diff --git a/Doc/UserManual/AppendixListings.tex b/Doc/UserManual/AppendixListings.tex
new file mode 100644
index 0000000000000000000000000000000000000000..85d89975bfac04cb4f9c6309df4d777eb21e8be2
--- /dev/null
+++ b/Doc/UserManual/AppendixListings.tex
@@ -0,0 +1,143 @@
+\newpage{\pagestyle{empty}\cleardoublepage}
+
+
+%\mychapter{1}{Appendix}
+
+\chapter{Listings}
+
+\begin{lstlisting}[caption={Python script of example 1},
+ label=script_ex1,captionpos=b,escapeinside={@}{@} ,language=python,style=eclipse, numbers= none,frame = leftline ,
+ framerule = 2mm ,
+ rulecolor = \color{lightgrey},
+ breaklines = true]
+import sys, os, numpy
+
+sys.path.append(os.path.abspath(os.path.join(os.path.split(__file__)[0],'..', '..', '..', 'lib')))
+
+from libBornAgainCore import *
+
+def RunSimulation():
+ # defining materials
+ mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
+ mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate",
+ 6e-6, 2e-8)
+ mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
+ # collection of particles
+ cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
+ cylinder = Particle(mParticle, cylinder_ff)
+ prism_ff = FormFactorPrism3(5*nanometer, 5*nanometer)
+ prism = Particle(mParticle, prism_ff)
+ particle_decoration = ParticleDecoration()
+ particle_decoration.addParticle(cylinder, 0.0, 0.5)
+ particle_decoration.addParticle(prism, 0.0, 0.5)
+ interference = InterferenceFunctionNone()
+ particle_decoration.addInterferenceFunction(interference)
+ # air layer with particles and substrate form multi layer
+ air_layer = Layer(mAmbience)
+ air_layer.setDecoration(particle_decoration)
+ substrate_layer = Layer(mSubstrate, 0)
+ multi_layer = MultiLayer()
+ multi_layer.addLayer(air_layer)
+ multi_layer.addLayer(substrate_layer)
+
+ # build and run simulation
+ simulation = Simulation()
+ simulation.setDetectorParameters(100,-1.0*degree, 1.0*degree,
+ 100, 0.0*degree, 2.0*degree, True)
+ simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree)
+ simulation.setSample(multi_layer)
+ simulation.runSimulation()
+
+ # retrieving intensity data
+ return GetOutputData(simulation)
+\end{lstlisting}
+
+
+\begin{lstlisting}[caption={Python script of fitting example},
+ label=script_exfit1,captionpos=b,escapeinside={@}{@} ,language=python,style=eclipse, numbers= none,frame = leftline ,
+ framerule = 2mm ,
+ rulecolor = \color{lightgrey},
+ breaklines = true]
+import sys, os, numpy
+import math
+
+sys.path.append(os.path.abspath(
+ os.path.join(os.path.split(__file__)[0],
+ '..', '..', '..', 'lib')))
+
+from libBornAgainCore import *
+from libBornAgainFit import *
+
+# values we want to find
+cylinder_height = 5.0*nanometer
+cylinder_radius = 5.0*nanometer
+prism3_half_side = 5.0*nanometer
+prism3_height = 5.0*nanometer
+# ----------------------------------
+# create sample : cylinders and prisms in the air on substrate layer
+# ----------------------------------
+def buildSample():
+ # defining materials
+ mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
+ mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate",
+ 6e-6, 2e-8 )
+ mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
+ # collection of particles
+ cylinder_ff = FormFactorCylinder(cylinder_height, cylinder_radius)
+ cylinder = Particle(mParticle, cylinder_ff)
+ prism_ff = FormFactorPrism3(prism3_height, prism3_half_side)
+ prism = Particle(mParticle, prism_ff)
+ particle_decoration = ParticleDecoration()
+ particle_decoration.addParticle(cylinder, 0.0, 0.5)
+ particle_decoration.addParticle(prism,0.0, 0.5)
+ interference = InterferenceFunctionNone()
+ particle_decoration.addInterferenceFunction(interference)
+ # air layer with particles and substrate form multi layer
+ air_layer = Layer(mAmbience)
+ air_layer.setDecoration(particle_decoration)
+ substrate_layer = Layer(mSubstrate, 0)
+ multi_layer = MultiLayer()
+ multi_layer.addLayer(air_layer)
+ multi_layer.addLayer(substrate_layer)
+ return multi_layer
+# ----------------------------------
+# create sample : input beam and detector - characteristics
+# ----------------------------------
+def createSimulation():
+ simulation = Simulation()
+ simulation.setDetectorParameters(100, 0.0*degree, 2.0*degree,100 , 0.0*degree, 2.0*degree)
+ simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree)
+ return simulation
+# ----------------------------------
+# read "real" data from file
+# ----------------------------------
+def GetRealData():
+ real_data = OutputDataIOFactory.getOutputData('Refdata_fitcylinderprisms.txt')
+ return real_data
+# ----------------------------------
+# run fitting
+# ----------------------------------
+def run_fitting():
+ sample = buildSample()
+ simulation = createSimulation()
+ simulation.setSample(sample)
+ # get the real data, which is simply results of our simulation with default values
+ real_data = GetRealData()
+ # run the simulation
+ simulation.runSimulation()
+ # linking real and numerical (to be fitted) data
+ fitSuite = FitSuite()
+ fitSuite.addSimulationAndRealData(simulation, real_data)
+ # setting fitting minimizer
+ fitSuite.setMinimizer( MinimizerFactory.createMinimizer("Minuit2","Migrad") )
+ # setting fitting parameters
+ fitSuite.addFitParameter("*FormFactorCylinder/height", 4.*nanometer, 0.01*nanometer, AttLimits.lowerLimited(0.01) )
+ fitSuite.addFitParameter("*FormFactorCylinder/radius", 6.*nanometer, 0.01*nanometer, AttLimits.lowerLimited(0.01) )
+ fitSuite.addFitParameter("*FormFactorPrism3/height", 4.*nanometer, 0.01*nanometer, AttLimits.lowerLimited(0.01) )
+ fitSuite.addFitParameter("*FormFactorPrism3/half_side", 6*nanometer, 0.01*nanometer, AttLimits.lowerLimited(0.01) )
+ # run fit
+ fitSuite.runFit()
+ # print fit results
+ fitSuite.printResults()
+\end{lstlisting}
+
diff --git a/Doc/UserManual/Appendix.tex b/Doc/UserManual/AppendixPhysics.tex
similarity index 100%
rename from Doc/UserManual/Appendix.tex
rename to Doc/UserManual/AppendixPhysics.tex
diff --git a/Doc/UserManual/FittingExamples.tex b/Doc/UserManual/FittingExamples.tex
index 4a2e7eaa8feffac57e79cf683e8c4d19310fc986..5831abfea0af6d27d0a671a9acdcd86336585784 100644
--- a/Doc/UserManual/FittingExamples.tex
+++ b/Doc/UserManual/FittingExamples.tex
@@ -611,93 +611,6 @@ Listing~\ref{script_exfit1}, the text given in~\ref{output_exfit1} should be dis
screen (generated using \Code{PrintResults}).
-\begin{lstlisting}[caption={Python script of fitting example},
- label=script_exfit1,captionpos=b,escapeinside={@}{@} ,language=python,style=eclipse, numbers= none,frame = leftline ,
- framerule = 2mm ,
- rulecolor = \color{lightgrey},
- breaklines = true]
-import sys, os, numpy
-import math
-
-sys.path.append(os.path.abspath(
- os.path.join(os.path.split(__file__)[0],
- '..', '..', '..', 'lib')))
-
-from libBornAgainCore import *
-from libBornAgainFit import *
-
-# values we want to find
-cylinder_height = 5.0*nanometer
-cylinder_radius = 5.0*nanometer
-prism3_half_side = 5.0*nanometer
-prism3_height = 5.0*nanometer
-# ----------------------------------
-# create sample : cylinders and prisms in the air on substrate layer
-# ----------------------------------
-def buildSample():
- # defining materials
- mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
- mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate",
- 6e-6, 2e-8 )
- mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
- # collection of particles
- cylinder_ff = FormFactorCylinder(cylinder_height, cylinder_radius)
- cylinder = Particle(mParticle, cylinder_ff)
- prism_ff = FormFactorPrism3(prism3_height, prism3_half_side)
- prism = Particle(mParticle, prism_ff)
- particle_decoration = ParticleDecoration()
- particle_decoration.addParticle(cylinder, 0.0, 0.5)
- particle_decoration.addParticle(prism,0.0, 0.5)
- interference = InterferenceFunctionNone()
- particle_decoration.addInterferenceFunction(interference)
- # air layer with particles and substrate form multi layer
- air_layer = Layer(mAmbience)
- air_layer.setDecoration(particle_decoration)
- substrate_layer = Layer(mSubstrate, 0)
- multi_layer = MultiLayer()
- multi_layer.addLayer(air_layer)
- multi_layer.addLayer(substrate_layer)
- return multi_layer
-# ----------------------------------
-# create sample : input beam and detector - characteristics
-# ----------------------------------
-def createSimulation():
- simulation = Simulation()
- simulation.setDetectorParameters(100, 0.0*degree, 2.0*degree,100 , 0.0*degree, 2.0*degree)
- simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree)
- return simulation
-# ----------------------------------
-# read "real" data from file
-# ----------------------------------
-def GetRealData():
- real_data = OutputDataIOFactory.getOutputData('Refdata_fitcylinderprisms.txt')
- return real_data
-# ----------------------------------
-# run fitting
-# ----------------------------------
-def run_fitting():
- sample = buildSample()
- simulation = createSimulation()
- simulation.setSample(sample)
- # get the real data, which is simply results of our simulation with default values
- real_data = GetRealData()
- # run the simulation
- simulation.runSimulation()
- # linking real and numerical (to be fitted) data
- fitSuite = FitSuite()
- fitSuite.addSimulationAndRealData(simulation, real_data)
- # setting fitting minimizer
- fitSuite.setMinimizer( MinimizerFactory.createMinimizer("Minuit2","Migrad") )
- # setting fitting parameters
- fitSuite.addFitParameter("*FormFactorCylinder/height", 4.*nanometer, 0.01*nanometer, AttLimits.lowerLimited(0.01) )
- fitSuite.addFitParameter("*FormFactorCylinder/radius", 6.*nanometer, 0.01*nanometer, AttLimits.lowerLimited(0.01) )
- fitSuite.addFitParameter("*FormFactorPrism3/height", 4.*nanometer, 0.01*nanometer, AttLimits.lowerLimited(0.01) )
- fitSuite.addFitParameter("*FormFactorPrism3/half_side", 6*nanometer, 0.01*nanometer, AttLimits.lowerLimited(0.01) )
- # run fit
- fitSuite.runFit()
- # print fit results
- fitSuite.printResults()
-\end{lstlisting}
\begin{lstlisting}[caption={Output of fit using Python script~\ref{script_exfit1}},language=bash,basicstyle=\small\lstfontfamily,% style=commandline,
label=output_exfit1,captionpos=b,escapeinside={@}{@}, numbers=
diff --git a/Doc/UserManual/SimulationExamples.tex b/Doc/UserManual/SimulationExamples.tex
index 3f873951527172f9f3998effb514612774a65519..c5ade8dec3f9ff65704db19da15d94d5007c6ca7 100644
--- a/Doc/UserManual/SimulationExamples.tex
+++ b/Doc/UserManual/SimulationExamples.tex
@@ -1,5 +1,5 @@
\newpage
-\chapter{Simulation} \SecLabel{Simulation}
+\chapter{Simulation examples} \SecLabel{Simulation}
\section{General methodology}
A simulation of GISAXS using \BornAgain\ consists of following steps:
@@ -364,53 +364,6 @@ is associated with the output intensity in arbitrary units. }
\label{fig:output_ex1}
\end{figure}
-\newpage
-\begin{lstlisting}[caption={Python script of example 1},
- label=script_ex1,captionpos=b,escapeinside={@}{@} ,language=python,style=eclipse, numbers= none,frame = leftline ,
- framerule = 2mm ,
- rulecolor = \color{lightgrey},
- breaklines = true]
-import sys, os, numpy
-
-sys.path.append(os.path.abspath(os.path.join(os.path.split(__file__)[0],'..', '..', '..', 'lib')))
-
-from libBornAgainCore import *
-
-def RunSimulation():
- # defining materials
- mAmbience = MaterialManager.getHomogeneousMaterial("Air", 0.0, 0.0 )
- mSubstrate = MaterialManager.getHomogeneousMaterial("Substrate",
- 6e-6, 2e-8)
- mParticle = MaterialManager.getHomogeneousMaterial("Particle", 6e-4, 2e-8 )
- # collection of particles
- cylinder_ff = FormFactorCylinder(5*nanometer, 5*nanometer)
- cylinder = Particle(mParticle, cylinder_ff)
- prism_ff = FormFactorPrism3(5*nanometer, 5*nanometer)
- prism = Particle(mParticle, prism_ff)
- particle_decoration = ParticleDecoration()
- particle_decoration.addParticle(cylinder, 0.0, 0.5)
- particle_decoration.addParticle(prism, 0.0, 0.5)
- interference = InterferenceFunctionNone()
- particle_decoration.addInterferenceFunction(interference)
- # air layer with particles and substrate form multi layer
- air_layer = Layer(mAmbience)
- air_layer.setDecoration(particle_decoration)
- substrate_layer = Layer(mSubstrate, 0)
- multi_layer = MultiLayer()
- multi_layer.addLayer(air_layer)
- multi_layer.addLayer(substrate_layer)
-
- # build and run simulation
- simulation = Simulation()
- simulation.setDetectorParameters(100,-1.0*degree, 1.0*degree,
- 100, 0.0*degree, 2.0*degree, True)
- simulation.setBeamParameters(1.0*angstrom, 0.2*degree, 0.0*degree)
- simulation.setSample(multi_layer)
- simulation.runSimulation()
-
- # retrieving intensity data
- return GetOutputData(simulation)
-\end{lstlisting}
% \newpage
% \subsection{Hello, minted}
diff --git a/Doc/UserManual/UserManual.pdf b/Doc/UserManual/UserManual.pdf
index 2016a5dddeb80ae768c2adf3eaede37fbe8ae60c..9aa6542b119d284e96b757509b8914f02b8e4c4f 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 df4f185246834854ecf94b0b736f3c9b5993b3ad..3bd6810b165ea02323d67c93216b54463f4785ae 100644
--- a/Doc/UserManual/UserManual.tex
+++ b/Doc/UserManual/UserManual.tex
@@ -180,10 +180,14 @@ Forschungszentrum J\"ulich GmbH
\input{Introduction}
\input{QuickStart}
\input{Installation}
-\input{SoftwareArchitecture}
-\input{SoftwareDesignOverview}
\input{SimulationExamples}
\input{FittingExamples}
+\input{SoftwareArchitecture}
+\input{SoftwareDesignOverview}
+\appendix
+\input{AppendixListings}
+\input{AppendixPhysics}
+
%List of notations\\ Bugs\\ License agreement\\ Directory layout \\ FAQ \\ Future development.