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bug fixes

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Kohlbrecher committed Nov 20, 2017
1 parent 0635720 commit e152e93db87e0340830780a40a244c1b80b9ca7a
Showing with 31,867 additions and 30,580 deletions.
  1. BIN CHANGES.txt
  2. +1 −1 doc/manual/DatenRed.tex
  3. +2 −2 doc/manual/SASfit_absInt.tex
  4. +1 −1 doc/manual/SASfit_ch2_EllipsoidalObj.tex
  5. +4 −4 doc/manual/SASfit_ch2_cylindricalObj.tex
  6. +4 −4 doc/manual/SASfit_ch2_otherObj.tex
  7. +3 −3 doc/manual/SASfit_ch2_polymers_micelles.tex
  8. +1 −1 doc/manual/SASfit_ch3.tex
  9. +5 −0 doc/manual/SASfit_history.tex
  10. +2 −2 doc/manual/SASfit_pluginsFF_anisotropic.tex
  11. +40 −16 doc/manual/SASfit_pluginsFF_cylindrical_obj.tex
  12. +2 −2 doc/manual/SASfit_pluginsFF_magnetic_structures.tex
  13. +1 −1 doc/manual/SASfit_pluginsFF_nonparticular.tex
  14. +3 −3 doc/manual/fittingstrategies.tex
  15. +4 −5 doc/manual/intro.tex
  16. +260 −260 doc/manual/sasfit.aux
  17. +447 −455 doc/manual/sasfit.log
  18. +74 −74 doc/manual/sasfit.out
  19. BIN doc/manual/sasfit.pdf
  20. +30,249 −29,499 doc/manual/sasfit.synctex
  21. +74 −74 doc/manual/sasfit.toc
  22. +5 −5 doc/manual/sasfit_OZsolver.tex
  23. +11 −6 sasfit.vfs/lib/app-sasfit/tcl/sasfit_addfiles.tcl
  24. +14 −9 sasfit.vfs/lib/app-sasfit/tcl/sasfit_main.tcl
  25. BIN src/external_libs/sundials-3.1.0.tar.gz
  26. +3 −3 src/plugins/groups.form_fac.def
  27. +0 −10 src/plugins/helix/sasfit_ff_superhelices_coiled.c
  28. +0 −9 src/plugins/helix/sasfit_ff_superhelices_straight.c
  29. +1 −1 src/plugins/{non_particular → non_particulate}/CMakeLists.txt
  30. +3 −3 src/plugins/{non_particular → non_particulate}/include/private.h
  31. +81 −81 ...on_particular/include/sasfit_non_particular.h → non_particulate/include/sasfit_non_particulate.h}
  32. 0 src/plugins/{non_particular → non_particulate}/interface.c
  33. 0 src/plugins/{non_particular → non_particulate}/sasfit_ff_beaucage_exppowlaw.c
  34. 0 src/plugins/{non_particular → non_particulate}/sasfit_ff_beaucage_exppowlaw_2.c
  35. 0 src/plugins/{non_particular → non_particulate}/sasfit_ff_broad_peak.c
  36. 0 src/plugins/{non_particular → non_particulate}/sasfit_ff_debye_anderson_brumberger.c
  37. 0 src/plugins/{non_particular → non_particulate}/sasfit_ff_extended_guinier_law.c
  38. 0 src/plugins/{non_particular → non_particulate}/sasfit_ff_g_dab.c
  39. 0 src/plugins/{non_particular → non_particulate}/sasfit_ff_generalized_guinier_porod_law.c
  40. 0 src/plugins/{non_particular → non_particulate}/sasfit_ff_ornstein_zernike.c
  41. 0 src/plugins/{non_particular → non_particulate}/sasfit_ff_spinodal.c
  42. 0 src/plugins/{non_particular → non_particulate}/sasfit_ff_teubner_strey.c
  43. +4 −0 src/plugins/parallel_epiped/CMakeLists.txt
  44. +18 −0 src/plugins/parallel_epiped/include/private.h
  45. +159 −0 src/plugins/parallel_epiped/include/sasfit_parallel_epiped.h
  46. +4 −1 src/plugins/parallel_epiped/interface.c
  47. +24 −45 src/plugins/parallel_epiped/sasfit_ff_parallelepiped_abc.c
  48. +92 −0 src/plugins/parallel_epiped/sasfit_ff_parallelepiped_abc1.c
  49. +91 −0 src/plugins/parallel_epiped/sasfit_ff_parallelepiped_abc2.c
  50. +91 −0 src/plugins/parallel_epiped/sasfit_ff_parallelepiped_abc3.c
  51. +89 −0 src/plugins/parallel_epiped/sasfit_parallelepiped_utils.c
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@@ -29,7 +29,7 @@ \section{Correction and Normalization of SANS-Raw data}
\item scattering of the isolated sample $I_S$
\end{enumerate}
Furthermore the detector elements can have different efficiencies $\epsilon_i$.
To determine the differential cross-section of of the sample all the different
To determine the differential cross-section of the sample all the different
contribution to the total scattering intensity have to be considered and determined
separately by different measurements. The quantity to be known is the scattering
contribution of the isolated sample $I_S$, which in general can not be measured directly.
@@ -71,7 +71,7 @@ \section{Fitting absolute intensities}
For fitting a form factor to experimental data one needs next to the size parameter also a
scaling parameter. For the simplest case this is done by choosing as a distribution function
\texttt{Delta}. \texttt{Delta} simply multiplies a constant value $N$ to the form factor.
The meaning and the unit of $N$ now depends on the unit of the cross-section, wether it is
The meaning and the unit of $N$ now depends on the unit of the cross-section, whether it is
normalized or not normalized on the sample volume. \SASfit calculates in the case of
a form factor of \texttt{Sphere} with \texttt{Delta} as a distribution function
\begin{align}
@@ -339,7 +339,7 @@ \section{Moments of scattering curves and size distribution}
values for each scattering contribution having a size distribution
and also for the sum of all scattering contributions. Next to the
integral structural parameters also the different moments of the
size distribution up the the $8^\textrm{th}$ moment are supplied.
size distribution up the $8^\textrm{th}$ moment are supplied.
\section{Volume fractions}
\label{sec:volumefraction}
@@ -210,7 +210,7 @@ \subsection{triaxial ellipsoidal core shell structure}
\begin{center}
\includegraphics[width=0.768\textwidth,height=0.588\textwidth]{../images/form_factor/Ellipsoid/triax_ellipsoidal_core_shell.png}
\end{center}
\caption{Form factor of an triaxial ellipsoidal core shell with semi
\caption{Form factor of a triaxial ellipsoidal core shell with semi
axis $a$, $b$ and $c$ and a shell thickness $t$.}
\label{fig:I_triax_ellipsoidal_core_shell}
\end{figure}
@@ -131,7 +131,7 @@ \subsection{Porod's approximation for a long cylinder \cite{Porod1948}}
\includegraphics[width=0.668\textwidth,height=0.488\textwidth]{../images/form_factor/cylindrical_obj/LongCylinder.png}
\end{center}
\caption{Scattering intensity of a cylinder with radius $R=10$ nm and lengths of $L=20$ nm
and $L=50$ nm. Next to Porod's axproximation for long cylinders also
and $L=50$ nm. Next to Porod's approximation for long cylinders also
the exact integral solution is shown for comparison.
The scattering length density contrast is set to 1.}
\label{fig:LongCylinder}
@@ -183,7 +183,7 @@ \subsection{Porod's approximation for a flat cylinder \cite{Porod1948}}
\includegraphics[width=0.668\textwidth,height=0.488\textwidth]{../images/form_factor/cylindrical_obj/FlatCylinder.png}
\end{center}
\caption{Scattering intensity of a cylinder with radius $R=10$ nm and lengths of $L=2$ nm
and $L=20$ nm. Next to Porod's axproximation for flat cylinders also
and $L=20$ nm. Next to Porod's approximation for flat cylinders also
the exact integral solution is shown for comparison.
The scattering length density contrast is set to 1.}
\label{fig:FlatCylinder}
@@ -233,7 +233,7 @@ \subsection{Porod's approximations for cylinder \cite{Porod1948}}
\includegraphics[width=0.55\textwidth,height=0.4\textwidth]{../images/form_factor/cylindrical_obj/PorodCylinder.png}
\end{center}
\caption{Scattering intensity of a cylinder with radius $R=10$ nm and lengths of $L=2$ nm,
$L=20$ nm, and $L=50$ nm. Next to Porod's axproximation for a cylinders also
$L=20$ nm, and $L=50$ nm. Next to Porod's approximation for a cylinders also
the exact integral solution is shown for comparison.
The scattering length density contrast is set to 1.}
\label{fig:PorodCylinder}
@@ -552,7 +552,7 @@ \subsection{partly aligned cylindrical shell \cite{Hayter1984}}
\begin{align}
p(\theta) & = \sum_{l=0,even}^\infty \frac{2l+1}{2} \left\langle P_l\right\rangle\, P_l(\cos(\theta))
\end{align}
Due to the symmetrie $p(\theta)=p(\pi-\theta)$ all terms with odd values for $l$ are zero and only the
Due to the symmetry $p(\theta)=p(\pi-\theta)$ all terms with odd values for $l$ are zero and only the
even terms needs to be considered. For this form factor the first three terms up to $l=6$ are implemented.
As $\int_0^\pi p(\theta) \sin\theta \, d\theta =1$ the zero order parameter is one $\left\langle P_0 \right\rangle=1$.
@@ -6,8 +6,8 @@ \subsection{DLS\_Sphere\_RDG} ~\\
signal $g_2(t)-1 = g_1^2(t)$ of a DLS (dynamic light scattering)
measurement. The $Q$ dependent contribution to the relaxation
signal by particles of different radius $R$ is considered by
weighting $g_2(t)-1$ with the form factor of sperical particles in
Raylay-Debye-Gans approximation:
weighting $g_2(t)-1$ with the form factor of spherical particles in
Rayleigh-Debye-Gans approximation:
\begin{align}
I_\text{DLS\_Sphere\_RDG} (t,\eta,T,Q) &= \int\limits_0^\infty N(R) \; K^2_\text{sp}(Q,R)
\: e^{-D Q^2t} \; dR
@@ -272,8 +272,8 @@ \subsection{SuperParStroboPsi} ~\\
magnetic field due to phase shifts in the amplifier.
If the neutron polarization can follow adiabatically the varying magnetic field needs to be verified
experimentally. Therefore we introduce here a parameter $a_\text{ad} \in [0;1]$ which takes into account
wether ($a_\text{ad}=1$) or not ($a_\text{ad}=0$) the neutron spin adiabatically follows the change
of of magnetic field direction ($\text{sgn}(B(t))$).
whether ($a_\text{ad}=1$) or not ($a_\text{ad}=0$) the neutron spin adiabatically follows the change
of magnetic field direction ($\text{sgn}(B(t))$).
\begin{align}
\BM{r}_\text{ad} =
\left(
@@ -10,7 +10,7 @@ \subsection{Gaussian chain}
\includegraphics[width=0.744\textwidth,height=0.823\textwidth]{Walk3d_0.png}
\end{center}
\caption{The underlying model for a polymer chain is an
isotropic random walk on the euclidean lattice $\mathbb{Z}^3$.
isotropic random walk on the Euclidean lattice $\mathbb{Z}^3$.
This picture shows three different walks after 10 000 unit steps,
all three starting from the origin. \label{fig:RandomWalk3D}}
\end{figure}
@@ -99,7 +99,7 @@ \subsection{Gaussian chain}
\SASfit has implemented the generalized form of a Gaussian (\texttt{generalized Gaussian coil}) coil and the standard
Debye formula \texttt{Gauss}. In both cases three version are implemented which only differ in their parametrization of
the forward scattering. In case of the the Debye-formula also the polydisperse \texttt{GaussPoly} is implemented.
the forward scattering. In case of the Debye-formula also the polydisperse \texttt{GaussPoly} is implemented.
\textcolor[rgb]{1.00,1.00,1.00}{Gauss}\\
\subsubsection{Gauss \cite{Debye1947}}
@@ -212,7 +212,7 @@ \subsubsection{Polydisperse flexible polymers with Gaussian statistics \cite{Ped
\end{figure}
\textcolor[rgb]{1.00,1.00,1.00}{Gauss}\\
\subsubsection{generalalized Gaussian coil \cite{Hammouda,Hammouda2012,Hammouda1993,Hammouda2016}}
\subsubsection{generalized Gaussian coil \cite{Hammouda,Hammouda2012,Hammouda1993,Hammouda2016}}
\label{sect:generalized_gaussian_coil}
~\\
The scattering function for the generalized Gaussian coil is according to eq.\ \ref{eq:generalizedGauss}
@@ -156,7 +156,7 @@ \subsection{van der Waals one-fluid approximation}
\label{sec:SQvdW1}
~\\
This approximation is similar to the scaling approximation introduced by Gazzillo
et al. \cite{Gazzillo1999}. The exact formular is given by
et al. \cite{Gazzillo1999}. The exact formula is given by
%\begin{subequations}
\begin{align}
\frac{d\sigma_i}{d\Omega}(Q) =
@@ -1,5 +1,10 @@
\appendix{History}
\begin{description}
\item[201x-xx-xx] \SASfit 0.94.10
\begin{itemize}
\item bug fix in the algorithm for calculating the resolution parameter in case of averaging neighbouring data points
\item plugin implementation of several variants of helices
\end{itemize}
\item[2017-08-16] \SASfit 0.94.9
\begin{itemize}
\item changed scaling of SESANS correlation functions by factor $1/(2\pi)^2$
@@ -726,11 +726,11 @@ \subsubsection{P'(Q): Kholodenko's worm} ~\\
\label{fig:KholodenkoWorm}
\end{figure}
By using the analogy between Diracs fermions
By using the analogy between Dirac's fermions
and semi-flexible polymers
Kholodenko \cite{kholodenko93} could give a simple expression for the
scattering behaviour of wormlike structures. The form factor $P_0(Q)$ resulting
from Kholodenkos approach is designed to reproduce
from Kholodenko's approach is designed to reproduce
correctly the rigid-rod limit and the random-coil limit.
Defining $x = 3L/l_b$ ($L$: contour length, $l_b$: Kuhn length), it is given by
\begin{align}
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