height $H$.
-\end{itemize}
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V = \dfrac{3\sqrt{3}}{2}H R^2$,
-\item particle surface seen from above $S =\dfrac{3\sqrt{3}R^2}{2}$.
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-\begin{align*}
-F(\mathbf{q}, R, H) &= \frac{4H\sqrt{3}}{3q_y^2 - q_x^2}
-\sinc\left(q_z\frac{H}{2}\right) \exp\left(-i q_z\frac{ H}{2}\right)\times\\
-&\left\{\frac{3q_y^2R^2}{4} \sinc\left(\frac{q_x
-  R}{2}\right)\sinc\left(\frac{\sqrt{3}q_yR }{2}\right)+ \cos(q_x R)-\cos\left(q_y
-\frac{\sqrt{3}R}{2}\right) \cos\left(\frac{q_x R}{2}\right)\right\},
-\end{align*}
-with $\sinc(x)=\sin(x)/x$.
-
-\paragraph{Syntax:} \Code{FormFactorPrism6(radius, height)} 
-
-\newpage
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:FFprism6Ex} shows the normalized intensity
-$|F|^2/V^2$, computed with $R=5$~nm and \mbox{$H=11$~nm.}
-
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffprism6}
-\end{center}
-\caption{Normalized intensity for the form factor of a Prism6 plotted against ($q_y$, $q_z$) and ($q_x$, $q_y$) and computed with \Code{FormFactorPrism6(5.*nanometer, 11.*nanometer)}.}
-\label{fig:FFprism6Ex}
-\end{figure}
-
-%\FloatBarrier
-
-%\subsection{References}
-%The hexagonal base is parametrized in the different way compared with
-%\Code{IsGISXAXS}. In \BornAgain\, we use $R = 2/\sqrt{3}R_{\text{\Code{IsGiSaXs}}}$.
-%A factor $H$ is missing in the expression of the form factor given in
-%\Code{IsGISAXS}'s manual. 
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Cone6} \SecLabel{Cone6} 
-
-\paragraph{Real-space geometry}\mbox{}\\
-It is a truncated hexagonal pyramid (see fig.~\ref{fig:cone6}). 
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Cone62dxz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Cone62dxy}}
-\hfill
-\caption{Sketch of a Cone6.  The implementation of this shape uses angle
-  $\alpha$, which is linked to $\beta$ via $\tan \alpha = \dfrac{2}{\sqrt{3}} \tan 
-  \beta$. $\alpha$ is measured along one of the base lines and $\beta$
-  at one of the base vertices.}
-\label{fig:cone6}
-\end{figure}
-
-\FloatBarrier
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item radius of the regular hexagonal base $R$,
-\item height $H$,
-\item angle $\alpha$ is considered between one of the side faces and
-  the middle of a base length. 
-\end{itemize}
-
-\paragraph{Restrictions on the parameters:} 
-$\dfrac{2H}{\sqrt{3}R}< \tan{\alpha}$.
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V = \dfrac{3}{4} \tan(\alpha) R^3 \left[
-            1 - \left(1- \dfrac{2H}{ \tan(\alpha) R\sqrt{3}}\right)^3
-            \right]$,
-\item  particle surface seen from above $S =\dfrac{3\sqrt{3}R^2}{2}$.
-\end{itemize}
-
-\paragraph{Expression of the form factor}\mbox{}\\
-The
-calculation can be derived from ``Prism6'' (\SecRef{Prism6}) by
-considering a side length varying with the vertical position:
-
-\begin{align*}
-F(\mathbf{q}, R, H, \alpha) = \frac{4\sqrt{3}}{3q_y ^2 - q_x^2}\int_0 ^H &\exp(iq_z z)
-\Big[\frac{3}{4}R_z^2q_y^2 \sinc\left(\frac{q_xR_z}{2}\right)\sinc\left(\frac{\sqrt{3}q_y
-R_z}{2}\right)\\
-&+\cos(q_xR_z)-\cos\left(\frac{\sqrt{3}q_y R_z}{2}\right)\cos\left(\frac{q_xR_z}{2}\right) \Big]dz
-\end{align*}
-with $R_z=R-\dfrac{2z}{\sqrt{3}\tan(\alpha)}$ and $\sinc(x)=\sin(x)/x$.
-
-\paragraph{Syntax:} \Code{FormFactorCone6(radius,height, alpha)} 
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:FFCone6Ex} shows the normalized intensity
-$|F|^2/V^2$, computed with $R=10$~nm, $H=13$~nm, and
-$\alpha=60^{\circ}$.
-
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffcone6}
-\end{center}
-\caption{Normalized intensity for the form factor of a Cone6 plotted against ($q_y$, $q_z$) and ($q_x$, $q_y$) and computed with \Code{FormFactorCone6(10.*nanometer,13.*nanometer, 60.*degree)}.}
-\label{fig:FFCone6Ex}
-\end{figure}
-
-%\FloatBarrier
-
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Pyramid}\SecLabel{Pyramid}
-
-\paragraph{Real-space geometry}\mbox{}\\
-This shape is a  truncated pyramid with a square base as shown in fig.~\ref{fig:pyramid}.
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Pyramid2dxz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Pyramid2dxy}}
-\hfill
-\caption{Sketch of a Pyramid}
-\label{fig:pyramid}
-\end{figure}
-
-\FloatBarrier
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item length of one side of the square base $L$,  
-\item height $H$,
-\item  $\alpha$ is the angle between the base and the
-  side faces, taken in the middle of the base lines.
-\end{itemize}
-
-\paragraph{Restrictions on the parameters:}  $\dfrac{2H}{L} < \tan(\alpha)$.
-
-\paragraph{Properties:}
-\begin{itemize}
-\item  volume $V = \dfrac{1}{6} \tan(\alpha) L^3\left[ 1
-             - \left(1 - \dfrac{2H}{\tan(\alpha)L}\right)^3 \right],$
-\item particle surface seen from above $S = L^2$.
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-\begin{align*}
-&F(\mathbf{q},L, H, \alpha) =
-\frac{H}{q_x q_y} \times \nonumber \\ &\left\{ K_1 \cos\left[
-  (q_x-q_y)\frac{L}{2} \right] + K_2 \sin\left[ (q_x-q_y)\frac{L}{2} \right]
-- K_3 \cos\left[ (q_x+q_y) \frac{L}{2} \right] - K_4 \sin\left[ (q_x+q_y)\frac{L}{2} \right]\right\},
-\end{align*}
-with $\sinc(x)=\sin(x)/x$,
-\begin{align*}
-       q_1 &=\frac{1}{2}\Big[\frac{q_x-q_y}{\tan(\alpha)} + q_z\Big],\quad       q_2 =\frac{1}{2}\Big[\frac{q_x-q_y}{\tan(\alpha)} - q_z\Big]\\
-        q_3 &=\frac{1}{2}\Big[\frac{q_x+q_y}{\tan(\alpha)} + q_z\Big],\quad       q_4 =\frac{1}{2}\Big[\frac{q_x+q_y}{\tan(\alpha)} - q_z\Big]\\
-        K_1 &= \sinc(q_1 H)\exp(i q_1 H)  + \sinc(q_2 H) \exp(-i q_2 H)\\
-        K_2 &= -i \sinc(q_1 H) \exp(i q_1 H) +i \sinc(q_2 H) \exp(-i q_2 H)\\
-        K_3 &= \sinc(q_3 H) \exp(i q_3 H)    + \sinc(q_4 H) \exp(-i q_4 H)\\
-        K_4 &= -i \sinc(q_3 H) \exp(i q_3 H) + i \sinc(q_4 H) \exp(-i q_4 H) 
-   \end{align*}
-
-\paragraph{Syntax:}  \Code{FormFactorPyramid(length, height, alpha)}
-
-\paragraph{Examples}
-Figure~\ref{fig:FFPyramidEx} shows the normalized intensity
-$|F|^2/V^2$, computed with $L=18$~nm, $H=13$~nm and
-$\alpha=60^{\circ}$.
-
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffpyramid}
-\end{center}
-\caption{Normalized intensity for the form factor of a
-  pyramid plotted against ($q_y$, $q_z$) and  
-  ($q_x$, $q_y$) and computed with  \Code{FormFactorPyramid(18.*nanometer, 13.*nanometer, 60.*degree)}.}
-\label{fig:FFPyramidEx}
-\end{figure}
-
-%\FloatBarrier
-%\subsection{References}
-%The output of equation~(\ref{eq:ffpyramid}) agrees with the \lq\lq
-%pyramid\rq\rq ~form factor of \IsGISAXS~\cite{Laz02}.
-%In \BornAgain\, the base of the pyramid is characterized by the full
-%length of one of its side and not by half this value: $L=2R_{\rm{\Code{IsGISXAXS}}}$. 
-%Pyramid: problem with signs of K2 and K4
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Anisotropic pyramid} \SecLabel{AnisoPyramid} 
-
-\paragraph{Real-space geometry}\mbox{}\\
-This shape is a truncated right pyramid with a rectangular base as
-shown in fig.~\ref{fig:anisopyramid}.
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/AnisoPyramid2dxz.eps}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/AnisoPyramid2dxy.eps}}
-\hfill
-\caption{Sketch of an Anisotropic Pyramid.}
-\label{fig:anisopyramid}
-\end{figure}
-
-\FloatBarrier
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item full length of the base $L$,
-\item full width of the base $W$,
-\item height $H$,
-\item $\alpha$ is the angle between the base and the
-  side faces, taken in the middle of the base lines.
-\end{itemize}
-
-\paragraph{Restrictions on the parameters:} $\dfrac{2H}{L}< \tan(\alpha)$ and $\dfrac{2H}{W}< \tan(\alpha)$.
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V= H \Big[LW - \dfrac{(L + W)H}{\tan(\alpha)}
-   + \dfrac{4}{3} \dfrac{H^2}{\tan^2(\alpha)}\Big]$,
-\item particle surface seen from above $S = LW$.
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-\begin{align*}
-&F(\mathbf{q}, L, W, H, \alpha)=
-\frac{H}{q_xq_y} \times \\
-&\Big\{
-K_1\cos\Big(q_x \frac{L}{2} -q_y \frac{W}{2}\Big)+  K_2 \sin \Big (q_x
-\frac{L}{2}- q_y \frac{W}{2}\Big) - K_3 \cos \Big (q_x \frac{L}{2} +q_y \frac{W}{2}\Big)-
-K_4 \sin \Big (q_x \frac{L}{2} + q_y \frac{W}{2}\Big)
-\Big\},
-\end{align*}
-with $\sinc(x)=\sin(x)/x$,
-\begin{align*}
-K_1 &= \exp(-i q_2 H) \sinc(q_2 H) + \exp(iq_1 H) \sinc(q_1 H) \\
-K_2 &= i \exp(-iq_2 H) \sinc(q_2 H) -i \exp(iq_1 H) \sinc(q_1 H) \\
-K_3 &= \exp(-iq_4 H) \sinc(q_4 H) + \exp(iq_3 H) \sinc(q_3 H) \\
-K_4 &= i \exp(i q_4 H) \sinc(q_4 H) -i \exp(iq_3 H) \sinc(q_3 H)\\
-q_1 &= \frac{1}{2}\left[\frac{q_x -q_y}{\tan \alpha} +q_z \right],\quad q_2 = \frac{1}{2}\left[\frac{q_x -q_y}{\tan \alpha} -q_z \right]\\
-q_3 &= \frac{1}{2}\left[\frac{q_x +q_y}{\tan \alpha} +q_z \right] , \quad q_4 = \frac{1}{2}\left[\frac{q_x +q_y}{\tan \alpha} -q_z \right]
-\end{align*}
-
-\paragraph{Syntax:} \Code{FormFactorAnisoPyramid(length, width, height, alpha)}
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:FFAnisoPyramidEx} shows the normalized intensity
-$|F|^2/V^2$, computed with $L=20$~nm, $W=16$~nm, $H=13$~nm, and
-$\alpha=60^{\circ}$.
-
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffanisopyramid}
-\end{center}
-\caption{Normalized intensity for the form factor of an anisotropic
-  pyramid $|F|^2/V^2$, plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$) and computed with \Code{FormFactorAnisoPyramid(20.*nanometer, 16.*nanometer, 60.*degree)}.}
-\label{fig:FFAnisoPyramidEx}
-\end{figure}
-
-%\FloatBarrier
-
-%\subsection{References}
-%Like in \Code{IsGISAXS}, the base angle $\alpha$ is the same for both unequal
-%side. This means that a full anisotropic pyramid is not a limit case. \\
-%But \BornAgain\ uses a different convention of the parameters relative
-%to the base. We input the full length and width instead of half values.
-%Condition on the parameters: 
-%Should not it be: H/R < tan(alpha) and  H/W < tan(alpha) instead of H/R < tan(alpha) and  
-%W/R < tan(alpha) where H is the height and R, W the side-lengths of the rectangular base?
-
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Cuboctahedron} \SecLabel{Cuboctahedron} 
-
-\paragraph{Real-space geometry}\mbox{}\\
-It is a combination of two pyramids with square bases, as shown in fig.~\ref{fig:cuboctahedron}: the bottom one
-is upside down with an height $H$ and the top one has the opposite
-orientation (the standard one) and an height $r_H \times H$.
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Cuboctahedron2dxz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Cuboctahedron2dxy}}
-\hfill
-\caption{Sketch of a Cuboctahedron.}
-\label{fig:cuboctahedron}
-\end{figure}
-
-\FloatBarrier
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item length of the shared square base $L$,
-\item height $H$,
-\item height\_ratio $r_H$,
-\item $\alpha$ is the angle between the base and the
-  side faces, taken in the middle of the base lines (see
-  fig.~\ref{fig:pyramid} in \SecRef{Pyramid}).
-\end{itemize}
-
-\paragraph{Restrictions on the parameters:} $\dfrac{2H}{L}< \tan(\alpha)$ and $\dfrac{2r_HH}{L}< \tan(\alpha)$.
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $ V= \dfrac{1}{6} \tan(\alpha)L^3 \Big[ 2
-         - \Big(1 - \dfrac{2H }{L\tan(\alpha)} \Big)^3
-           - \Big(1 - \dfrac{2 r_H
-             H}{L\tan(\alpha) }\Big)^3\Big]$,
-\item particle surface seen from above $S =L^2$.
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-\begin{equation*}
-F(\mathbf{q}, L, H, r_H, \alpha)=\exp(iq_z
-H)\Big[F_{\rm{Pyramid}}(q_x,q_y, q_z, L, r_H H,
-\alpha)+F_{\rm{Pyramid}}(q_x, q_y, -q_z, L, H, \alpha))\Big]
-\end{equation*}
-
-\paragraph{Syntax:} \Code{FormFactorCuboctahedron(length, height, height\_ratio,
-  alpha)}
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:FFcuboctahEx} shows the normalized intensity $|F|^2/V^2$, computed with $L=20$~nm, $H=13$~nm, $r_H=0.7$, and $\alpha=60^{\circ}$.
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffcuboctah}
-\end{center}
-\caption{Normalized intensity for the form factor of a cuboctahedron plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$) and computed with \Code{FormFactorCuboctahedron(20.*nanometer, 13.*nanometer, 0.7, 60.*degree)}.}
-\label{fig:FFcuboctahEx}
-\end{figure}
-
-%\FloatBarrier
-
-%\subsection{References}
-%In comparison with \Code{IsGISAXS}, as for the  form factor of a  Pyramid,
-%we use the full length of a side of the square base:
-%$L=2R_{\rm{\Code{IsGISAXS}}}$. 
-
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
-\section{Cylinder} \SecLabel{Cylinder}
- 
-\paragraph{Real-space geometry}\mbox{}\\
-This shape is a right circular cylinder (see fig.~\ref{fig:cylinder}).
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Cylinder2dxz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Cylinder2dxy}}
-\hfill
-\caption{Sketch of a Cylinder.}
-\label{fig:cylinder}
-\end{figure}
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item radius of the circular base $R$, 
-\item height $H$.
-\end{itemize}
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V = \pi R^2 H$,
-\item particle surface seen from above $S=\pi R^2$.
-
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-  \begin{equation*}
-F(\mathbf{q},R, H)=  2\pi
- R^2 H  \sinc\left(q_ z \frac{H}{2}\right) \exp\left(i q_ z \frac{H}{2}\right) \frac{J_1(q_{\parallel} R )}{q_{\parallel} R },
- \end{equation*}
-with $q_{\parallel}=\sqrt{q_x^2+q_y^2}$ and $J_1(x)$ is the first order
-Bessel function of the first kind \cite{AbSt64}.
-
-\paragraph{Syntax:} \Code{FormFactorCylinder(radius, height)}
-
-\newpage
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:FFcylinderEx} shows the normalized intensity
-$|F|^2/V^2$, computed with $R=8$~nm and \mbox{$H=16$~nm.}
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffcylinder}
-\end{center}
-\caption{Normalized intensity for the form factor of a cylinder plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$.) It
-has been  computed with \Code{FormFactorCylinder(8.*nanometer, 16.*nanometer)}.}
-\label{fig:FFcylinderEx}
-\end{figure}
-%\FloatBarrier
-
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Ellipsoidal cylinder} \SecLabel{EllipsoidalCylinder} 
-
-\paragraph{Real-space geometry}\mbox{}\\
-This is a cylinder whose cross section is an ellipse.
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/EllipsoidalCylinder2dxz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/EllipsoidalCylinder2dxy}}
-\hfill
-\caption{Sketch of an Ellipsoidal Cylinder.}
-\label{fig:ellipscylinder}
-\end{figure}
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item $r_a$ = half length of the ellipse main axis parallel to $x$,
-\item$r_b$ = half length of the ellipse main axis parallel to $y$, 
-\item height $H$.
-\end{itemize}
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V = \pi r_a r_bH$,
-\item particle surface seen from above $S = r_a r_b$.
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-The total form factor is given by 
-\begin{equation*}
-F(\mathbf{q},R,W,H) = 2\pi r_a r_b H \exp\left(i\frac{q_z
-  H}{2}\right)\sinc\left(\frac{q_z H}{2}\right) \frac{J_1(\gamma)}{\gamma},
-\end{equation*}
-with $\gamma=\sqrt{(q_x r_a)^2+(q_y r_b)^2}$ and $J_1(x)$ is the first order
-Bessel function of the first kind \cite{AbSt64}.
-
-\paragraph{Syntax:} \Code{FormFactorEllipsoidalCylinder($r_a$, $r_b$, height)}
-
-\newpage
-
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:FFellipscylinderEx} shows the normalized intensity
-$|F|^2/V^2$, computed with $r_a=13$~nm, $r_b=8$~nm, and $H=16$~nm.
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffellipscylinder}
-\end{center}
-\caption{Normalized intensity for the form factor of an ellipsoidal
-  cylinder plotted against ($q_y$, $q_z$) and ($q_x$,
-  $q_y$) and computed with \Code{FormFactorEllipsoidalCylinder(8.*nanometer, 13.*nanometer, 16*nanometer)}.}
-\label{fig:FFellipscylinderEx}
-\end{figure}
-
-%\subsection{References}
-%This form factor is referred to as "Ellipsoid'' in \Code{ISGISAXS}. 
-
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Cone} \SecLabel{Cone} 
-
-\paragraph{Real-space geometry}
-This shape is a truncated cone as shown in fig.~\ref{fig:cone}. 
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Cone2dxz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Cone2dxy}}
-\hfill
-\caption{Sketch of a Cone.}
-\label{fig:cone}
-\end{figure}
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item radius $R$,
-\item height $H$,
-\item $\alpha$ is the angle between the side and the circular base.
-\end{itemize}
-
-\paragraph{Restrictions on the parameters:} $\dfrac{H}{R}< \tan(\alpha)$.
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V = \dfrac{\pi}{3} \tan(\alpha) R^3 \left[ 
-            1 - \left(1- \dfrac{H}{\tan(\alpha)R}\right)^3\right]$,
-\item  particle surface seen from above $S=\pi R^2$.
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-\begin{equation*}
-F(\mathbf{q}, R, H, \alpha) = \int_0 ^H 2\pi R_z^2
-\frac{J_1(q_{\parallel}R_z)}{q_{\parallel} R_z}\exp(iq_z z)dz,
-\end{equation*}
-with $R_z =R-\dfrac{z}{\tan \alpha}$, $\mathbf{q}_{\parallel}=\sqrt{q_x^2+ q_y^2}$ and $J_1(x)$ is the first order
-Bessel function of the first kind \cite{AbSt64}.
-
-\paragraph{Syntax:}  \Code{FormFactorCone(radius, height, alpha)}. 
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:FFConeEx} shows the normalized intensity
-$|F|^2/V^2$, computed with $R=10$~nm, $H=13$~nm, and $\alpha=60^{\circ}$.
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffcone}
-\end{center}
-\caption{Normalized intensity for the form factor of a Cone plotted against ($q_y$, $q_z$) and ($q_x$, $q_y$.) It
-  has been  computed with \Code{FormFactorCone(10.*nanometer,13.*nanometer, 60.*degree)}.}
-\label{fig:FFConeEx}
-\end{figure}
-
-%\subsection{References}
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Full Sphere} \SecLabel{FullSphere}
-
-\paragraph{Real-space geometry}\mbox{}\\
-The full sphere is parametrized by its radius $R$. 
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/FullSphere2dxz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/FullSphere2dxy}}
-\hfill
-\caption{Sketch of a Full Sphere.}
-\label{fig:fullsphere}
-\end{figure}
-
-\FloatBarrier
-
-\paragraph{Parameters:} radius $R$.
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V = \dfrac{4\pi}{3}R^3$,
-\item particle surface seen from above $S= \pi R^2$.
-%\item radius of gyration
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-\begin{equation*}
-F(\mathbf{q},R) = 4\pi R^3 \exp(iq_z R)\frac{\sin(q R) - q R \cos(q R)}{(qR)^3},
-\end{equation*}
-where $q=\sqrt{q_x^2 + q_y^2 + q_z^2}$.
-
-\paragraph{Syntax:} \Code{FormFactorFullSphere(radius)}
-
-\newpage
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:FFfSphereEx} shows the normalized intensity $|F|^2/V^2$, computed with $R=8$~nm.
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figfffsphere}
-\end{center}
-\caption{Normalized intensity for the
-  form factor of a Full Sphere plotted against ($q_y$, $q_z$) and ($q_x$, $q_y$) and computed with \Code{FormFactorFullSphere(8.*nanometer)}.}
-\label{fig:FFfSphereEx}
-\end{figure}
-
-%\FloatBarrier
-
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Truncated Sphere}\SecLabel{Sphere}
-  
-\paragraph{Real-space geometry}\mbox{}\\
-This shape is a spherical dome, \textit{i.e.} a portion of a sphere cut off by a plane (perpendicular
-to $z$-axis) as shown in fig.~\ref{fig:sphere}.
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Sphere2dxz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Sphere2dxy}}
-\hfill
-\caption{Sketch of a Truncated Sphere.}
-\label{fig:sphere}
-\end{figure}
-\FloatBarrier
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item radius $R$,
-\item height $H$.
-\end{itemize}
-
-\paragraph{Restrictions on the parameters:} $0 \leq H\leq 2R$.
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V=\pi R^3 \left[\dfrac{2}{3} + \dfrac{H-R}{R} - \dfrac{1}{3}\left(\dfrac{H-R}{R}\right)^3\right]$,
-\item particle surface seen from above $S = \left\{\begin{array}{ll} \pi R^2, & H \geq R \\
-         \pi\left(2RH-H^2\right), & H < R \end{array}\right. $.
-%\item gyration radius along $z$ axis %$R_g = \left\{\begin{array}{ll}
-%R, & H > R \\ \sqrt{2RH-H^2}, & H < R \end{array}\right. .$
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-\begin{equation*}  
-F(\mathbf{q},R, H)= 2\pi \exp[i q_z (H-R)]\int_{R-H} ^{R} R_z^2 \frac{J_1(q_{\parallel} R_z) }{q_{\parallel} R_z} \exp(i q_z z) dz,
-\end{equation*}
-with $J_1(x)$ the first order
-Bessel function of the first kind \cite{AbSt64}, $q_{\parallel} =
-\sqrt{q_x^2+q_y^2}$, and $R_z = \sqrt{R^2-z^2}$
-
-\paragraph{Syntax:} \Code{FormFactorTruncatedSphere(radius, height)}
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:SphereEx} shows the normalized intensity $|F|^2/V^2$, computed with $R=5$~nm and $H=7$~nm:
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffsphere}
-\end{center}
-\caption{Normalized intensity for the form factor of a Truncated Sphere plotted against ($q_y$, $q_z$) and ($q_x$, $q_y$) and
-  computed with \Code{FormFactorTruncatedSphere(5.*nanometer, 7.*nanometer)}.}
-\label{fig:SphereEx}
-\end{figure}
-
-%\FloatBarrier
-
-%\subsection{References}
-%Equation~(\ref{eq:ffsphere}) agrees with the \lq\lq Sphere\rq\rq ~form
-%factor of \IsGISAXS~\cite{Laz02}.
-
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Full Spheroid} \SecLabel{FullSpheroid}  
-
-\paragraph{Real-space geometry}\mbox{}\\
-A full spheroid is generated by rotating an ellipse around the vertical
-axis (see fig.~\ref{fig:fullspheroid}).
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/FullSpheroid2dxz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/FullSpheroid2dxy}}
-\hfill
-\caption{Sketch of a Full Spheroid. }
-\label{fig:fullspheroid}
-\end{figure}
-
-\FloatBarrier
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item radius $R$,
-\item height $H$.
-\end{itemize}
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V =\dfrac{2}{3}R^2H$,
-\item particle surface seen from above $S =\pi R^2$. 
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-\begin{equation*}
-F(\mathbf{q}, R, H) = 4\pi \exp(i q_z H/2) \int_0 ^{H/2}R_z ^2
-\frac{J_1(q_{\parallel}R_z)}{q_{\parallel}R_z} \cos(q_z z) dz,
-\end{equation*}
-with $J_1(x)$ the first order
-Bessel function of the first kind \cite{AbSt64},
-$R_z = R\sqrt{1-\frac{4z^2}{H^2}}$, $\gamma_z = \sqrt{(q_x R_z)^2+(q_y R_z)^2}$.
-
-
-\paragraph{Syntax:} \Code{FormFactorFullSpheroid(radius,height)}
-\newpage
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:FFfspheroidEx} shows the normalized intensity
-$|F|^2/V^2$, computed with $R=10$~nm, and $H=13$~nm.
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figfffspheroid}
-\end{center}
-\caption{Normalized intensity for the form factor of a full spheroid plotted against ($q_y$, $q_z$) and ($q_x$, $q_y$) and
-  computed with \Code{FormFactorFullSpheroid(10.*nanometer, 13.*nanometer)}.}
-\label{fig:FFfspheroidEx}
-\end{figure}
-
-%\FloatBarrier
-
-%\subsection{References}
-%The expression is identical to \Code{IsGISAXS} manual. In the code,
-%the integration is over $[-H/2, H/2]$ with $\exp(iq_z z)$ instead of
-%the cosine.
-%In \Code{IsGISAXS}, factor 4 instead of 2 in the expression of the
-%volume. In the code there is also a problem with an extra factor 2 in the function to integrate.
-
-\newpage%{\cleardoublepage}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Truncated Spheroid} \SecLabel{Spheroid}
-
-\paragraph{Real-space geometry}\mbox{}\\
-This shape is a spheroidal dome: a portion of a full spheroid cut off
-by a plane perpendicular to the $z$-axis.
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Spheroid2dxz.eps}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Spheroid2dxy.eps}}
-\hfill
-\caption{Sketch of a Truncated Spheroid.}
-\label{fig:spheroid}
-\end{figure}
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item radius $R$,
-\item height $H$,
-\item height\_flattening coefficient in the perpendicular direction $f_p$.
-\end{itemize}
-
-\paragraph{Restrictions on the parameters:} $0< \dfrac{H}{R}< 2f_p$.
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V = \dfrac{\pi R H^2}{f_p}  \Big(1-\dfrac{H}{3f_p R}\Big)$,
-\item particle surface seen from above $S = \left\{\begin{array}{ll} \pi R^2, & H \geq f_pR \\
-         \pi\left(\dfrac{2RH}{f_p}-\dfrac{H^2}{f_p^2}\right), & H < R \end{array}\right.$.
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-\begin{equation*} 
-F(\mathbf{q},R, H,f_p) =   2\pi \exp[iq_z(H-f_pR)] \int_{f_p R-H} ^{f_p R} R_z
-        ^2\frac{J_1(q_{\parallel}R_z)}{q_{\parallel}R_z} \exp(i q_z z) dz
-\end{equation*}
-with $J_1(x)$ the first order
-Bessel function of the first kind \cite{AbSt64}, $q_{\parallel}=\sqrt{q_x^2+q_y^2} $ and $R_z=\sqrt{R^2-z^2/f_p^2}$.
-
-\paragraph{Syntax:} \Code{FormFactorTruncatedSpheroid(radius, height, height\_flattening)}
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:FFspheroidEx} shows the normalized intensity
-$|F|^2/V^2$, computed with $R=7.5$~nm, $H=9$~nm and $f_p=1.2$.
-
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffspheroid}
-\end{center}
-\caption{Normalized intensity for the form factor of a Truncated Spheroid plotted against ($q_z$, $q_y$) and ($q_x$, $q_y$) and
-  computed with \Code{FormFactorTruncatedSpheroid(7.5*nanometer, 9.*nanometer, 1.2)}.}
-\label{fig:FFspheroidEx}
-\end{figure}
-
-%\FloatBarrier
-
-%\subsection{References}
-%In \Code{IsGISAXS}'s manual there is an extra factor 2 in the
-%expression of the volume.
-
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Hemi ellipsoid} \SecLabel{HemiEllipsoid}  
-
-\paragraph{Real-space geometry}\mbox{}\\
-This shape is a truncated ellipsoid as shown in fig.~\ref{fig:hemiellipsoid}.
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/HemiEllipsoid2dxz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/HemiEllipsoid2dxy}}
-\hfill
-\caption{Sketch of an Hemi-ellipsoid.}
-\label{fig:hemiellipsoid}
-\end{figure}
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item $r_a$ = half length of the ellipse main axis parallel to $x$,
-\item$r_b$ = half length of the ellipse main axis parallel to $y$, 
-\item $H$ = height (half length of the vertical main axis of a full ellipsoid).
-\end{itemize}
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V = \dfrac{2}{3}\pi r_a r_bH$,
-\item particle surface seen from above $S =\pi r_a r_b$.
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-\begin{equation*}
-F(\mathbf{q},r_a,r_b,H) = 2\pi \int_0 ^{H} r_{a,z} r_{b,z}
-\frac{J_1(\gamma_z)}{\gamma_z}\exp(iq_z z)dz,
-\end{equation*}
-with $J_1(x)$ the first order
-Bessel function of the first kind \cite{AbSt64}, $r_{a,z} = r_a \sqrt{1-\left(\dfrac{z}{H} \right)^2}$, ${r_{b,z} = r_b
-\sqrt{1-\left(\dfrac{z}{H} \right)^2}}$ and $\gamma_z =\sqrt{(q_x r_{a,z})^2+(q_y r_{b,z})^2}$.
-
-\paragraph{Syntax:} \Code{FormFactorHemiEllipsoid($r_a$, $r_b$, height)}
-
-\newpage
-
-\paragraph{Example} \mbox{}\\
-Figure~\ref{fig:FFhemiellipsEx} shows the normalized intensity
-$|F|^2/V^2$, computed with $r_a=10$~nm, $r_b=6$~nm and $H=8$~nm.
-
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffhemiellips}
-\end{center}
-\caption{Normalized intensity for the form factor of an Hemi-Ellipsoid plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$)
-  computed with \Code{FormFactorHemiEllipsoid(10.*nanometer, 6.*nanometer, 8.*nanometer)}.}
-\label{fig:FFhemiellipsEx}
-\end{figure}
-
-%\FloatBarrier
-
-%\subsection{References}
-%This shape is referred to as ``Anisotropic hemi ellipsoid'' in  \Code{ISGISAXS}.
-%Problem when running  \Code{ISGISAXS}.
-%In \Code{IsGISAXS} manual, where does the minus sign in exp(-iq\_z z)
-%come from?
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Ripple1} \SecLabel{Ripple1}  
-
-\paragraph{Real-space geometry}\mbox{}\\
-This shape has a sinusoidal profile (see fig.~\ref{fig:ripple1}).
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Ripple12dyz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Ripple12dxy}}
-\hfill
-\caption{Sketch of a Ripple1.}
-\label{fig:ripple1}
-\end{figure}
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item length $L$, 
-\item width $W$, 
-\item height $H$. 
-\end{itemize}
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V = \dfrac{L W H}{2} $,
-\item particle surface seen from above $S = L W$.
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-\begin{align*}
-F(\mathbf{q},L,W,H) &=L \cdot \frac{W}{\pi}\cdot \sinc\left(\frac{q_xL}{2}\right)\times \\ &\int_0^H{dz \arccos\left(\frac{2z}{H}-1\right)\sinc\left[\frac{q_yW}{2\pi}\arccos\left(\frac{2z}{H} - 1\right)\right]\exp\left(iq_zz\right)},
-\end{align*}
-where $\arccos$ is the  arc cosine (\textit{i.e.} the inverse
-operation of cosine).
-
-\paragraph{Syntax:} \Code{FormFactorRipple1(length, width, height)}
-
-\paragraph{Example}\mbox{}\\
-Figure~\ref{fig:FFripple1Ex} shows the normalized intensity
-$|F|^2/V^2$, computed with $L=27$~nm, $W=20$~nm and $H=14$~nm.
-
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffripple1}
-\end{center}
-\caption{Normalized intensity for the form factor of a ripple1
-  $|F|^2/V^2$, plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$)
-  computed with \Code{FormFactorRipple1(27.*nanometer, 20.*nanometer, 14.*nanometer)}.}
-\label{fig:FFripple1Ex}
-\end{figure}
-%\FloatBarrier
-
-\newpage%{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section{Ripple2} \SecLabel{Ripple2}  
-
-\paragraph{Real-space geometry}\mbox{}\\
-This shape has an asymmetric sawtooth profile.
-
-\begin{figure}[ht]
-\hfill
-\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Ripple22dyz}}
-\hfill
-\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Ripple22dxy}}
-\hfill
-\caption{Sketch of a Ripple2.}
-\label{fig:ripple2}
-\end{figure}
-
-\FloatBarrier
-
-\paragraph{Parameters:}
-\begin{itemize}
-\item length $L$, 
-\item width $W$, 
-\item height $H$,
-\item asymmetry $d$. 
-\end{itemize}
-
-\paragraph{Restriction on the parameters:} $|d| < \frac{W}{2} $.
-
-\paragraph{Properties:}
-\begin{itemize}
-\item volume $V = \dfrac{L W H}{2}$,
-\item particle surface seen from above $S = L W$.
-\end{itemize}
-
-\paragraph{Expression of the form factor}
-\begin{align*}
-F(\mathbf{q},L,W,H,d) &=L W
-\sinc\left(\frac{q_xL}{2}\right)\times \\ &
-\int_0^H 
-\left(1-\frac{z}{H}\right)
- \sinc\left[\frac{q_y
-    W}{2}\left(1-\frac{z}{H}\right)\right] 
-\exp\left\{ i\left[q_zz -
-    q_yd\left(1-\frac{z}{H}\right)\right]\right\} 
-dz
-\end{align*}
-
-\paragraph{Syntax:} \Code{FormFactorRipple2(length, width, height, asymmetry)}
-
-\paragraph{Examples}
-Figure~\ref{fig:FFripple2Ex} shows the normalized intensity
-$|F|^2/V^2$, computed with $L=36$~nm, $W=25$~nm, $H=14$~nm, and $d=3$~nm.
-
-\begin{figure}[h]
-\begin{center}
-\includegraphics[width=\textwidth]{Figures/figffripple2}
-\end{center}
-\caption{Normalized intensity for the form factor of a ripple2 plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$)
-  computed with \Code{FormFactorRipple2(36.*nanometer, 25.*nanometer, 14.*nanometer, 3.*nanometer)}.}
-\label{fig:FFripple2Ex}
-\end{figure}
-
-%\FloatBarrier
-
-%\newpage{\cleardoublepage}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%\section{Distorted Wave Born Approximation}
-%The previous sections of this appendix on form factors have dealt with the Born approximation. In this case the form factor is given by a single integral over the particle shape (see equation~\ref{ffformulaBA}). But this 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 will be dealt with in Section~\ref{appendixinterf}.  We also do not take any polarization effects into account. They will be described in...\\
-
-% In the DWBA, the form factor of a particle in a multilayer system is given by
-
-%\begin{align}
-%F_{\rm{DWBA}} (\vect{k}_i,\vect{k}_f, r_z) & = T_i T_f F_{\rm{BA}} (\vect{k}_i-\vect{k}_f) e^{i (k_{i,z}-k_{f,z}) r_z} + R_i T_f F_{\rm{BA}}(\vect{\widetilde{k}}_i-\vect{k}_f) e^{i(-k_{i,z}-k_{f,z})r_z}
- %\nonumber \\
- % &+ T_i R_f F_{\rm{BA}}(\vect{k}_i-\vect{\widetilde{k}}_f)e^{i(k_{i,z}+k_{f,z})r_z} + R_iR_fF_{\rm{BA}} (\vect{\widetilde{k}}_i-\vect{\widetilde{k}}_f)e^{i(-k_{i,z}+k_{f,z})r_z} \; , \label{eq:dwbageneral}
-%\end{align}
-%where $F_{\rm{BA}}$ is the expression of the form factor in the Born approximation, $r_z$ is the $z$-coordinate of the particle's position (measured from the bottom of the particle), $\vect{k}_i=(k_{i,x}, k_{i,y}, k_{i,z})$ $\vect{k}_f=(k_{f,x}, k_{f,y}, k_{f,z})$ are the incident and scattered wave vectors in air, respectively \cite{Raus95}. With a tilde (\~{}), these wavevectors components are evaluated in the multilayer system (the refractive indices of the different constituting materials have to be taken into account). 
-%$T_i$, $T_f$, $R_i$, $R_f$ are the transmission and reflection coefficients for the incident wave (index $i$) or the scattered one (index $f$). These coefficients can be calculated using the Parratt formalism \cite{Parr54} or the matrix method \cite{BoWo99}. $\vect{k}_i-\vect{k}_f$ is equal to the scattering vector $\vect{q}$ and the $z$-axis is pointing upwards.\\
-
-%\ImportantPoint{Remark:}{The particles cannot sit in between layers. At most they can be sitting on any inner interfaces.}
-
-%\vspace{18pt}
-
-%In the followings, the DWBA will be illustrated for two different layouts of particles: 
-%\begin{itemize}
-%\item particles deposited on a substrate,
-%\item particles buried in a layer on a substrate.
-%\end{itemize}
-
-%\ImportantPoint{Remark:}{In \BornAgain\ There is no limitation to the number of layers composing the sample.}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%\subsection{Particles deposited on a substrate}
-%%Substrate modified Born approximation
-%In this configuration, the particles are sitting on top of a substrate layer, in the air as shown in fig.~\ref{fig:SchemDWBA}. In the DWBA the expression of a form factor becomes 
-%\begin{align}
-%F_{\rm{DWBA}}(q_{\parallel}, k_{i,z}, k_{f,z}) &= F_{\rm{BA}}(q_{\parallel}, k_{i,z}-k_{f,z})+ R_i F_{\rm{BA}}(q_{\parallel}, -k_{i,z}-k_{f,z}) \nonumber \\
-%&+ R_f F_{\rm{BA}}(q_{\parallel}, k_{i,z}+k_{f,z}) + R_i R_f F_{\rm{BA}}(q_{\parallel},-k_{i,z}+k_{f,z}), \label{eq:dwbaair}
-%\end{align}
-%where $q_{\parallel}$ is the component of the scattering beam in the plane of the interface ($\vect{q}=\vect{k}_i-\vect{k}_f$), $k_{i,z}$ and $k_{f,z}$ are the z-component of the incident and scattered beam, respectively. $R_i$, $R_f$ are the reflection coefficients in incidence and reflection. They are defined as\\ $R=\dfrac{k_z+\sqrt{n_s^2k_0^2-|k_{\parallel}|^2}}{k_z-\sqrt{n_s^2 k_0^2-|k_{\parallel}|^2}}$, where $n_s=1-\delta_s -i \beta_s$ is the refractive index of the substrate, $k_0$ is the wavelength in vacuum ($2\pi /\lambda$), $k_z$ and $k_{\parallel}$ are the $z$-component and the in-plane component of $\vect{k}_i$ or $\vect{k}_f$. \\
-
-%\ImportantPoint{Remark:}{If the particles are sitting on a multilayered system, the expression of the form factor in the DWBA is obtained by replacing the Fresnel coefficient by the corresponding coefficients of the underlying layers \cite{Parr54,BoWo99}.}
-
-%\vspace{18pt}
-
-%Figure~\ref{fig:SchemDWBA} illustrates the four scattering processes for a supported particle, taken into account in the DWBA. The first term of eq.~\ref{eq:dwbaair}  corresponds to the Born approximation. Each term of $F_{\rm{DWBA}}$ is weighted by a Fresnel coefficient. 
-
-%\begin{figure}[h]
-%\begin{center}
-%\includegraphics[width=\textwidth]{Figures/drawingDWBA}
-%\end{center}
-%\caption{Schematic views of the different terms appearing in the expression of the form factor under DWBA for particles sitting on a substrate layer.}
-%\label{fig:SchemDWBA}
-%\end{figure}
-
-%Script~\ref{lst:badwba} illustrates the difference between BA and DWBA in \BornAgain\ when generating the sample.  We consider the simple case of:
-%\begin{itemize}
-%\item one kind of particles' shape,
-%\item no interference between the particles,
-%\item in the DWBA, a sample made of a layer of substrate on which are deposited the particles,
-%\item in the BA, a sample composed of the particles in air.
-%\end{itemize} 
-
-%Figure~\ref{fig:spheroidbadwba} shows the intensity contourplot generated using this script with truncated spheroids as particles. Note that the full \Python\ script UMFormFactorBA\_DWBA.py is available in folder Examples/Python/UserManual/.
-
-%\newpage
-
-%\begin{lstlisting}[language=python, style=eclipseboxed,numbers=none,nolol,caption={\Code{Python} script to generate a sample using Born or Distorted Wave Born Approximation. The difference between BA and DWBA in this simple case is the absence or presence of a substrate layer in the sample.},label={lst:badwba}]
-%def get_sample():
-%    """
-%    Build and return the sample to calculate form factor of 
-%    truncated spheroid in Born or Distorted Wave Born Approximation.
-%    """
-%    # defining materials
-%    m_ambience = HomogeneousMaterial("Air", 0.0, 0.0)
-%    m_substrate = HomogeneousMaterial("Substrate", 6e-6, 2e-8)
-%    m_particle = HomogeneousMaterial("Particle", 6e-4, 2e-8)
-
-%    # collection of particles
-%    ff= FormFactorTruncatedSpheroid(7.5*nanometer, 9.0*nanometer, 1.2)
-%    particleshape = Particle(m_particle, ff)
-%    particle_layout = ParticleLayout()
-%    particle_layout.addParticle(particleshape, 0.0, 1.0)
-
-%    # interferences
-%    interference = InterferenceFunctionNone()
-%    particle_layout.addInterferenceFunction(interference)
-
-%    # assembling the sample
-%    air_layer = Layer(m_ambience)
-%    air_layer.setLayout(particle_layout)
-%    substrate_layer = Layer(m_substrate, 0)
-
-%    multi_layer = MultiLayer()
-%    multi_layer.addLayer(air_layer)
-%    # Comment the following line out for Born Approximation
-%    multi_layer.addLayer(substrate_layer)
-%    return multi_layer
-%\end{lstlisting}
-
-%\begin{figure}[ht]
-%\hfill
-%\subfigure[Born Approximation]{\includegraphics[width=6cm]{Figures/ffspheroidBA}}
-%\hfill
-%\subfigure[DWB Approximation]{\includegraphics[width=6cm]{Figures/ffspheroidDWBA}}
-%\hfill
-%\caption{Intensity map of TruncatedSpheroid form factor in BA and DWBA computing using script~\ref{lst:badwba} for the sample.}
-%\label{fig:spheroidbadwba}
-%\end{figure}
-
-%\FloatBarrier 
-
-%\ImportantPoint{Remark:}{In \BornAgain, the DWBA is implemented automatically when assembling the sample with more than the air layer.}
-
-%\subsection{Buried particles} 
-%The system considered in this section consists of particles encapsulated in a layer, which is sitting on a substrate (see fig.~\ref{fig:SchemDWBAburied}). In this case the form factor in the DWBA is given by
-
-%\begin{align}
-%F_{\rm{DWBA}}(q_{\parallel}, k_{i,z}, k_{f,z}) &= T_i T_f F_{\rm{BA}}(q_{\parallel}, k_{i,z}-k_{f,z})e^{i(k_{i,z}-k_{f,z})d}+ R_i T_f F_{\rm{BA}}(q_{\parallel}, -k_{i,z}-k_{f,z})e^{i(-k_{i,z}-k_{f,z})d} \nonumber \\
-%&+ R_f T_i F_{\rm{BA}}(q_{\parallel}, k_{i,z}+k_{f,z}) e^{i(k_{i,z}+k_{f,z})d}+ R_f R_iF_{\rm{BA}}(q_{\parallel},-k_{i,z}+k_{f,z})e^{i(-k_{i,z}+k_{f,z})d}, \label{eq:dwbaburied}
-%\end{align}
-
-%\begin{equation*}
-%R_j =\frac{t^{j}_{0,1}r^{j}_{1,2}\exp(2ik_{j,z}t)}{1+r^{j}_{0,1}r^{j}_{1,2}\exp(2ik_{j,z}t)}, \quad %T_j=\frac{t^{j}_{0,1}}{1+r^{j}_{0,1}r^{j}_{1,2}\exp(2ik_{j,z}t)}, j=i,f 
-%\end{equation*}
-%where $q_{\parallel}$ is the component of the scattering beam in the plane of the interface, $k_{i,z}$ and $k_{f,z}$ are the z-component of the incident and scattered beams, respectively.  $d$ is the depth at which the particles are sitting in the layer. Note that this value is given relative to the top of this layer and it is not the coordinate in the absolute referential (linked with the full sample) and it is measured up to the bottom of the particle. $t$ is the thickness of the intermediate layer containing the particles. $R_{i,f}$ and $T_{i,f}$  are the reflection  and transmission coefficients in incidence and reflection (they can be calculated using Parratt or matrix formalism). $r^j_{0,1}$, $r^j_{1,2}$ $t^j_{0,1}$ are the reflection and transmission coefficients between layers; the indices are related to different boundaries with 0: air, 1: intermediate layer and 2: substrate layer and the superscript $j$ is associated with the incident or scattered beams:
-%\begin{equation*}
-%r^j_{n,n+1}=\frac{k_{j,z,n}-k_{j,z,n+1}}{k_{j,z,n}-k_{j,z,n+1}}, \qquad t^j_{n,n+1}= \frac{2k_{j,z,n}}{k_{j,z,n}-k_{j,z,n+1}}, \quad n=0,1, \quad j=i,f,
-%\end{equation*}
-%where index $n$ is related to the layers, $z$ to the vertical component, and $j$ to the beams (incident and outgoing).
-
-%\begin{figure}[h]
-%\begin{center}
-%\includegraphics[width=\textwidth]{Figures/drawingDWBAburied}
-%\end{center}
-%\caption{Schematic views of the different terms appearing in the expression of the form factor under the DWBA for buried particles.}
-%\label{fig:SchemDWBAburied}
-%\end{figure}
-
-%%For example, for a three layer system (particles embbedded in the middle layer of thickness $t$), 
-%%\begin{align*}
-%%F=A_1T_i T_fF_{\rm{BA}}(q_{\parallel}, k_{i,z}-k_{f,z})+ R_i T_f F_{\rm{BA}}(q_{\parallel}, -k_{i,z}-k_{f,z}) \\
-%%&+ R_f T_i F_{\rm{BA}}(q_{\parallel}, k_{i,z}+k_{f,z}) + R_f R_iF_{\rm{BA}}(q_{\parallel},-k_{i,z}+k_{f,z})
-%%\end{align*} 
-
-%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} (The full script UMFormFactor\_Buried\_DWBA.py can be found in /Examples/Python/UserManual.
-
-%\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}]
-%def get_sample():
-%    """
-%    Build and return the sample with buried spheres in DWBA.
-%    """
-%    # defining materials
-%    m_ambience = HomogeneousMaterial("Air", 0.0, 0.0)
-%    m_interm_layer = HomogeneousMaterial("IntermLayer",3.45e-6, 5.24e-9)
-%    m_substrate = HomogeneousMaterial("Substrate", 7.43e-6, 1.72e-7)
-%    m_particle = HomogeneousMaterial("Particle", 0.0, 0.0)
-
-%    # collection of particles 
-%    ff = FormFactorFullSphere(10.2*nanometer)
-%    particleshape = Particle(m_particle, ff)
-%    particle_layout = ParticleLayout()
-%    particle_layout.addParticle(particleshape,20.1,1.0)
-
-%    # interferences 
-%    interference = InterferenceFunctionNone()
-%    particle_layout.addInterferenceFunction(interference)
-
-%    # assembling the sample 
-%    air_layer = Layer(m_ambience)
-%    intermediate_layer = Layer(m_interm_layer, 30.*nanometer)
-%    intermediate_layer.setLayout(particle_layout)
-%    substrate_layer = Layer(m_substrate, 0)
-   
-%    multi_layer = MultiLayer()
-%    multi_layer.addLayer(air_layer)
-%    multi_layer.addLayer(intermediate_layer)
-%    multi_layer.addLayer(substrate_layer)
-%    return multi_layer
-%\end{lstlisting}
-
-%\begin{figure}[ht]
-%\centering
-%\includegraphics[width=0.6\textwidth]{Figures/figIntBuriedPart}
-%\caption{Map of intensity scattered from a sample made of spherical particles embedded in the middle of a 30~nm-thick layer on a substrate (see Script~\ref{lst:dwbaburied} for details about the sample).}
-%\label{fig:dwbaburied}
-%\end{figure}
-
-%\newpage
-
-%\ImportantPoint{Remark:}{For layers different from the air layer, the top interface is considered as the reference level to position the encapsulated particles. For example, spheres positioned at depth $d$ (positive) are located at a distance $d$ from the top of the layer up to the bottom of these particles. This convention is different for the top air layer, where particles sitting at the interface with an underlying layer (\textit{i.e.} the bottom of the air layer) are located at depth 0 (see fig.~\ref{fig:depthpartBA}).}
-
-%\begin{figure}[ht]
-%\centering
-%\includegraphics[width=0.5\textwidth]{Figures/drawingDepthParticle}
-%\caption{Illustration of the convention about \Code{depth} used in \BornAgain\ to encapsulate particles in %layers.}
-%\label{fig:depthpartBA}
-%\end{figure}
-
-%\newpage
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%\section{Core-shell particles}
-% \BornAgain\ also offers the possibility to simulate more complicated shapes of particles by combining those listed in the previous sections. To generate a core-shell particle, the combination is performed using the following command:\\
-%\Code{ParticleCoreShell(shell\_particle, core\_particle, relative\_core\_position)},\\
-%where \Code{shell\_particle} and \Code{core\_particle} are the outer and inner parts of the core-shell particle, respectively. They refer to one of the form factors defined previously and to an associated material. For example, for the outer part,\\ \Code{shell\_particle=Particle(material\_shell, outer\_form\_factor)},\\ where \Code{material\_shell} is the material of the shell and \Code{outer\_form\_factor} is the shape of the outer part (cf. listing~\ref{lst:cshellsample}). \\ \Code{relative\_core\_position} defines the position of the centre of gravity of the inner shape with respect to the outer one. An example in fig.~\ref{fig:coreshell} shows a core shell particle made of a box for the outer part and of a shifted pyramidal shape for the inner one.\\
-
-%Figure~\ref{fig:FFCoreShellBA} displays the output intensity scattered in the Born Approximation using the code listed in~\ref{lst:cshellsample} to generate the core-shell particle. The full script can be found at /Examples/python/UserManual/UMFormFactor\_CoreShell.py. 
-
-%\begin{figure}[ht]
-%\hfill
-%\subfigure[Side view]{\includegraphics[width=5cm]{Figures/CoreShellParallPyrxz}}
-%\hfill
-%\subfigure[Top view]{\includegraphics[width=5cm]{Figures/CoreShellParallPyrxy}}
-%\hfill
-%\caption{Example of a core-shell particle composed of a box with a pyramidal  inset. The relative core shell position is marked %by the position of its center of gravity (blue point $\color{blue}\bullet$) with respect to the center of gravity of the box (red %point $\color{red}\bullet$). }
-%\label{fig:coreshell}
-%\end{figure}
-
-%\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}]
- %   outer_ff = FormFactorBox(16.0*nanometer, 16.0*nanometer, 8.0*nanometer) 
- %   inner_ff = FormFactorPyramid(12.0*nanometer, 7.0*nanometer, 60.0*degree)
- %   shell_particle = Particle(m_shell, outer_ff)
- %   core_particle = Particle(m_core, inner_ff)
- %   core_position = kvector_t(1.5, 0.0, 0.0)
-
-%   particle = ParticleCoreShell(shell_particle, core_particle, core_position)
-%\end{lstlisting}
-
-%\begin{figure}[h]
-%\begin{center}
-%\includegraphics[width=0.6\textwidth]{Figures/CoreShellParallPyr}
-%\end{center}
-%\caption{Intensity map of a core-shell form factor in Born Approximation using  \Code{FormFactorBox(16*nanometer, %16*nanometer, 8*nanometer)} and \Code{FormFactorPyramid(12*nanometer, 7*nanometer, 60*degree)} for the outer and inner %shells, respectively. The core particle is shifted by 1.5~nm in the $x$-direction with respect to the centre of the outer shell. The %sample used to generate the particle is listed in~\ref{lst:cshellsample}.  There is no substrate and no interference between the %particles.}
-%\label{fig:FFCoreShellBA}
-%\end{figure}
-
-%%outer_ff = FormFactorParallelepiped(16*nanometer, 8*nanometer) 
-%%inner_ff = FormFactorPyramid(12*nanometer, 7*nanometer, 60*degree)
-%%  shell_particle = Particle(m_shell, outer_ff)
-%%  core_particle = Particle(m_core, inner_ff)
-%% core_position = kvector_t(1.5, 0.0, 0.0)
-%% alphai=0.2*degree
-%%    phii=0.*degree
+%\newpage
+\chapter{Form factors} \label{appendixff}
+In \BornAgain\ the expression of the form factor has been implemented in the Born approximation. Each of them is defined as
+\begin{equation*}
+F(\mathbf{q})=\int_V \exp (i\mathbf{q}.\mathbf{r}) d^3 \mathbf{r},
+\end{equation*}
+where $V$ is the volume of the particle's shape,
+$\mathbf{q}=\mathbf{k}_i - \mathbf{k}_f$ is the scattering vector with
+$\mathbf{k}_f$ and $\mathbf{k}_i$ the scattered and incident wave
+vector, respectively. The Distorted Wave Born Approximation can be taken into account as it has been explained in \SecRef{sect:dwba}.\\
+
+The particle's shape is parametrized in a cartesian frame, with its
+$z$-axis pointing upwards and its origin at the center of the bottom
+of the particle: $\mathbf{r}=(x,y,z)$. In the followings, a schematic view will depict this layout for each
+form factor.\\
+
+
+All form factors have been implemented with complex scattering vectors
+in order to take any material absorption into account.\\
+
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Box} \SecLabel{Box} 
+
+\paragraph{Real-space geometry}\mbox{}\\
+This shape is a rectangular cuboid as
+shown in fig.~\ref{fig:box}. 
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Box2dxz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Box2dxy}}
+\hfill
+\caption{Sketch of a Box.}
+\label{fig:box}
+\end{figure}
+
+\FloatBarrier
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item length of the base $L$,
+\item width of the base $W$,
+\item height  $H$.
+\end{itemize}
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V= LWH$,
+\item particle surface seen from above $S = LW$.
+%\item radius of gyration
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+\begin{equation*}
+F(\mathbf{q},L,W,H)= L W H\exp\left(i q_z \frac{H}{2}\right) \sinc\left(q_x \frac{L}{2}\right)
+\sinc\left(q_y \frac{W}{2}\right) \sinc\left(q_z \frac{H}{2}\right),
+\end{equation*}
+   
+where $\sinc(x)=\sin(x)/x$ is the cardinal sine.
+
+\paragraph{Syntax:} \Code{FormFactorBox(length, width, height)}
+
+\newpage
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:FFBoxEx} shows the normalized intensity
+$|F|^2/V^2$, computed with $L=20$~nm, $W=16$~nm, and $H=13$~nm:
+
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffbox}
+\end{center}
+\caption{Normalized intensity for the form factor of a Box plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$) and computed with \Code{FormFactorBox(20.*nanometer, 16.*nanometer, 13.*nanometer)}.}
+\label{fig:FFBoxEx}
+\end{figure}
+
+\FloatBarrier
+%\subsection{References}
+%\BornAgain\ uses a different convention for the parameters in comparison with \Code{IsGISAXS}, where the half length
+%values are used (see fig.~\ref{box}).
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Prism3} \SecLabel{Prism3} 
+
+\paragraph{Real-space geometry}\mbox{}\\
+This shape is a triangular prism, whose base is an equilateral
+triangle as shown in fig.~\ref{fig:prism3}.
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Prism32dxz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Prism32dxy}}
+\hfill
+\caption{Sketch of a Prism3.}
+\label{fig:prism3}
+\end{figure}
+
+\FloatBarrier
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item length $L$ of one side of the base, 
+\item height $H$.
+\end{itemize}
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V= \dfrac{\sqrt{3}}{4} H L^2$,
+\item particle surface seen from above $S =\dfrac{\sqrt{3}}{4}L^2$.
+
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+\begin{align*}
+F(\mathbf{q},L, H) &= \frac{2 \sqrt{3}}{q_x^2-3q_y^2}  \exp\left(-i q_y\frac{L}{2\sqrt{3}}\right)\left[\exp\left(i \sqrt{3} q_y \frac{L}{2} \right)-\cos\left(q_x \frac{L}{2}\right)-i \sqrt{3} q_y \frac{L}{2} \sinc\left(q_x \frac{L}{2}\right) \right] \\
+  &
+\times  H \sinc\left(q_z \frac{H}{2} \right) \exp\left(i q_z \frac{H}{2}\right),
+\end{align*}
+where $\sinc(x)=\sin(x)/x$ is the cardinal sine.
+
+\paragraph{Syntax:} \Code{FormFactorPrism3(length, height)}
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:FFprism3Ex} shows the normalized intensity
+$|F|^2/V^2$, computed with $L=10$~nm and \mbox{$H=13$~nm.}
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffprism3}
+\end{center}
+\caption{Normalized intensity for the form factor of a Prism3
+ plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$) and
+  computed with \Code{FormFactorPrism3(10.*nanometer, 13.*nanometer)}.}
+\label{fig:FFprism3Ex}
+\end{figure}
+
+%\subsection{References}
+%In the $x,y$ plane , we use the full side length of the triangular
+%base instead of  half as implemented in \Code{IsGISAXS}: $L= 2
+%R_{\rm{\Code{IsGISAXS}}}$.
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Tetrahedron}  \SecLabel{Tetrahedron} 
+ 
+\paragraph{Real-space geometry}\mbox{}\\
+This shape is a truncated tetrahedron as shown in fig.~\ref{fig:tetrahedron}.
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Tetrahedron2dxz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Tetrahedron2dxy}}
+\hfill
+\caption{Sketch of a Tetrahedron. The implementation of this shape uses angle
+  $\alpha$, which is linked to $\beta$ via $\tan \alpha = 2 \tan 
+  \beta$. $\alpha$ is measured along one of the base lines and $\beta$
+  at one of the base vertices.}
+\label{fig:tetrahedron}
+\end{figure}
+
+\FloatBarrier
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item length of one side of the equilateral triangular base $L$,
+\item height $H$,
+\item angle $\alpha$ is the angle between the base and the
+  side faces, taken in the middle of the base lines.
+\end{itemize}
+
+\paragraph{Restrictions on the parameters:} 
+$\dfrac{H}{L}< \dfrac{\tan{\alpha}}{2\sqrt{3}}$.
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V= \dfrac{\tan(\alpha) L^3}{24} \left[1- \left(1 -
+  \dfrac{2\sqrt{3} H}{L \tan(\alpha)} \right)^3\right]$,
+\item particle surface seen from above $S =\dfrac{\sqrt{3}}{4}L^2$.
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+
+\begin{align*}
+&F(\mathbf{q}, L, H, \alpha)=\frac{\sqrt{3}H}{q_x (q_x^2-3q_y^2)}
+\exp\left(i\frac{q_z L}{2\tan (\alpha)\sqrt{3}}\right) \times \\
+&\Big\{2q_x \exp(iq_3 D)\sinc(q_3 H) - (q_x +\sqrt{3}q_y)
+\exp(iq_1 D)\sinc(q_1 D) -(q_x-\sqrt{3}q_y)\exp(-iq_2
+D)\sinc(q_2 H) \Big\}, 
+\end{align*}
+with $\sinc(x)=\sin(x)/x$,
+\begin{equation*}
+q_1  =\frac{1}{2}\left[\frac{q_x\sqrt{3} -q_y}{\tan \alpha}-q_z \right],
+\quad q_2 = \frac{1}{2}\left[\frac{q_x\sqrt{3} +q_y}{\tan \alpha}+q_z
+\right], \quad 
+q_3 = \frac{q_y}{\tan \alpha} -\frac{q_z}{2}, \quad D = \frac{L \tan \alpha}{\sqrt{3}} -H.
+\end{equation*}
+
+\paragraph{Syntax:} \Code{FormFactorTetrahedron(length, height, alpha)}
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:FFtetrahEx} shows the normalized intensity
+$|F|^2/V^2$, computed with $L=15$~nm, $H=6$~nm and $\alpha =60
+^{\circ}$.
+
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figfftetrahedron}
+\end{center}
+\caption{Normalized intensity for the form factor of a Tetrahedron
+  plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$) and
+  computed with \Code{FormFactorTetrahedron(15.*nanometer, 6.*nanometer, 60.*degree)}.}
+\label{fig:FFtetrahEx}
+\end{figure}
+
+%\FloatBarrier
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Prism6} \SecLabel{Prism6}
+
+\paragraph{Real-space geometry}\mbox{}\\
+This shape is an hexagonal prism (see fig.~\ref{fig:prism6}).
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Prism62dxz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Prism62dxy}}
+\hfill
+\caption{Sketch of a Prism6.}
+\label{fig:prism6}
+\end{figure}
+
+\FloatBarrier
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item radius of the hexagonal base $R$,
+\item height $H$.
+\end{itemize}
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V = \dfrac{3\sqrt{3}}{2}H R^2$,
+\item particle surface seen from above $S =\dfrac{3\sqrt{3}R^2}{2}$.
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+\begin{align*}
+F(\mathbf{q}, R, H) &= \frac{4H\sqrt{3}}{3q_y^2 - q_x^2}
+\sinc\left(q_z\frac{H}{2}\right) \exp\left(-i q_z\frac{ H}{2}\right)\times\\
+&\left\{\frac{3q_y^2R^2}{4} \sinc\left(\frac{q_x
+  R}{2}\right)\sinc\left(\frac{\sqrt{3}q_yR }{2}\right)+ \cos(q_x R)-\cos\left(q_y
+\frac{\sqrt{3}R}{2}\right) \cos\left(\frac{q_x R}{2}\right)\right\},
+\end{align*}
+with $\sinc(x)=\sin(x)/x$.
+
+\paragraph{Syntax:} \Code{FormFactorPrism6(radius, height)} 
+
+\newpage
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:FFprism6Ex} shows the normalized intensity
+$|F|^2/V^2$, computed with $R=5$~nm and \mbox{$H=11$~nm.}
+
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffprism6}
+\end{center}
+\caption{Normalized intensity for the form factor of a Prism6 plotted against ($q_y$, $q_z$) and ($q_x$, $q_y$) and computed with \Code{FormFactorPrism6(5.*nanometer, 11.*nanometer)}.}
+\label{fig:FFprism6Ex}
+\end{figure}
+
+%\FloatBarrier
+
+%\subsection{References}
+%The hexagonal base is parametrized in the different way compared with
+%\Code{IsGISXAXS}. In \BornAgain\, we use $R = 2/\sqrt{3}R_{\text{\Code{IsGiSaXs}}}$.
+%A factor $H$ is missing in the expression of the form factor given in
+%\Code{IsGISAXS}'s manual. 
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Cone6} \SecLabel{Cone6} 
+
+\paragraph{Real-space geometry}\mbox{}\\
+It is a truncated hexagonal pyramid (see fig.~\ref{fig:cone6}). 
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Cone62dxz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Cone62dxy}}
+\hfill
+\caption{Sketch of a Cone6.  The implementation of this shape uses angle
+  $\alpha$, which is linked to $\beta$ via $\tan \alpha = \dfrac{2}{\sqrt{3}} \tan 
+  \beta$. $\alpha$ is measured along one of the base lines and $\beta$
+  at one of the base vertices.}
+\label{fig:cone6}
+\end{figure}
+
+\FloatBarrier
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item radius of the regular hexagonal base $R$,
+\item height $H$,
+\item angle $\alpha$ is considered between one of the side faces and
+  the middle of a base length. 
+\end{itemize}
+
+\paragraph{Restrictions on the parameters:} 
+$\dfrac{2H}{\sqrt{3}R}< \tan{\alpha}$.
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V = \dfrac{3}{4} \tan(\alpha) R^3 \left[
+            1 - \left(1- \dfrac{2H}{ \tan(\alpha) R\sqrt{3}}\right)^3
+            \right]$,
+\item  particle surface seen from above $S =\dfrac{3\sqrt{3}R^2}{2}$.
+\end{itemize}
+
+\paragraph{Expression of the form factor}\mbox{}\\
+The
+calculation can be derived from ``Prism6'' (\SecRef{Prism6}) by
+considering a side length varying with the vertical position:
+
+\begin{align*}
+F(\mathbf{q}, R, H, \alpha) = \frac{4\sqrt{3}}{3q_y ^2 - q_x^2}\int_0 ^H &\exp(iq_z z)
+\Big[\frac{3}{4}R_z^2q_y^2 \sinc\left(\frac{q_xR_z}{2}\right)\sinc\left(\frac{\sqrt{3}q_y
+R_z}{2}\right)\\
+&+\cos(q_xR_z)-\cos\left(\frac{\sqrt{3}q_y R_z}{2}\right)\cos\left(\frac{q_xR_z}{2}\right) \Big]dz
+\end{align*}
+with $R_z=R-\dfrac{2z}{\sqrt{3}\tan(\alpha)}$ and $\sinc(x)=\sin(x)/x$.
+
+\paragraph{Syntax:} \Code{FormFactorCone6(radius,height, alpha)} 
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:FFCone6Ex} shows the normalized intensity
+$|F|^2/V^2$, computed with $R=10$~nm, $H=13$~nm, and
+$\alpha=60^{\circ}$.
+
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffcone6}
+\end{center}
+\caption{Normalized intensity for the form factor of a Cone6 plotted against ($q_y$, $q_z$) and ($q_x$, $q_y$) and computed with \Code{FormFactorCone6(10.*nanometer,13.*nanometer, 60.*degree)}.}
+\label{fig:FFCone6Ex}
+\end{figure}
+
+%\FloatBarrier
+
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Pyramid}\SecLabel{Pyramid}
+
+\paragraph{Real-space geometry}\mbox{}\\
+This shape is a  truncated pyramid with a square base as shown in fig.~\ref{fig:pyramid}.
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Pyramid2dxz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Pyramid2dxy}}
+\hfill
+\caption{Sketch of a Pyramid}
+\label{fig:pyramid}
+\end{figure}
+
+\FloatBarrier
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item length of one side of the square base $L$,  
+\item height $H$,
+\item  $\alpha$ is the angle between the base and the
+  side faces, taken in the middle of the base lines.
+\end{itemize}
+
+\paragraph{Restrictions on the parameters:}  $\dfrac{2H}{L} < \tan(\alpha)$.
+
+\paragraph{Properties:}
+\begin{itemize}
+\item  volume $V = \dfrac{1}{6} \tan(\alpha) L^3\left[ 1
+             - \left(1 - \dfrac{2H}{\tan(\alpha)L}\right)^3 \right],$
+\item particle surface seen from above $S = L^2$.
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+\begin{align*}
+&F(\mathbf{q},L, H, \alpha) =
+\frac{H}{q_x q_y} \times \nonumber \\ &\left\{ K_1 \cos\left[
+  (q_x-q_y)\frac{L}{2} \right] + K_2 \sin\left[ (q_x-q_y)\frac{L}{2} \right]
+- K_3 \cos\left[ (q_x+q_y) \frac{L}{2} \right] - K_4 \sin\left[ (q_x+q_y)\frac{L}{2} \right]\right\},
+\end{align*}
+with $\sinc(x)=\sin(x)/x$,
+\begin{align*}
+       q_1 &=\frac{1}{2}\Big[\frac{q_x-q_y}{\tan(\alpha)} + q_z\Big],\quad       q_2 =\frac{1}{2}\Big[\frac{q_x-q_y}{\tan(\alpha)} - q_z\Big]\\
+        q_3 &=\frac{1}{2}\Big[\frac{q_x+q_y}{\tan(\alpha)} + q_z\Big],\quad       q_4 =\frac{1}{2}\Big[\frac{q_x+q_y}{\tan(\alpha)} - q_z\Big]\\
+        K_1 &= \sinc(q_1 H)\exp(i q_1 H)  + \sinc(q_2 H) \exp(-i q_2 H)\\
+        K_2 &= -i \sinc(q_1 H) \exp(i q_1 H) +i \sinc(q_2 H) \exp(-i q_2 H)\\
+        K_3 &= \sinc(q_3 H) \exp(i q_3 H)    + \sinc(q_4 H) \exp(-i q_4 H)\\
+        K_4 &= -i \sinc(q_3 H) \exp(i q_3 H) + i \sinc(q_4 H) \exp(-i q_4 H) 
+   \end{align*}
+
+\paragraph{Syntax:}  \Code{FormFactorPyramid(length, height, alpha)}
+
+\paragraph{Examples}
+Figure~\ref{fig:FFPyramidEx} shows the normalized intensity
+$|F|^2/V^2$, computed with $L=18$~nm, $H=13$~nm and
+$\alpha=60^{\circ}$.
+
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffpyramid}
+\end{center}
+\caption{Normalized intensity for the form factor of a
+  pyramid plotted against ($q_y$, $q_z$) and  
+  ($q_x$, $q_y$) and computed with  \Code{FormFactorPyramid(18.*nanometer, 13.*nanometer, 60.*degree)}.}
+\label{fig:FFPyramidEx}
+\end{figure}
+
+%\FloatBarrier
+%\subsection{References}
+%The output of equation~(\ref{eq:ffpyramid}) agrees with the \lq\lq
+%pyramid\rq\rq ~form factor of \IsGISAXS~\cite{Laz02}.
+%In \BornAgain\, the base of the pyramid is characterized by the full
+%length of one of its side and not by half this value: $L=2R_{\rm{\Code{IsGISXAXS}}}$. 
+%Pyramid: problem with signs of K2 and K4
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Anisotropic pyramid} \SecLabel{AnisoPyramid} 
+
+\paragraph{Real-space geometry}\mbox{}\\
+This shape is a truncated right pyramid with a rectangular base as
+shown in fig.~\ref{fig:anisopyramid}.
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/AnisoPyramid2dxz.eps}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/AnisoPyramid2dxy.eps}}
+\hfill
+\caption{Sketch of an Anisotropic Pyramid.}
+\label{fig:anisopyramid}
+\end{figure}
+
+\FloatBarrier
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item full length of the base $L$,
+\item full width of the base $W$,
+\item height $H$,
+\item $\alpha$ is the angle between the base and the
+  side faces, taken in the middle of the base lines.
+\end{itemize}
+
+\paragraph{Restrictions on the parameters:} $\dfrac{2H}{L}< \tan(\alpha)$ and $\dfrac{2H}{W}< \tan(\alpha)$.
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V= H \Big[LW - \dfrac{(L + W)H}{\tan(\alpha)}
+   + \dfrac{4}{3} \dfrac{H^2}{\tan^2(\alpha)}\Big]$,
+\item particle surface seen from above $S = LW$.
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+\begin{align*}
+&F(\mathbf{q}, L, W, H, \alpha)=
+\frac{H}{q_xq_y} \times \\
+&\Big\{
+K_1\cos\Big(q_x \frac{L}{2} -q_y \frac{W}{2}\Big)+  K_2 \sin \Big (q_x
+\frac{L}{2}- q_y \frac{W}{2}\Big) - K_3 \cos \Big (q_x \frac{L}{2} +q_y \frac{W}{2}\Big)-
+K_4 \sin \Big (q_x \frac{L}{2} + q_y \frac{W}{2}\Big)
+\Big\},
+\end{align*}
+with $\sinc(x)=\sin(x)/x$,
+\begin{align*}
+K_1 &= \exp(-i q_2 H) \sinc(q_2 H) + \exp(iq_1 H) \sinc(q_1 H) \\
+K_2 &= i \exp(-iq_2 H) \sinc(q_2 H) -i \exp(iq_1 H) \sinc(q_1 H) \\
+K_3 &= \exp(-iq_4 H) \sinc(q_4 H) + \exp(iq_3 H) \sinc(q_3 H) \\
+K_4 &= i \exp(i q_4 H) \sinc(q_4 H) -i \exp(iq_3 H) \sinc(q_3 H)\\
+q_1 &= \frac{1}{2}\left[\frac{q_x -q_y}{\tan \alpha} +q_z \right],\quad q_2 = \frac{1}{2}\left[\frac{q_x -q_y}{\tan \alpha} -q_z \right]\\
+q_3 &= \frac{1}{2}\left[\frac{q_x +q_y}{\tan \alpha} +q_z \right] , \quad q_4 = \frac{1}{2}\left[\frac{q_x +q_y}{\tan \alpha} -q_z \right]
+\end{align*}
+
+\paragraph{Syntax:} \Code{FormFactorAnisoPyramid(length, width, height, alpha)}
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:FFAnisoPyramidEx} shows the normalized intensity
+$|F|^2/V^2$, computed with $L=20$~nm, $W=16$~nm, $H=13$~nm, and
+$\alpha=60^{\circ}$.
+
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffanisopyramid}
+\end{center}
+\caption{Normalized intensity for the form factor of an anisotropic
+  pyramid $|F|^2/V^2$, plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$) and computed with \Code{FormFactorAnisoPyramid(20.*nanometer, 16.*nanometer, 60.*degree)}.}
+\label{fig:FFAnisoPyramidEx}
+\end{figure}
+
+%\FloatBarrier
+
+%\subsection{References}
+%Like in \Code{IsGISAXS}, the base angle $\alpha$ is the same for both unequal
+%side. This means that a full anisotropic pyramid is not a limit case. \\
+%But \BornAgain\ uses a different convention of the parameters relative
+%to the base. We input the full length and width instead of half values.
+%Condition on the parameters: 
+%Should not it be: H/R < tan(alpha) and  H/W < tan(alpha) instead of H/R < tan(alpha) and  
+%W/R < tan(alpha) where H is the height and R, W the side-lengths of the rectangular base?
+
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Cuboctahedron} \SecLabel{Cuboctahedron} 
+
+\paragraph{Real-space geometry}\mbox{}\\
+It is a combination of two pyramids with square bases, as shown in fig.~\ref{fig:cuboctahedron}: the bottom one
+is upside down with an height $H$ and the top one has the opposite
+orientation (the standard one) and an height $r_H \times H$.
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Cuboctahedron2dxz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Cuboctahedron2dxy}}
+\hfill
+\caption{Sketch of a Cuboctahedron.}
+\label{fig:cuboctahedron}
+\end{figure}
+
+\FloatBarrier
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item length of the shared square base $L$,
+\item height $H$,
+\item height\_ratio $r_H$,
+\item $\alpha$ is the angle between the base and the
+  side faces, taken in the middle of the base lines (see
+  fig.~\ref{fig:pyramid} in \SecRef{Pyramid}).
+\end{itemize}
+
+\paragraph{Restrictions on the parameters:} $\dfrac{2H}{L}< \tan(\alpha)$ and $\dfrac{2r_HH}{L}< \tan(\alpha)$.
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $ V= \dfrac{1}{6} \tan(\alpha)L^3 \Big[ 2
+         - \Big(1 - \dfrac{2H }{L\tan(\alpha)} \Big)^3
+           - \Big(1 - \dfrac{2 r_H
+             H}{L\tan(\alpha) }\Big)^3\Big]$,
+\item particle surface seen from above $S =L^2$.
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+\begin{equation*}
+F(\mathbf{q}, L, H, r_H, \alpha)=\exp(iq_z
+H)\Big[F_{\rm{Pyramid}}(q_x,q_y, q_z, L, r_H H,
+\alpha)+F_{\rm{Pyramid}}(q_x, q_y, -q_z, L, H, \alpha))\Big]
+\end{equation*}
+
+\paragraph{Syntax:} \Code{FormFactorCuboctahedron(length, height, height\_ratio,
+  alpha)}
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:FFcuboctahEx} shows the normalized intensity $|F|^2/V^2$, computed with $L=20$~nm, $H=13$~nm, $r_H=0.7$, and $\alpha=60^{\circ}$.
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffcuboctah}
+\end{center}
+\caption{Normalized intensity for the form factor of a cuboctahedron plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$) and computed with \Code{FormFactorCuboctahedron(20.*nanometer, 13.*nanometer, 0.7, 60.*degree)}.}
+\label{fig:FFcuboctahEx}
+\end{figure}
+
+%\FloatBarrier
+
+%\subsection{References}
+%In comparison with \Code{IsGISAXS}, as for the  form factor of a  Pyramid,
+%we use the full length of a side of the square base:
+%$L=2R_{\rm{\Code{IsGISAXS}}}$. 
+
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
+\section{Cylinder} \SecLabel{Cylinder}
+ 
+\paragraph{Real-space geometry}\mbox{}\\
+This shape is a right circular cylinder (see fig.~\ref{fig:cylinder}).
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Cylinder2dxz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Cylinder2dxy}}
+\hfill
+\caption{Sketch of a Cylinder.}
+\label{fig:cylinder}
+\end{figure}
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item radius of the circular base $R$, 
+\item height $H$.
+\end{itemize}
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V = \pi R^2 H$,
+\item particle surface seen from above $S=\pi R^2$.
+
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+  \begin{equation*}
+F(\mathbf{q},R, H)=  2\pi
+ R^2 H  \sinc\left(q_ z \frac{H}{2}\right) \exp\left(i q_ z \frac{H}{2}\right) \frac{J_1(q_{\parallel} R )}{q_{\parallel} R },
+ \end{equation*}
+with $q_{\parallel}=\sqrt{q_x^2+q_y^2}$ and $J_1(x)$ is the first order
+Bessel function of the first kind \cite{AbSt64}.
+
+\paragraph{Syntax:} \Code{FormFactorCylinder(radius, height)}
+
+\newpage
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:FFcylinderEx} shows the normalized intensity
+$|F|^2/V^2$, computed with $R=8$~nm and \mbox{$H=16$~nm.}
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffcylinder}
+\end{center}
+\caption{Normalized intensity for the form factor of a cylinder plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$.) It
+has been  computed with \Code{FormFactorCylinder(8.*nanometer, 16.*nanometer)}.}
+\label{fig:FFcylinderEx}
+\end{figure}
+%\FloatBarrier
+
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Ellipsoidal cylinder} \SecLabel{EllipsoidalCylinder} 
+
+\paragraph{Real-space geometry}\mbox{}\\
+This is a cylinder whose cross section is an ellipse.
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/EllipsoidalCylinder2dxz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/EllipsoidalCylinder2dxy}}
+\hfill
+\caption{Sketch of an Ellipsoidal Cylinder.}
+\label{fig:ellipscylinder}
+\end{figure}
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item $r_a$ = half length of the ellipse main axis parallel to $x$,
+\item$r_b$ = half length of the ellipse main axis parallel to $y$, 
+\item height $H$.
+\end{itemize}
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V = \pi r_a r_bH$,
+\item particle surface seen from above $S = r_a r_b$.
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+The total form factor is given by 
+\begin{equation*}
+F(\mathbf{q},R,W,H) = 2\pi r_a r_b H \exp\left(i\frac{q_z
+  H}{2}\right)\sinc\left(\frac{q_z H}{2}\right) \frac{J_1(\gamma)}{\gamma},
+\end{equation*}
+with $\gamma=\sqrt{(q_x r_a)^2+(q_y r_b)^2}$ and $J_1(x)$ is the first order
+Bessel function of the first kind \cite{AbSt64}.
+
+\paragraph{Syntax:} \Code{FormFactorEllipsoidalCylinder($r_a$, $r_b$, height)}
+
+\newpage
+
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:FFellipscylinderEx} shows the normalized intensity
+$|F|^2/V^2$, computed with $r_a=13$~nm, $r_b=8$~nm, and $H=16$~nm.
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffellipscylinder}
+\end{center}
+\caption{Normalized intensity for the form factor of an ellipsoidal
+  cylinder plotted against ($q_y$, $q_z$) and ($q_x$,
+  $q_y$) and computed with \Code{FormFactorEllipsoidalCylinder(8.*nanometer, 13.*nanometer, 16*nanometer)}.}
+\label{fig:FFellipscylinderEx}
+\end{figure}
+
+%\subsection{References}
+%This form factor is referred to as "Ellipsoid'' in \Code{ISGISAXS}. 
+
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Cone} \SecLabel{Cone} 
+
+\paragraph{Real-space geometry}
+This shape is a truncated cone as shown in fig.~\ref{fig:cone}. 
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Cone2dxz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Cone2dxy}}
+\hfill
+\caption{Sketch of a Cone.}
+\label{fig:cone}
+\end{figure}
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item radius $R$,
+\item height $H$,
+\item $\alpha$ is the angle between the side and the circular base.
+\end{itemize}
+
+\paragraph{Restrictions on the parameters:} $\dfrac{H}{R}< \tan(\alpha)$.
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V = \dfrac{\pi}{3} \tan(\alpha) R^3 \left[ 
+            1 - \left(1- \dfrac{H}{\tan(\alpha)R}\right)^3\right]$,
+\item  particle surface seen from above $S=\pi R^2$.
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+\begin{equation*}
+F(\mathbf{q}, R, H, \alpha) = \int_0 ^H 2\pi R_z^2
+\frac{J_1(q_{\parallel}R_z)}{q_{\parallel} R_z}\exp(iq_z z)dz,
+\end{equation*}
+with $R_z =R-\dfrac{z}{\tan \alpha}$, $\mathbf{q}_{\parallel}=\sqrt{q_x^2+ q_y^2}$ and $J_1(x)$ is the first order
+Bessel function of the first kind \cite{AbSt64}.
+
+\paragraph{Syntax:}  \Code{FormFactorCone(radius, height, alpha)}. 
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:FFConeEx} shows the normalized intensity
+$|F|^2/V^2$, computed with $R=10$~nm, $H=13$~nm, and $\alpha=60^{\circ}$.
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffcone}
+\end{center}
+\caption{Normalized intensity for the form factor of a Cone plotted against ($q_y$, $q_z$) and ($q_x$, $q_y$.) It
+  has been  computed with \Code{FormFactorCone(10.*nanometer,13.*nanometer, 60.*degree)}.}
+\label{fig:FFConeEx}
+\end{figure}
+
+%\subsection{References}
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Full Sphere} \SecLabel{FullSphere}
+
+\paragraph{Real-space geometry}\mbox{}\\
+The full sphere is parametrized by its radius $R$. 
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/FullSphere2dxz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/FullSphere2dxy}}
+\hfill
+\caption{Sketch of a Full Sphere.}
+\label{fig:fullsphere}
+\end{figure}
+
+\FloatBarrier
+
+\paragraph{Parameters:} radius $R$.
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V = \dfrac{4\pi}{3}R^3$,
+\item particle surface seen from above $S= \pi R^2$.
+%\item radius of gyration
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+\begin{equation*}
+F(\mathbf{q},R) = 4\pi R^3 \exp(iq_z R)\frac{\sin(q R) - q R \cos(q R)}{(qR)^3},
+\end{equation*}
+where $q=\sqrt{q_x^2 + q_y^2 + q_z^2}$.
+
+\paragraph{Syntax:} \Code{FormFactorFullSphere(radius)}
+
+\newpage
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:FFfSphereEx} shows the normalized intensity $|F|^2/V^2$, computed with $R=8$~nm.
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figfffsphere}
+\end{center}
+\caption{Normalized intensity for the
+  form factor of a Full Sphere plotted against ($q_y$, $q_z$) and ($q_x$, $q_y$) and computed with \Code{FormFactorFullSphere(8.*nanometer)}.}
+\label{fig:FFfSphereEx}
+\end{figure}
+
+%\FloatBarrier
+
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Truncated Sphere}\SecLabel{Sphere}
+  
+\paragraph{Real-space geometry}\mbox{}\\
+This shape is a spherical dome, \textit{i.e.} a portion of a sphere cut off by a plane (perpendicular
+to $z$-axis) as shown in fig.~\ref{fig:sphere}.
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Sphere2dxz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Sphere2dxy}}
+\hfill
+\caption{Sketch of a Truncated Sphere.}
+\label{fig:sphere}
+\end{figure}
+\FloatBarrier
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item radius $R$,
+\item height $H$.
+\end{itemize}
+
+\paragraph{Restrictions on the parameters:} $0 \leq H\leq 2R$.
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V=\pi R^3 \left[\dfrac{2}{3} + \dfrac{H-R}{R} - \dfrac{1}{3}\left(\dfrac{H-R}{R}\right)^3\right]$,
+\item particle surface seen from above $S = \left\{\begin{array}{ll} \pi R^2, & H \geq R \\
+         \pi\left(2RH-H^2\right), & H < R \end{array}\right. $.
+%\item gyration radius along $z$ axis %$R_g = \left\{\begin{array}{ll}
+%R, & H > R \\ \sqrt{2RH-H^2}, & H < R \end{array}\right. .$
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+\begin{equation*}  
+F(\mathbf{q},R, H)= 2\pi \exp[i q_z (H-R)]\int_{R-H} ^{R} R_z^2 \frac{J_1(q_{\parallel} R_z) }{q_{\parallel} R_z} \exp(i q_z z) dz,
+\end{equation*}
+with $J_1(x)$ the first order
+Bessel function of the first kind \cite{AbSt64}, $q_{\parallel} =
+\sqrt{q_x^2+q_y^2}$, and $R_z = \sqrt{R^2-z^2}$
+
+\paragraph{Syntax:} \Code{FormFactorTruncatedSphere(radius, height)}
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:SphereEx} shows the normalized intensity $|F|^2/V^2$, computed with $R=5$~nm and $H=7$~nm:
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffsphere}
+\end{center}
+\caption{Normalized intensity for the form factor of a Truncated Sphere plotted against ($q_y$, $q_z$) and ($q_x$, $q_y$) and
+  computed with \Code{FormFactorTruncatedSphere(5.*nanometer, 7.*nanometer)}.}
+\label{fig:SphereEx}
+\end{figure}
+
+%\FloatBarrier
+
+%\subsection{References}
+%Equation~(\ref{eq:ffsphere}) agrees with the \lq\lq Sphere\rq\rq ~form
+%factor of \IsGISAXS~\cite{Laz02}.
+
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Full Spheroid} \SecLabel{FullSpheroid}  
+
+\paragraph{Real-space geometry}\mbox{}\\
+A full spheroid is generated by rotating an ellipse around the vertical
+axis (see fig.~\ref{fig:fullspheroid}).
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/FullSpheroid2dxz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/FullSpheroid2dxy}}
+\hfill
+\caption{Sketch of a Full Spheroid. }
+\label{fig:fullspheroid}
+\end{figure}
+
+\FloatBarrier
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item radius $R$,
+\item height $H$.
+\end{itemize}
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V =\dfrac{2}{3}R^2H$,
+\item particle surface seen from above $S =\pi R^2$. 
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+\begin{equation*}
+F(\mathbf{q}, R, H) = 4\pi \exp(i q_z H/2) \int_0 ^{H/2}R_z ^2
+\frac{J_1(q_{\parallel}R_z)}{q_{\parallel}R_z} \cos(q_z z) dz,
+\end{equation*}
+with $J_1(x)$ the first order
+Bessel function of the first kind \cite{AbSt64},
+$R_z = R\sqrt{1-\frac{4z^2}{H^2}}$, $\gamma_z = \sqrt{(q_x R_z)^2+(q_y R_z)^2}$.
+
+
+\paragraph{Syntax:} \Code{FormFactorFullSpheroid(radius,height)}
+\newpage
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:FFfspheroidEx} shows the normalized intensity
+$|F|^2/V^2$, computed with $R=10$~nm, and $H=13$~nm.
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figfffspheroid}
+\end{center}
+\caption{Normalized intensity for the form factor of a full spheroid plotted against ($q_y$, $q_z$) and ($q_x$, $q_y$) and
+  computed with \Code{FormFactorFullSpheroid(10.*nanometer, 13.*nanometer)}.}
+\label{fig:FFfspheroidEx}
+\end{figure}
+
+%\FloatBarrier
+
+%\subsection{References}
+%The expression is identical to \Code{IsGISAXS} manual. In the code,
+%the integration is over $[-H/2, H/2]$ with $\exp(iq_z z)$ instead of
+%the cosine.
+%In \Code{IsGISAXS}, factor 4 instead of 2 in the expression of the
+%volume. In the code there is also a problem with an extra factor 2 in the function to integrate.
+
+\newpage%{\cleardoublepage}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Truncated Spheroid} \SecLabel{Spheroid}
+
+\paragraph{Real-space geometry}\mbox{}\\
+This shape is a spheroidal dome: a portion of a full spheroid cut off
+by a plane perpendicular to the $z$-axis.
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Spheroid2dxz.eps}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Spheroid2dxy.eps}}
+\hfill
+\caption{Sketch of a Truncated Spheroid.}
+\label{fig:spheroid}
+\end{figure}
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item radius $R$,
+\item height $H$,
+\item height\_flattening coefficient in the perpendicular direction $f_p$.
+\end{itemize}
+
+\paragraph{Restrictions on the parameters:} $0< \dfrac{H}{R}< 2f_p$.
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V = \dfrac{\pi R H^2}{f_p}  \Big(1-\dfrac{H}{3f_p R}\Big)$,
+\item particle surface seen from above $S = \left\{\begin{array}{ll} \pi R^2, & H \geq f_pR \\
+         \pi\left(\dfrac{2RH}{f_p}-\dfrac{H^2}{f_p^2}\right), & H < R \end{array}\right.$.
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+\begin{equation*} 
+F(\mathbf{q},R, H,f_p) =   2\pi \exp[iq_z(H-f_pR)] \int_{f_p R-H} ^{f_p R} R_z
+        ^2\frac{J_1(q_{\parallel}R_z)}{q_{\parallel}R_z} \exp(i q_z z) dz
+\end{equation*}
+with $J_1(x)$ the first order
+Bessel function of the first kind \cite{AbSt64}, $q_{\parallel}=\sqrt{q_x^2+q_y^2} $ and $R_z=\sqrt{R^2-z^2/f_p^2}$.
+
+\paragraph{Syntax:} \Code{FormFactorTruncatedSpheroid(radius, height, height\_flattening)}
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:FFspheroidEx} shows the normalized intensity
+$|F|^2/V^2$, computed with $R=7.5$~nm, $H=9$~nm and $f_p=1.2$.
+
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffspheroid}
+\end{center}
+\caption{Normalized intensity for the form factor of a Truncated Spheroid plotted against ($q_z$, $q_y$) and ($q_x$, $q_y$) and
+  computed with \Code{FormFactorTruncatedSpheroid(7.5*nanometer, 9.*nanometer, 1.2)}.}
+\label{fig:FFspheroidEx}
+\end{figure}
+
+%\FloatBarrier
+
+%\subsection{References}
+%In \Code{IsGISAXS}'s manual there is an extra factor 2 in the
+%expression of the volume.
+
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Hemi ellipsoid} \SecLabel{HemiEllipsoid}  
+
+\paragraph{Real-space geometry}\mbox{}\\
+This shape is a truncated ellipsoid as shown in fig.~\ref{fig:hemiellipsoid}.
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/HemiEllipsoid2dxz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/HemiEllipsoid2dxy}}
+\hfill
+\caption{Sketch of an Hemi-ellipsoid.}
+\label{fig:hemiellipsoid}
+\end{figure}
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item $r_a$ = half length of the ellipse main axis parallel to $x$,
+\item$r_b$ = half length of the ellipse main axis parallel to $y$, 
+\item $H$ = height (half length of the vertical main axis of a full ellipsoid).
+\end{itemize}
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V = \dfrac{2}{3}\pi r_a r_bH$,
+\item particle surface seen from above $S =\pi r_a r_b$.
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+\begin{equation*}
+F(\mathbf{q},r_a,r_b,H) = 2\pi \int_0 ^{H} r_{a,z} r_{b,z}
+\frac{J_1(\gamma_z)}{\gamma_z}\exp(iq_z z)dz,
+\end{equation*}
+with $J_1(x)$ the first order
+Bessel function of the first kind \cite{AbSt64}, $r_{a,z} = r_a \sqrt{1-\left(\dfrac{z}{H} \right)^2}$, ${r_{b,z} = r_b
+\sqrt{1-\left(\dfrac{z}{H} \right)^2}}$ and $\gamma_z =\sqrt{(q_x r_{a,z})^2+(q_y r_{b,z})^2}$.
+
+\paragraph{Syntax:} \Code{FormFactorHemiEllipsoid($r_a$, $r_b$, height)}
+
+\newpage
+
+\paragraph{Example} \mbox{}\\
+Figure~\ref{fig:FFhemiellipsEx} shows the normalized intensity
+$|F|^2/V^2$, computed with $r_a=10$~nm, $r_b=6$~nm and $H=8$~nm.
+
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffhemiellips}
+\end{center}
+\caption{Normalized intensity for the form factor of an Hemi-Ellipsoid plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$)
+  computed with \Code{FormFactorHemiEllipsoid(10.*nanometer, 6.*nanometer, 8.*nanometer)}.}
+\label{fig:FFhemiellipsEx}
+\end{figure}
+
+%\FloatBarrier
+
+%\subsection{References}
+%This shape is referred to as ``Anisotropic hemi ellipsoid'' in  \Code{ISGISAXS}.
+%Problem when running  \Code{ISGISAXS}.
+%In \Code{IsGISAXS} manual, where does the minus sign in exp(-iq\_z z)
+%come from?
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Ripple1} \SecLabel{Ripple1}  
+
+\paragraph{Real-space geometry}\mbox{}\\
+This shape has a sinusoidal profile (see fig.~\ref{fig:ripple1}).
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Ripple12dyz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Ripple12dxy}}
+\hfill
+\caption{Sketch of a Ripple1.}
+\label{fig:ripple1}
+\end{figure}
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item length $L$, 
+\item width $W$, 
+\item height $H$. 
+\end{itemize}
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V = \dfrac{L W H}{2} $,
+\item particle surface seen from above $S = L W$.
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+\begin{align*}
+F(\mathbf{q},L,W,H) &=L \cdot \frac{W}{\pi}\cdot \sinc\left(\frac{q_xL}{2}\right)\times \\ &\int_0^H{dz \arccos\left(\frac{2z}{H}-1\right)\sinc\left[\frac{q_yW}{2\pi}\arccos\left(\frac{2z}{H} - 1\right)\right]\exp\left(iq_zz\right)},
+\end{align*}
+where $\arccos$ is the  arc cosine (\textit{i.e.} the inverse
+operation of cosine).
+
+\paragraph{Syntax:} \Code{FormFactorRipple1(length, width, height)}
+
+\paragraph{Example}\mbox{}\\
+Figure~\ref{fig:FFripple1Ex} shows the normalized intensity
+$|F|^2/V^2$, computed with $L=27$~nm, $W=20$~nm and $H=14$~nm.
+
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffripple1}
+\end{center}
+\caption{Normalized intensity for the form factor of a ripple1
+  $|F|^2/V^2$, plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$)
+  computed with \Code{FormFactorRipple1(27.*nanometer, 20.*nanometer, 14.*nanometer)}.}
+\label{fig:FFripple1Ex}
+\end{figure}
+%\FloatBarrier
+
+\newpage%{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Ripple2} \SecLabel{Ripple2}  
+
+\paragraph{Real-space geometry}\mbox{}\\
+This shape has an asymmetric sawtooth profile.
+
+\begin{figure}[ht]
+\hfill
+\subfigure[Side view]{\includegraphics[width=5cm]{Figures/Ripple22dyz}}
+\hfill
+\subfigure[Top view]{\includegraphics[width=5cm]{Figures/Ripple22dxy}}
+\hfill
+\caption{Sketch of a Ripple2.}
+\label{fig:ripple2}
+\end{figure}
+
+\FloatBarrier
+
+\paragraph{Parameters:}
+\begin{itemize}
+\item length $L$, 
+\item width $W$, 
+\item height $H$,
+\item asymmetry $d$. 
+\end{itemize}
+
+\paragraph{Restriction on the parameters:} $|d| < \frac{W}{2} $.
+
+\paragraph{Properties:}
+\begin{itemize}
+\item volume $V = \dfrac{L W H}{2}$,
+\item particle surface seen from above $S = L W$.
+\end{itemize}
+
+\paragraph{Expression of the form factor}
+\begin{align*}
+F(\mathbf{q},L,W,H,d) &=L W
+\sinc\left(\frac{q_xL}{2}\right)\times \\ &
+\int_0^H 
+\left(1-\frac{z}{H}\right)
+ \sinc\left[\frac{q_y
+    W}{2}\left(1-\frac{z}{H}\right)\right] 
+\exp\left\{ i\left[q_zz -
+    q_yd\left(1-\frac{z}{H}\right)\right]\right\} 
+dz
+\end{align*}
+
+\paragraph{Syntax:} \Code{FormFactorRipple2(length, width, height, asymmetry)}
+
+\paragraph{Examples}
+Figure~\ref{fig:FFripple2Ex} shows the normalized intensity
+$|F|^2/V^2$, computed with $L=36$~nm, $W=25$~nm, $H=14$~nm, and $d=3$~nm.
+
+\begin{figure}[h]
+\begin{center}
+\includegraphics[width=\textwidth]{Figures/figffripple2}
+\end{center}
+\caption{Normalized intensity for the form factor of a ripple2 plotted against ($q_y$, $q_z$) and  ($q_x$, $q_y$)
+  computed with \Code{FormFactorRipple2(36.*nanometer, 25.*nanometer, 14.*nanometer, 3.*nanometer)}.}
+\label{fig:FFripple2Ex}
+\end{figure}
+
+%\FloatBarrier
+
+%\newpage{\cleardoublepage}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\section{Distorted Wave Born Approximation}
+%The previous sections of this appendix on form factors have dealt with the Born approximation. In this case the form factor is given by a single integral over the particle shape (see equation~\ref{ffformulaBA}). But this 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 will be dealt with in Section~\ref{appendixinterf}.  We also do not take any polarization effects into account. They will be described in...\\
+
+% In the DWBA, the form factor of a particle in a multilayer system is given by
+
+%\begin{align}
+%F_{\rm{DWBA}} (\vect{k}_i,\vect{k}_f, r_z) & = T_i T_f F_{\rm{BA}} (\vect{k}_i-\vect{k}_f) e^{i (k_{i,z}-k_{f,z}) r_z} + R_i T_f F_{\rm{BA}}(\vect{\widetilde{k}}_i-\vect{k}_f) e^{i(-k_{i,z}-k_{f,z})r_z}
+ %\nonumber \\
+ % &+ T_i R_f F_{\rm{BA}}(\vect{k}_i-\vect{\widetilde{k}}_f)e^{i(k_{i,z}+k_{f,z})r_z} + R_iR_fF_{\rm{BA}} (\vect{\widetilde{k}}_i-\vect{\widetilde{k}}_f)e^{i(-k_{i,z}+k_{f,z})r_z} \; , \label{eq:dwbageneral}
+%\end{align}
+%where $F_{\rm{BA}}$ is the expression of the form factor in the Born approximation, $r_z$ is the $z$-coordinate of the particle's position (measured from the bottom of the particle), $\vect{k}_i=(k_{i,x}, k_{i,y}, k_{i,z})$ $\vect{k}_f=(k_{f,x}, k_{f,y}, k_{f,z})$ are the incident and scattered wave vectors in air, respectively \cite{Raus95}. With a tilde (\~{}), these wavevectors components are evaluated in the multilayer system (the refractive indices of the different constituting materials have to be taken into account). 
+%$T_i$, $T_f$, $R_i$, $R_f$ are the transmission and reflection coefficients for the incident wave (index $i$) or the scattered one (index $f$). These coefficients can be calculated using the Parratt formalism \cite{Parr54} or the matrix method \cite{BoWo99}. $\vect{k}_i-\vect{k}_f$ is equal to the scattering vector $\vect{q}$ and the $z$-axis is pointing upwards.\\
+
+%\ImportantPoint{Remark:}{The particles cannot sit in between layers. At most they can be sitting on any inner interfaces.}
+
+%\vspace{18pt}
+
+%In the followings, the DWBA will be illustrated for two different layouts of particles: 
+%\begin{itemize}
+%\item particles deposited on a substrate,
+%\item particles buried in a layer on a substrate.
+%\end{itemize}
+
+%\ImportantPoint{Remark:}{In \BornAgain\ There is no limitation to the number of layers composing the sample.}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\subsection{Particles deposited on a substrate}
+%%Substrate modified Born approximation
+%In this configuration, the particles are sitting on top of a substrate layer, in the air as shown in fig.~\ref{fig:SchemDWBA}. In the DWBA the expression of a form factor becomes 
+%\begin{align}
+%F_{\rm{DWBA}}(q_{\parallel}, k_{i,z}, k_{f,z}) &= F_{\rm{BA}}(q_{\parallel}, k_{i,z}-k_{f,z})+ R_i F_{\rm{BA}}(q_{\parallel}, -k_{i,z}-k_{f,z}) \nonumber \\
+%&+ R_f F_{\rm{BA}}(q_{\parallel}, k_{i,z}+k_{f,z}) + R_i R_f F_{\rm{BA}}(q_{\parallel},-k_{i,z}+k_{f,z}), \label{eq:dwbaair}
+%\end{align}
+%where $q_{\parallel}$ is the component of the scattering beam in the plane of the interface ($\vect{q}=\vect{k}_i-\vect{k}_f$), $k_{i,z}$ and $k_{f,z}$ are the z-component of the incident and scattered beam, respectively. $R_i$, $R_f$ are the reflection coefficients in incidence and reflection. They are defined as\\ $R=\dfrac{k_z+\sqrt{n_s^2k_0^2-|k_{\parallel}|^2}}{k_z-\sqrt{n_s^2 k_0^2-|k_{\parallel}|^2}}$, where $n_s=1-\delta_s -i \beta_s$ is the refractive index of the substrate, $k_0$ is the wavelength in vacuum ($2\pi /\lambda$), $k_z$ and $k_{\parallel}$ are the $z$-component and the in-plane component of $\vect{k}_i$ or $\vect{k}_f$. \\
+
+%\ImportantPoint{Remark:}{If the particles are sitting on a multilayered system, the expression of the form factor in the DWBA is obtained by replacing the Fresnel coefficient by the corresponding coefficients of the underlying layers \cite{Parr54,BoWo99}.}
+
+%\vspace{18pt}
+
+%Figure~\ref{fig:SchemDWBA} illustrates the four scattering processes for a supported particle, taken into account in the DWBA. The first term of eq.~\ref{eq:dwbaair}  corresponds to the Born approximation. Each term of $F_{\rm{DWBA}}$ is weighted by a Fresnel coefficient. 
+
+%\begin{figure}[h]
+%\begin{center}
+%\includegraphics[width=\textwidth]{Figures/drawingDWBA}
+%\end{center}
+%\caption{Schematic views of the different terms appearing in the expression of the form factor under DWBA for particles sitting on a substrate layer.}
+%\label{fig:SchemDWBA}
+%\end{figure}
+
+%Script~\ref{lst:badwba} illustrates the difference between BA and DWBA in \BornAgain\ when generating the sample.  We consider the simple case of:
+%\begin{itemize}
+%\item one kind of particles' shape,
+%\item no interference between the particles,
+%\item in the DWBA, a sample made of a layer of substrate on which are deposited the particles,
+%\item in the BA, a sample composed of the particles in air.
+%\end{itemize} 
+
+%Figure~\ref{fig:spheroidbadwba} shows the intensity contourplot generated using this script with truncated spheroids as particles. Note that the full \Python\ script UMFormFactorBA\_DWBA.py is available in folder Examples/Python/UserManual/.
+
+%\newpage
+
+%\begin{lstlisting}[language=python, style=eclipseboxed,numbers=none,nolol,caption={\Code{Python} script to generate a sample using Born or Distorted Wave Born Approximation. The difference between BA and DWBA in this simple case is the absence or presence of a substrate layer in the sample.},label={lst:badwba}]
+%def get_sample():
+%    """
+%    Build and return the sample to calculate form factor of 
+%    truncated spheroid in Born or Distorted Wave Born Approximation.
+%    """
+%    # defining materials
+%    m_ambience = HomogeneousMaterial("Air", 0.0, 0.0)
+%    m_substrate = HomogeneousMaterial("Substrate", 6e-6, 2e-8)
+%    m_particle = HomogeneousMaterial("Particle", 6e-4, 2e-8)
+
+%    # collection of particles
+%    ff= FormFactorTruncatedSpheroid(7.5*nanometer, 9.0*nanometer, 1.2)
+%    particleshape = Particle(m_particle, ff)
+%    particle_layout = ParticleLayout()
+%    particle_layout.addParticle(particleshape, 0.0, 1.0)
+
+%    # interferences
+%    interference = InterferenceFunctionNone()
+%    particle_layout.addInterferenceFunction(interference)
+
+%    # assembling the sample
+%    air_layer = Layer(m_ambience)
+%    air_layer.setLayout(particle_layout)
+%    substrate_layer = Layer(m_substrate, 0)
+
+%    multi_layer = MultiLayer()
+%    multi_layer.addLayer(air_layer)
+%    # Comment the following line out for Born Approximation
+%    multi_layer.addLayer(substrate_layer)
+%    return multi_layer
+%\end{lstlisting}
+
+%\begin{figure}[ht]
+%\hfill
+%\subfigure[Born Approximation]{\includegraphics[width=6cm]{Figures/ffspheroidBA}}
+%\hfill
+%\subfigure[DWB Approximation]{\includegraphics[width=6cm]{Figures/ffspheroidDWBA}}
+%\hfill
+%\caption{Intensity map of TruncatedSpheroid form factor in BA and DWBA computing using script~\ref{lst:badwba} for the sample.}
+%\label{fig:spheroidbadwba}
+%\end{figure}
+
+%\FloatBarrier 
+
+%\ImportantPoint{Remark:}{In \BornAgain, the DWBA is implemented automatically when assembling the sample with more than the air layer.}
+
+%\subsection{Buried particles} 
+%The system considered in this section consists of particles encapsulated in a layer, which is sitting on a substrate (see fig.~\ref{fig:SchemDWBAburied}). In this case the form factor in the DWBA is given by
+
+%\begin{align}
+%F_{\rm{DWBA}}(q_{\parallel}, k_{i,z}, k_{f,z}) &= T_i T_f F_{\rm{BA}}(q_{\parallel}, k_{i,z}-k_{f,z})e^{i(k_{i,z}-k_{f,z})d}+ R_i T_f F_{\rm{BA}}(q_{\parallel}, -k_{i,z}-k_{f,z})e^{i(-k_{i,z}-k_{f,z})d} \nonumber \\
+%&+ R_f T_i F_{\rm{BA}}(q_{\parallel}, k_{i,z}+k_{f,z}) e^{i(k_{i,z}+k_{f,z})d}+ R_f R_iF_{\rm{BA}}(q_{\parallel},-k_{i,z}+k_{f,z})e^{i(-k_{i,z}+k_{f,z})d}, \label{eq:dwbaburied}
+%\end{align}
+
+%\begin{equation*}
+%R_j =\frac{t^{j}_{0,1}r^{j}_{1,2}\exp(2ik_{j,z}t)}{1+r^{j}_{0,1}r^{j}_{1,2}\exp(2ik_{j,z}t)}, \quad %T_j=\frac{t^{j}_{0,1}}{1+r^{j}_{0,1}r^{j}_{1,2}\exp(2ik_{j,z}t)}, j=i,f 
+%\end{equation*}
+%where $q_{\parallel}$ is the component of the scattering beam in the plane of the interface, $k_{i,z}$ and $k_{f,z}$ are the z-component of the incident and scattered beams, respectively.  $d$ is the depth at which the particles are sitting in the layer. Note that this value is given relative to the top of this layer and it is not the coordinate in the absolute referential (linked with the full sample) and it is measured up to the bottom of the particle. $t$ is the thickness of the intermediate layer containing the particles. $R_{i,f}$ and $T_{i,f}$  are the reflection  and transmission coefficients in incidence and reflection (they can be calculated using Parratt or matrix formalism). $r^j_{0,1}$, $r^j_{1,2}$ $t^j_{0,1}$ are the reflection and transmission coefficients between layers; the indices are related to different boundaries with 0: air, 1: intermediate layer and 2: substrate layer and the superscript $j$ is associated with the incident or scattered beams:
+%\begin{equation*}
+%r^j_{n,n+1}=\frac{k_{j,z,n}-k_{j,z,n+1}}{k_{j,z,n}-k_{j,z,n+1}}, \qquad t^j_{n,n+1}= \frac{2k_{j,z,n}}{k_{j,z,n}-k_{j,z,n+1}}, \quad n=0,1, \quad j=i,f,
+%\end{equation*}
+%where index $n$ is related to the layers, $z$ to the vertical component, and $j$ to the beams (incident and outgoing).
+
+%\begin{figure}[h]
+%\begin{center}
+%\includegraphics[width=\textwidth]{Figures/drawingDWBAburied}
+%\end{center}
+%\caption{Schematic views of the different terms appearing in the expression of the form factor under the DWBA for buried particles.}
+%\label{fig:SchemDWBAburied}
+%\end{figure}
+
+%%For example, for a three layer system (particles embbedded in the middle layer of thickness $t$), 
+%%\begin{align*}
+%%F=A_1T_i T_fF_{\rm{BA}}(q_{\parallel}, k_{i,z}-k_{f,z})+ R_i T_f F_{\rm{BA}}(q_{\parallel}, -k_{i,z}-k_{f,z}) \\
+%%&+ R_f T_i F_{\rm{BA}}(q_{\parallel}, k_{i,z}+k_{f,z}) + R_f R_iF_{\rm{BA}}(q_{\parallel},-k_{i,z}+k_{f,z})
+%%\end{align*} 
+
+%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} (The full script UMFormFactor\_Buried\_DWBA.py can be found in /Examples/Python/UserManual.
+
+%\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}]
+%def get_sample():
+%    """
+%    Build and return the sample with buried spheres in DWBA.
+%    """
+%    # defining materials
+%    m_ambience = HomogeneousMaterial("Air", 0.0, 0.0)
+%    m_interm_layer = HomogeneousMaterial("IntermLayer",3.45e-6, 5.24e-9)
+%    m_substrate = HomogeneousMaterial("Substrate", 7.43e-6, 1.72e-7)
+%    m_particle = HomogeneousMaterial("Particle", 0.0, 0.0)
+
+%    # collection of particles 
+%    ff = FormFactorFullSphere(10.2*nanometer)
+%    particleshape = Particle(m_particle, ff)
+%    particle_layout = ParticleLayout()
+%    particle_layout.addParticle(particleshape,20.1,1.0)
+
+%    # interferences 
+%    interference = InterferenceFunctionNone()
+%    particle_layout.addInterferenceFunction(interference)
+
+%    # assembling the sample 
+%    air_layer = Layer(m_ambience)
+%    intermediate_layer = Layer(m_interm_layer, 30.*nanometer)
+%    intermediate_layer.setLayout(particle_layout)
+%    substrate_layer = Layer(m_substrate, 0)
+   
+%    multi_layer = MultiLayer()
+%    multi_layer.addLayer(air_layer)
+%    multi_layer.addLayer(intermediate_layer)
+%    multi_layer.addLayer(substrate_layer)
+%    return multi_layer
+%\end{lstlisting}
+
+%\begin{figure}[ht]
+%\centering
+%\includegraphics[width=0.6\textwidth]{Figures/figIntBuriedPart}
+%\caption{Map of intensity scattered from a sample made of spherical particles embedded in the middle of a 30~nm-thick layer on a substrate (see Script~\ref{lst:dwbaburied} for details about the sample).}
+%\label{fig:dwbaburied}
+%\end{figure}
+
+%\newpage
+
+%\ImportantPoint{Remark:}{For layers different from the air layer, the top interface is considered as the reference level to position the encapsulated particles. For example, spheres positioned at depth $d$ (positive) are located at a distance $d$ from the top of the layer up to the bottom of these particles. This convention is different for the top air layer, where particles sitting at the interface with an underlying layer (\textit{i.e.} the bottom of the air layer) are located at depth 0 (see fig.~\ref{fig:depthpartBA}).}
+
+%\begin{figure}[ht]
+%\centering
+%\includegraphics[width=0.5\textwidth]{Figures/drawingDepthParticle}
+%\caption{Illustration of the convention about \Code{depth} used in \BornAgain\ to encapsulate particles in %layers.}
+%\label{fig:depthpartBA}
+%\end{figure}
+
+%\newpage
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%\section{Core-shell particles}
+% \BornAgain\ also offers the possibility to simulate more complicated shapes of particles by combining those listed in the previous sections. To generate a core-shell particle, the combination is performed using the following command:\\
+%\Code{ParticleCoreShell(shell\_particle, core\_particle, relative\_core\_position)},\\
+%where \Code{shell\_particle} and \Code{core\_particle} are the outer and inner parts of the core-shell particle, respectively. They refer to one of the form factors defined previously and to an associated material. For example, for the outer part,\\ \Code{shell\_particle=Particle(material\_shell, outer\_form\_factor)},\\ where \Code{material\_shell} is the material of the shell and \Code{outer\_form\_factor} is the shape of the outer part (cf. listing~\ref{lst:cshellsample}). \\ \Code{relative\_core\_position} defines the position of the centre of gravity of the inner shape with respect to the outer one. An example in fig.~\ref{fig:coreshell} shows a core shell particle made of a box for the outer part and of a shifted pyramidal shape for the inner one.\\
+
+%Figure~\ref{fig:FFCoreShellBA} displays the output intensity scattered in the Born Approximation using the code listed in~\ref{lst:cshellsample} to generate the core-shell particle. The full script can be found at /Examples/python/UserManual/UMFormFactor\_CoreShell.py. 
+
+%\begin{figure}[ht]
+%\hfill
+%\subfigure[Side view]{\includegraphics[width=5cm]{Figures/CoreShellParallPyrxz}}
+%\hfill
+%\subfigure[Top view]{\includegraphics[width=5cm]{Figures/CoreShellParallPyrxy}}
+%\hfill
+%\caption{Example of a core-shell particle composed of a box with a pyramidal  inset. The relative core shell position is marked %by the position of its center of gravity (blue point $\color{blue}\bullet$) with respect to the center of gravity of the box (red %point $\color{red}\bullet$). }
+%\label{fig:coreshell}
+%\end{figure}
+
+%\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}]
+ %   outer_ff = FormFactorBox(16.0*nanometer, 16.0*nanometer, 8.0*nanometer) 
+ %   inner_ff = FormFactorPyramid(12.0*nanometer, 7.0*nanometer, 60.0*degree)
+ %   shell_particle = Particle(m_shell, outer_ff)
+ %   core_particle = Particle(m_core, inner_ff)
+ %   core_position = kvector_t(1.5, 0.0, 0.0)
+
+%   particle = ParticleCoreShell(shell_particle, core_particle, core_position)
+%\end{lstlisting}
+
+%\begin{figure}[h]
+%\begin{center}
+%\includegraphics[width=0.6\textwidth]{Figures/CoreShellParallPyr}
+%\end{center}
+%\caption{Intensity map of a core-shell form factor in Born Approximation using  \Code{FormFactorBox(16*nanometer, %16*nanometer, 8*nanometer)} and \Code{FormFactorPyramid(12*nanometer, 7*nanometer, 60*degree)} for the outer and inner %shells, respectively. The core particle is shifted by 1.5~nm in the $x$-direction with respect to the centre of the outer shell. The %sample used to generate the particle is listed in~\ref{lst:cshellsample}.  There is no substrate and no interference between the %particles.}
+%\label{fig:FFCoreShellBA}
+%\end{figure}
+
+%%outer_ff = FormFactorParallelepiped(16*nanometer, 8*nanometer) 
+%%inner_ff = FormFactorPyramid(12*nanometer, 7*nanometer, 60*degree)
+%%  shell_particle = Particle(m_shell, outer_ff)
+%%  core_particle = Particle(m_core, inner_ff)
+%% core_position = kvector_t(1.5, 0.0, 0.0)
+%% alphai=0.2*degree
+%%    phii=0.*degree