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- added models for clipped random wave (CRW) with different two-point…

… correlation functions

- updated manual for those 5 CRW models
- an inverse erf function (sasfit_erfinv) made available in plugins
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Kohlbrecher committed Mar 22, 2019
1 parent 15acc37 commit d9f0a4208f5e810a18b3b0f41b654d6019a15c5c
Showing with 111,617 additions and 92,105 deletions.
  1. +1 −0 .gitignore
  2. BIN CHANGES.txt
  3. BIN doc/images/form_factor/nonparticular/Beaucage.png
  4. BIN doc/images/form_factor/nonparticular/BooleanUnionPhi0.png
  5. BIN doc/images/form_factor/nonparticular/BooleanUnionSigma.png
  6. BIN doc/images/form_factor/nonparticular/BroadPeak.png
  7. BIN doc/images/form_factor/nonparticular/CRW.opju
  8. BIN doc/images/form_factor/nonparticular/DAB.png
  9. BIN doc/images/form_factor/nonparticular/GuinierPorodIQ.png
  10. BIN doc/images/form_factor/nonparticular/IQCRW_10.png
  11. BIN doc/images/form_factor/nonparticular/IQCRW_80.png
  12. BIN doc/images/form_factor/nonparticular/OrnsteinZernicke.png
  13. BIN doc/images/form_factor/nonparticular/TeubnerStrey.png
  14. BIN doc/images/form_factor/nonparticular/boolean_union_3D.png
  15. BIN doc/images/form_factor/nonparticular/dead_leaves.png
  16. BIN doc/images/form_factor/nonparticular/dead_leaves_3D.png
  17. BIN doc/images/form_factor/nonparticular/gDAB.png
  18. BIN doc/images/form_factor/nonparticular/generalizedGuinierIQ.png
  19. BIN doc/images/form_factor/nonparticular/gyr0_10.png
  20. BIN doc/images/form_factor/nonparticular/gyr0_80.png
  21. BIN doc/images/form_factor/nonparticular/gyr2_10.png
  22. BIN doc/images/form_factor/nonparticular/gyr2_80.png
  23. BIN doc/images/form_factor/nonparticular/spinodalIQ.png
  24. BIN doc/images/form_factor/nonparticular/stochstic models.opju
  25. +2 −2 doc/manual/DatenRed.tex
  26. +3 −3 doc/manual/SASfit_absInt.tex
  27. +16 −16 doc/manual/SASfit_ch2_Spheres_Shells.tex
  28. +5 −5 doc/manual/SASfit_ch2_planar.tex
  29. +12 −12 doc/manual/SASfit_ch2_polymers_micelles.tex
  30. +16 −16 doc/manual/SASfit_ch3.tex
  31. +10 −10 doc/manual/SASfit_ch4.tex
  32. +65 −65 doc/manual/SASfit_ch5.tex
  33. +13 −0 doc/manual/SASfit_history.tex
  34. +2 −2 doc/manual/SASfit_pluginsFF_MieSLS.tex
  35. +19 −19 doc/manual/SASfit_pluginsFF_cluster.tex
  36. +24 −24 doc/manual/SASfit_pluginsFF_cylindrical_obj.tex
  37. +7 −7 doc/manual/SASfit_pluginsFF_elliptical_obj.tex
  38. +2 −2 doc/manual/SASfit_pluginsFF_magnetic_structures.tex
  39. +211 −16 doc/manual/SASfit_pluginsFF_nonparticular.tex
  40. +4 −4 doc/manual/basics.tex
  41. +1 −1 doc/manual/fittingstrategies.tex
  42. +3 −3 doc/manual/integral_structural_parameters.tex
  43. +1,539 −1 doc/manual/sasfit.aux
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  46. +4,683 −148 doc/manual/sasfit.log
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  48. BIN doc/manual/sasfit.pdf
  49. +100,959 −91,701 doc/manual/sasfit.synctex
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  51. +470 −0 doc/manual/sasfit.toc
  52. +31 −31 doc/manual/sasfit_OZsolver.tex
  53. +5 −0 src/plugins/stochastic_models/CMakeLists.txt
  54. +2,335 −0 src/plugins/stochastic_models/gy(r).nb
  55. +18 −1 src/plugins/stochastic_models/include/private.h
  56. +258 −0 src/plugins/stochastic_models/include/sasfit_stochastic_models.h
  57. +6 −1 src/plugins/stochastic_models/interface.c
  58. +1 −1 src/plugins/stochastic_models/sasfit_ff_boolean_union_model.c
  59. +50 −0 src/plugins/stochastic_models/sasfit_ff_clipped_random_waves_1.c
  60. +51 −0 src/plugins/stochastic_models/sasfit_ff_clipped_random_waves_2.c
  61. +51 −0 src/plugins/stochastic_models/sasfit_ff_clipped_random_waves_3.c
  62. +51 −0 src/plugins/stochastic_models/sasfit_ff_clipped_random_waves_4.c
  63. +51 −0 src/plugins/stochastic_models/sasfit_ff_clipped_random_waves_5.c
  64. +113 −1 src/plugins/stochastic_models/sasfit_stochastic_utils.c
  65. +5 −0 src/sasfit_common/include/sasfit_common_stubs.h
  66. +15 −5 src/sasfit_common/include/sasfit_utils.h
  67. +2 −0 src/sasfit_common/sasfit_common.c
  68. +5 −6 src/sasfit_common/sasfit_common.decls
  69. +45 −0 src/sasfit_common/sasfit_utils.c
@@ -63,3 +63,4 @@ saskit/saskit_*
/src/plugins/sin2/include/sasfit_sin2.h
/src/fftw/fftw-3.3.8.tar.gz
/sasfit.vfs/lib/app-sasfit/tcl/CET_CLB2.rgb
/doc/images/form_factor/nonparticular/BooleanUnionPhi1.png
BIN +626 Bytes (100%) CHANGES.txt
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@@ -2,7 +2,7 @@ \chapter{Experimental Setup of a Small Angle Scattering Instrument}
\section{SANS-Camera}
\begin{figure}[htb]
\begin{center}
\includegraphics[width=\textwidth,height=0.627\textwidth]{SANSAN.png}
\includegraphics[width=\textwidth]{SANSAN.png}
\caption{SANS-1 instrument at PSI, Switzerkand} \label{SANS1@PSI}
\end{center}
\end{figure}
@@ -11,7 +11,7 @@ \section{SAXS-Camera}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=\textwidth,height=0.598\textwidth]{CJUSIFA.png}
\includegraphics[width=\textwidth]{CJUSIFA.png}
\caption{Small angle x-ray scattering instrument Jusifa at the
synchrotron light source HASYLAB in Hamburg} \label{Jusifa}
\end{center}
@@ -269,12 +269,12 @@ \section{Moments of scattering curves and size distribution}
\begin{figure}[htb]
\begin{center}
\subfigure[GUI for defining fit ranges for Porod and Guinier
approximations]{\includegraphics[width=0.296\textwidth,height=0.464\textwidth]{QTintegralparameterGUI.png}}
approximations]{\includegraphics[width=0.296\textwidth]{QTintegralparameterGUI.png}}
\hfill \subfigure[Tabbed menu displaying the integral structural
parameters calculated via the different moments of the scattering
curve the Porod and Guinier extrapolations to $Q\rightarrow 0$ and
$Q\rightarrow\infty$.
]{\includegraphics[width=0.604\textwidth,height=0.576\textwidth]{QTintegralparameterTab.png}}
]{\includegraphics[width=0.604\textwidth]{QTintegralparameterTab.png}}
\end{center}
\caption{Menu and tabbed window for integral structural parameters.
\SASfit also supports analysis of series of data, whereby the
@@ -327,7 +327,7 @@ \section{Moments of scattering curves and size distribution}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.818\textwidth,height=0.637\textwidth]{QTmoments.png}
\includegraphics[width=0.818\textwidth]{QTmoments.png}
\end{center}
\caption{Menu displaying the different moments of a size
distribution. At the moment these values are only calculated for
@@ -6,7 +6,7 @@ \subsection{Sphere}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.2875\textwidth,height=0.359\textwidth]{../images/form_factor/spheres/sphere.png}
\includegraphics[width=0.2875\textwidth]{../images/form_factor/spheres/sphere.png}
\end{center}
\caption{Sphere with diameter $2R$} \label{fig:Sketch_sphere}
\end{figure}
@@ -41,7 +41,7 @@ \subsection{Sphere}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.768\textwidth,height=0.588\textwidth]{../images/form_factor/spheres/sphere_P.png}
\includegraphics[width=0.768\textwidth]{../images/form_factor/spheres/sphere_P.png}
\end{center}
\caption{Scattering intensity of spheres with radii $R=10$nm and $R=20$nm.
The scattering length density contrast is set to 1.} \label{fig:I_sphere}
@@ -55,7 +55,7 @@ \subsection{Spherical Shell i}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.38\textwidth,height=0.3575\textwidth]{../images/form_factor/spheres/shell1.png}
\includegraphics[width=0.38\textwidth]{../images/form_factor/spheres/shell1.png}
\end{center}
\caption{Spherical Shell i} \label{fig:shell1}
\end{figure}
@@ -95,7 +95,7 @@ \subsection{Spherical Shell i}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.768\textwidth,height=0.588\textwidth]{../images/form_factor/spheres/shell_i_P.png}
\includegraphics[width=0.768\textwidth]{../images/form_factor/spheres/shell_i_P.png}
\end{center}
\caption{Scattering intensity of spherical shell with outer radius of $R_1=14$nm
and inner radius of $R_2=11.2$nm. The scattering length density contrast the shell is set to 1
@@ -110,7 +110,7 @@ \subsection{Spherical Shell ii}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.38\textwidth,height=0.3575\textwidth]{../images/form_factor/spheres/shell2.png}
\includegraphics[width=0.38\textwidth]{../images/form_factor/spheres/shell2.png}
\end{center}
\caption{\texttt{Spherical Shell ii}} \label{fig:shell2}
\end{figure}
@@ -148,7 +148,7 @@ \subsection{Spherical Shell ii}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.768\textwidth,height=0.588\textwidth]{../images/form_factor/spheres/shell_ii_P.png}
\includegraphics[width=0.768\textwidth]{../images/form_factor/spheres/shell_ii_P.png}
\end{center}
\caption{Scattering intensity of spherical shell with outer radius of $R=14$nm
and inner radius of $\nu R=11.2$nm. The scattering length density contrast the shell is set to 1
@@ -162,7 +162,7 @@ \subsection{Spherical Shell iii}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.38\textwidth,height=0.3575\textwidth]{../images/form_factor/spheres/shell3.png}
\includegraphics[width=0.38\textwidth]{../images/form_factor/spheres/shell3.png}
\end{center}
\caption{Spherical Shell iii} \label{fig:shell3}
\end{figure}
@@ -202,7 +202,7 @@ \subsection{Spherical Shell iii}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.768\textwidth,height=0.588\textwidth]{../images/form_factor/spheres/shell_iii_P.png}
\includegraphics[width=0.768\textwidth]{../images/form_factor/spheres/shell_iii_P.png}
\end{center}
\caption{Scattering intensity of spherical shell with core radius of $R=11.2$nm
and shell thickness of $\Delta R=2.8$nm. The scattering length density contrast the shell is set to 1
@@ -219,7 +219,7 @@ \subsection{Bilayered Vesicle}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.5441\textwidth,height=0.5858\textwidth]{../images/form_factor/spheres/BiLayeredVesicle.png}
\includegraphics[width=0.5441\textwidth]{../images/form_factor/spheres/BiLayeredVesicle.png}
\end{center}
\caption{BiLayeredVesicle} \label{fig:BiLayeredVesicle}
\end{figure}
@@ -252,7 +252,7 @@ \subsection{Bilayered Vesicle}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.768\textwidth,height=0.588\textwidth]{../images/form_factor/spheres/bilayered_vesicle.png}
\includegraphics[width=0.768\textwidth]{../images/form_factor/spheres/bilayered_vesicle.png}
\end{center}
\caption{Scattering intensity of a bilayered vesicle. The scattering intensity has been calculated
with a lognormal $[\mathrm{LogNorm}(N\!=\!1,\sigma\!=\!0.05,p\!=\!1,R\!=\!30)]$ size distribution for the vesicle radius $R_c$.}
@@ -267,7 +267,7 @@ \subsection{Multi Lamellar Vesicle}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.537\textwidth,height=0.566\textwidth]{../images/form_factor/spheres/multilamellar_vesicle.png}
\includegraphics[width=0.537\textwidth]{../images/form_factor/spheres/multilamellar_vesicle.png}
\end{center}
\caption{MultiLamellarVesicle} \label{fig:MultiLamellarVesicle}
\end{figure}
@@ -300,7 +300,7 @@ \subsection{Multi Lamellar Vesicle}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.768\textwidth,height=0.588\textwidth]{../images/form_factor/spheres/multilamellar_vesicle_Iq.png}
\includegraphics[width=0.768\textwidth]{../images/form_factor/spheres/multilamellar_vesicle_Iq.png}
\end{center}
\caption{Scattering intensity of a multilamellar vesicle. The scattering intensities has been calculated
for a\&b) a distribution of the core radius $R_c$ by
@@ -318,7 +318,7 @@ \subsection{RNDMultiLamellarVesicle}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.537\textwidth,height=0.566\textwidth]{../images/form_factor/spheres/random_multilamellar_vesicle.png}
\includegraphics[width=0.537\textwidth]{../images/form_factor/spheres/random_multilamellar_vesicle.png}
\end{center}
\caption{randomMultiLamellarVesicle}
\label{fig:randomMultiLamellarVesicle}
@@ -369,7 +369,7 @@ \subsection{RNDMultiLamellarVesicle}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.768\textwidth,height=0.588\textwidth]{../images/form_factor/spheres/random_multilamellar_vesicle_Iq.png}
\includegraphics[width=0.768\textwidth]{../images/form_factor/spheres/random_multilamellar_vesicle_Iq.png}
\end{center}
\caption{Scattering intensity of a multilamellar vesicle where several distribution of parameters
within a single vesicle are calculated via a Monte Carlo algorithm. .}
@@ -383,7 +383,7 @@ \subsection{Vesicle with aligned flat capped ends \cite{Kaya:aj5008,Kaya:aj5016}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.492\textwidth,height=0.523\textwidth]{vesicle_capped_poles_aligned.png}
\includegraphics[width=0.492\textwidth]{vesicle_capped_poles_aligned.png}
\end{center}
\caption{Sketch of a vesicle with horizontally aligned flat
capped ends perpendicular to the incoming neutron beam}
@@ -538,7 +538,7 @@ \subsection{Vesicle with aligned flat capped ends \cite{Kaya:aj5008,Kaya:aj5016}

\begin{figure}[htb]
\begin{center}
%\includegraphics[width=0.768\textwidth,height=0.588\textwidth]{sphere_P.png}
%\includegraphics[width=0.768\textwidth]{sphere_P.png}
\end{center}
%\caption{Scattering intensity of spheres with radii $R=10$nm and $R=20$nm.
%The scattering length density contrast is set to 1.} \label{fig:I_sphere}
@@ -81,7 +81,7 @@ \subsubsection{homogeneousXS}
\hspace{1pt} \\
\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.6\textwidth,height=0.4\textwidth]{planarHomo.png}
\includegraphics[width=0.6\textwidth]{planarHomo.png}
\end{center}
\caption{Planar object with homogeneous cross-section.}
\label{fig:planarHomo}
@@ -98,7 +98,7 @@ \subsection{TwoInfinitelyThinPlates}
\hspace{1pt} \\
\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.6\textwidth,height=0.4\textwidth]{planar2thin.png}
\includegraphics[width=0.6\textwidth]{planar2thin.png}
\end{center}
\caption{planar2thin.}
\label{fig:planar2thin}
@@ -116,7 +116,7 @@ \subsection{LayeredCentroSymmetricXS}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.6\textwidth,height=0.4\textwidth]{planar2centrosymm.png}
\includegraphics[width=0.6\textwidth]{planar2centrosymm.png}
\end{center}
\caption{planar2centrosymHomo.}
\label{fig:planar2centrosymm}
@@ -139,8 +139,8 @@ \subsection{BiLayerGauss \cite{Pabst2000}}
~\\
\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.4\textwidth,height=0.5\textwidth]{BiLayers.png}
\includegraphics[width=0.5\textwidth,height=0.4\textwidth]{bilayerprofile.png}
\includegraphics[width=0.4\textwidth]{BiLayers.png}
\includegraphics[width=0.5\textwidth]{bilayerprofile.png}
\end{center}
\caption{bilayerprof.}
\label{fig:bilayerprof}
@@ -10,7 +10,7 @@ \subsection{Unified Exponential Power Law according to Beaucage \cite{beaucage95

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.952\textwidth,height=0.403\textwidth]{Beaucage.png}
\includegraphics[width=0.952\textwidth]{Beaucage.png}
\end{center}
\caption{A typical case in which two $R_g$'s are observed.
Particles composed of sub-particles where a radius of gyration for
@@ -93,7 +93,7 @@ \subsubsection{Beaucage} ~\\

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.75\textwidth,height=0.5\textwidth]{../images/form_factor/nonparticular/Beaucage.png}
\includegraphics[width=0.75\textwidth]{../images/form_factor/nonparticular/Beaucage.png}
\end{center}
\caption{}
\label{fig:Beaucage}
@@ -136,7 +136,7 @@ \subsubsection{Beaucage2} ~\\

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.75\textwidth,height=0.5\textwidth]{../images/form_factor/nonparticular/Beaucage2.png}
\includegraphics[width=0.75\textwidth]{../images/form_factor/nonparticular/Beaucage2.png}
\end{center}
\caption{}
\label{fig:Beaucage2}
@@ -158,7 +158,7 @@ \subsection{WormLikeChainEXV} \cite{Pedersen96Macrom}
~\\
\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.8\textwidth,height=0.4\textwidth]{wormlike2.png}
\includegraphics[width=0.8\textwidth]{wormlike2.png}
\end{center}
\caption{The chain of contour length, $L$, (the total length) can
be described a chain of some number of locally stiff segments of
@@ -193,7 +193,7 @@ \subsection{WormLikeChainEXV} \cite{Pedersen96Macrom}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.768\textwidth,height=0.588\textwidth]{wormlike_Iq.png}
\includegraphics[width=0.768\textwidth]{wormlike_Iq.png}
\end{center}
\caption{Comparison of wormlike micelles according to Pedersen \cite{Pedersen96Macrom}
and Kholodenko \cite{kholodenko93}} \label{fig:wormlike_Iq}
@@ -208,7 +208,7 @@ \subsection{KholodenkoWorm}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.617\textwidth,height=0.762\textwidth]{SemiflexiblePolymerTxt.png}
\includegraphics[width=0.617\textwidth]{SemiflexiblePolymerTxt.png}
\end{center}
\caption{}
\label{fig:KholodenkoWorm}
@@ -264,7 +264,7 @@ \subsection{KholodenkoWorm}

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.768\textwidth,height=0.588\textwidth]{wormlike_Iq.png}
\includegraphics[width=0.768\textwidth]{wormlike_Iq.png}
\end{center}
\caption{Comparison of wormlike micelles according to Pedersen \cite{Pedersen96Macrom}
and Kholodenko \cite{kholodenko93}. } \label{fig:wormlike_Iq2}
@@ -279,12 +279,12 @@ \subsection{Diblock copolymer micelles}
\begin{figure}[htb]
\centering
\subfigure[spherical
micelle]{\quad\includegraphics[width=0.25\textwidth,height=0.375\textwidth]{spheregauss.png}\quad}
micelle]{\quad\includegraphics[width=0.25\textwidth]{spheregauss.png}\quad}
\quad
\subfigure[ellipsoidal
micelle]{\quad\includegraphics[width=0.25\textwidth,height=0.41\textwidth]{ellipsoidgauss.png}\quad}
micelle]{\quad\includegraphics[width=0.25\textwidth]{ellipsoidgauss.png}\quad}
\quad
\subfigure[cylindrical micelle]{\quad\includegraphics[width=0.2\textwidth,height=0.4\textwidth]{cylindergauss.png}\quad}
\subfigure[cylindrical micelle]{\quad\includegraphics[width=0.2\textwidth]{cylindergauss.png}\quad}
\caption{Block copolymer forming micelles of different shapes}
\end{figure}

@@ -1068,7 +1068,7 @@ \subsubsection{Micelles with a homogeneous core

\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.55\textwidth,height=0.35\textwidth]{R_ma.png}
\includegraphics[width=0.55\textwidth]{R_ma.png}
\end{center}
\caption{radial profile.}
\label{R_ma_profile}
@@ -1523,7 +1523,7 @@ \subsubsection{spherical Micelles with a homogeneous core
\subsection{Sphere with Gaussian chains attached} ~\\
\begin{figure}[htb]
\begin{center}
\includegraphics[width=0.75\textwidth,height=0.55\textwidth]{agghalf.png}
\includegraphics[width=0.75\textwidth]{agghalf.png}
\end{center}
\caption{Block copolymer micelles.}
\label{SphereWithGaussChains}
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