Example 01 in Python (new figure for sample)

Core/Samples/inc/Layer.h

@@ -44,10 +44,10 @@ class BA_CORE_API_ Layer : public ICompositeSample
     //! Calls the ISampleVisitor's visit method
     virtual void accept(ISampleVisitor *p_visitor) const { p_visitor->visit(this); }
 
-    //! Sets layer thickness in Angstrom.
+    //! Sets layer thickness in nanometers.
     virtual void setThickness(double thickness);
 
-    //! Returns layer thickness in Angstrom.
+    //! Returns layer thickness in nanometers.
     virtual double getThickness() const { return m_thickness; }
 
     //! Sets _material_ of the layer.

Core/Samples/inc/LayerDecorator.h

@@ -44,7 +44,7 @@ class BA_CORE_API_ LayerDecorator : public Layer
     //! Sets _material_.
     virtual void setMaterial(const IMaterial* material);
 
-    //! Sets _material_ and _thickness_ in Angstrom.
+    //! Sets _material_ and _thickness_ in nanometers.
     virtual void setMaterial(const IMaterial* material, double thickness);
 
     //! Returns material

Core/Samples/src/Layer.cpp

@@ -43,7 +43,7 @@ void Layer::init_parameters()
 }
 
 
-//! Sets layer thickness in Angstrom.
+//! Sets layer thickness in nanometers.
 void Layer::setThickness(double thickness)
 {
     if (thickness < 0.)

Doc/UserManual/Appendix.tex

@@ -16,55 +16,66 @@
 \item Parallelepiped (\texttt{FormFactorParallelepiped})
 
 \begin{equation}
-F() = 4H R^2\exp(i q_z H/2) \frac{sin(q_xR)}{q_x R}\frac{ \sin(q_yR)}{q_y R}\frac{\sin(q_z H/2)}{q_z H/2}
+F(\mathbf{q},R, H) = 4H R^2\exp(i q_z H/2) \text{sinc}(q_xR)
+\text{sinc}(q_yR)\text{sinc}(q_z H/2)
 \end{equation}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \item Pyramid (\texttt{FormFactorPyramid})
 
 \begin{align*}
-        q_1 &=(H/2)((q_x-q_y)/\tan(\alpha) + q_z)\\
-        q_2 &=(H/2)((q_x-q_y)/\tan(\alpha) - q_z)\\
-        q_3 &=(H/2)((q_x+q_y)/\tan(\alpha) + q_z) \\
-        q_4 &=(H/2)((q_x+q_y)/\tan(\alpha) - q_z)\\
-        K_1 &= \frac{\sin(q_1)}{q_1} \exp(i q_1)  + i \frac{\sin(q_2)}{q_2} \exp(-i q_2)\\
-        K_2 &= -i \frac{sin(q_1)}{q_1} exp(i q_1) +i \frac{\sin(q_2)}{q_2} \exp(-i q_2)\\
-        K_3 &= \frac{\sin(q_3)}{q_3}\exp(i q_3)    + \frac{\sin(q_4)}{q_4} \exp(-i q_4)\\
-        K_4 &= -i \frac{\sin(q_3)}{q_3} \exp(i q_3) + i \frac{\sin(q_4)}{q_4} \exp(-i q_4)\\     
-  F() &= \frac{H}{q_x q_y} [ K_1 \cos( (q_x-q_y)R ) + K_2 \sin( (q_x-q_y)R ) - K_3 \cos( (q_x+q_y) R ) - K_4 \sin( (q_x+q_y) R )]
+        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]\quad
+        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 &= \text{sinc}(q_1 H)\exp(i q_1 H)  + i \text{sinc}(q_2 H) \exp(-i q_2 H)\\
+        K_2 &= -i \text{sinc}(q_1 H) \exp(i q_1 H) +i
+        \text{sinc}(q_2 H) \exp(-i q_2 H)\\
+        K_3 &= \text{sinc}(q_3 H) \exp(i q_3 H)    +
+        \text{sinc}(q_4 H) \exp(-i q_4 H)\\
+        K_4 &= -i \text{sinc}(q_3 H) \exp(i q_3 H) + i \text{sinc}(q_4 H) \exp(-i q_4 H)\\     
+  F(\mathbf{q},R, H, \alpha) &= \frac{H}{q_x q_y} \Big\{ K_1 \cos[ (q_x-q_y)R ] + K_2 \sin[ (q_x-q_y)R ] - K_3 \cos[ (q_x+q_y) R ] - K_4 \sin[ (q_x+q_y) R ]\Big\}
    \end{align*}
-	
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
 \item Cylinder (\texttt{FormFactorCylinder})
 
   \begin{equation}
- F()=   H  \frac{\sin(q_ z H/2)}{q_z H/2} \exp(i q_ z H/2) 2\pi R^2 \frac{J_1(|q_{\parallel} R |)}{|q_{\parallel} R| }
+ F(\mathbf{q},R, H)=   H  \text{sinc}(q_ z H/2) \exp(i q_ z H/2) 2\pi R^2 \frac{J_1(|q_{\parallel} R |)}{|q_{\parallel} R| }
  \end{equation}
  
-
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \item Prism3 (\texttt{FormFactorPrism3})
 
-\begin{equation}
-    F()= 2 \sqrt{3}\frac{\exp(-i q_y R/\sqrt{3})}{q_x^2-3q_y^2}[\exp(i \sqrt{3} q_y R ) -\cos(q_x R)-i \sqrt{3} q_y R \frac{\sin(q_x R)}{q_x R}]   H \frac{\sin(q_z H/2 )}{q_z H/2} \exp(i q_z H/2)
-\end{equation}
+\begin{align*}
+    F(\mathbf{q},R, H) &= 2 \sqrt{3}\frac{\exp(-i q_y
+      R/\sqrt{3})}{q_x^2-3q_y^2} \Big[\exp(i \sqrt{3} q_y R )
+    -\cos(q_x R)-i \sqrt{3} q_y R \text{sinc}(q_x R) \Big] \\
+   &\times  H \text{sinc}(q_z H/2 ) \exp(i q_z H/2)
+\end{align*}
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \item Sphere (\texttt{FormFactorSphere})
 
 \begin{equation}    
-return 2\pi \exp(i q_z (H-R))\int_{R-H} ^{R} R_z^2 \frac{J_1(|q_p*R_z|) }{|q_p*R_z|}
-        \exp(i q_z*Z)
+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}
 
+$R_z=\sqrt{R^2-z^2}$, $q_{\parallel}=\sqrt{q_x^2+q_y^2}$
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \item Full sphere (\texttt{FormFactorFullSphere})
 
 \begin{equation}
-radial = 4\pi R^3*\frac{\sin(q R) - q R*\cos(q R)}{(qR)^3}
+F(\mathbf{q},R) = 4\pi R^3 \frac{\sin(q R) - q R \cos(q R)}{(qR)^3}
 \end{equation}
-
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \item Box (\texttt{FormFactorBox})
 
 \begin{equation}
-F()= 4H R W\exp(i q_z H/2) \frac{\sin(q_x R)}{q_x R} \frac{  \sin(q_y W) }{q_y W}\frac{\sin(q_z H/2)}{q_z H/2}
+F(\mathbf{q},R,W,H)= 4H R W\exp(i q_z H/2) \text{sinc}(q_x R) \text{sinc}(q_y W) \text{sinc}(q_z H/2)
 \end{equation}
     
+where $\text{sinc}(x)=\sin(x)/x$ is the cardinal sine, $J_1(x)$ is the
+Bessel function of first order.
 	
 \end{itemize}
 
@@ -82,7 +93,7 @@ F()= 4H R W\exp(i q_z H/2) \frac{\sin(q_x R)}{q_x R} \frac{  \sin(q_y W) }{q_y W
 \begin{itemize}
 \item The Debye hard core 
 \item The gaussian
-\item The Lennard-Jonnes  	
+\item The Lennard-Jones  	
 \item The gate pair correlation 	
 \item The Debye hard core with power-law decrease  	
 \item The Zhu pair correlation function 	

Doc/UserManual/UserManual.tex

 \documentclass[a4paper,10pt]{report}
-\usepackage{cite}
+\usepackage{booktabs}
+\renewcommand{\arraystretch}{1.3}
 %----------------------------------------------------------------------------------------
 %	FONT
 %----------------------------------------------------------------------------------------
@@ -99,6 +100,7 @@
 
 \definecolor{Lightgray}{gray}{.80}
 \definecolor{lightgrey}{rgb}{0.9,0.9,0.9}
+
 %----------------------------------------------------------------------------------------
 %	TITLE PAGE
 %----------------------------------------------------------------------------------------
@@ -125,7 +127,7 @@ keepaspectratio]{results2_2.png}%
 
 \begin{document}
 
-%\AddToShipoutPicture*{\BackgroundPic} % add bakcground image to the
+%\AddToShipoutPicture*{\BackgroundPic} % add background image to the
 %first page
 \maketitle
 
@@ -177,7 +179,8 @@ For details about the theory (DWBA,\ldots), please refer to IsGISAXS manual (\ur
 %\input{Fitting}
 \input{Examples}
 
-Bugs\\ License agreement\\ Directory layout \\ FAQ \\ Future development.
+%List of notations\\  Bugs\\ License agreement\\ Directory layout \\ FAQ \\ Future development.
+
 %\appendix
 %\input{Appendix}
 

Doc/UserManual/lstcustom.sty

@@ -211,6 +211,11 @@ height, collapsed, true, false%
 \definecolor{lightblue}{rgb}{0.4,0.4,1}
 \definecolor{lightblue1}{rgb}{0 0.25 1}
 \definecolor{darkpink}{rgb}{1 0 0.75}
+\definecolor{dred}{rgb}{0.8,0,0}
+
+\definecolor{oneblue}{rgb}{0,0,0.75}
+\definecolor{dockerblue}{rgb}{0.11,0.56,0.98}
+\definecolor{MyDarkBlue1}{rgb}{0.1,0,0.55}
 
 \lstdefinestyle{eclipse}{
     basicstyle=\small\lstfontfamily,
@@ -219,8 +224,8 @@ height, collapsed, true, false%
     commentstyle=\color{darkgreen},
     stringstyle=\color{darkblue},
     numberstyle=\color{darkgrey}\lstfontfamily,
-    emph={Simulation,MaterialManager,MultiLayer}, 
-    emphstyle=\color{cyan}, %darkpink}, %red},
+    emph={Simulation,MaterialManager,MultiLayer,Layer,Particle,ParticleDecoration}, 
+    emphstyle=\color{dockerblue},%dred}, %darkpink}, %red},
     % get also javadoc style comments
     morecomment=[s][\color{lightblue}]{/**}{*/},
    %columns=fullflexible, %spaceflexible, %flexible, fullflexible             
@@ -254,7 +259,9 @@ breaklines = true
     commentstyle=\color{darkgreen},
     stringstyle=\color{darkblue},
     numberstyle=\color{darkgrey}\lstfontfamily,
-    emphstyle=\color{red},
+    emph={Simulation,MaterialManager,MultiLayer,Layer,Particle,ParticleDecoration}, 
+    emphstyle=\color{dockerblue},%dred}, %darkpink}, 
+   % emphstyle=\color{red},
     backgroundcolor=\color{lightgrey},
     morecomment=[s][\color{lightblue}]{/**}{*/},
   showstringspaces=false,