Releases: SASfit/SASfit
Releases · SASfit/SASfit
v0.94.12 2023-01-12
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- improved numerical stability of wormlike structure factor according to Koyama
- some older plugins are now using the new integration routines supplied in SASfit:
ellcylshell, torus, ellipsoidal shell, superhelices, stacked discs, ring polymers,
triaxial ellipsoidal shell, carved triaxial ellipsoidal shell, kholodenko worm,
ring and linear polymer under shearflow, sheared spheroids, sheared cylinders, koyama worm - made a variable substitution for the integration in sasfit_orient_avg to get more homogeneously distributed points on a spherical surface
- added form factor of cylinder with globular end caps
- the 1-Yukawa and 2-Yukawa structure factor stores now some previously calculated coefficients, which make it a bit more efficient.
- bugfix in calculating integral structural parameter.
In certain (nonphysical) cases the fit as well as the plot of the fit result crashed. - bugfix for star polymer with rigid arms
- due to flexible integration routines some of them calculate the function to integrate
at its integration limits. For mass fractals this caused an error using these integration routines.
There might be more such cases. The mass fractal plugins have been debugged. - corrected in "sq 2D hard disks Rosenfeld" bug:
$J_1(2x)/x = 2jinc(2x)$ instead
$J_1(2x)/x = 1/2 jinc(2x)$ - changed lognorm_fp-size distribution as plugin and included now also the other cases as described in the manual. So far only the shape 1 was implemented.
- renaming dodecahedra into rhombic dodecahedra
- added size distribution plugin based on generalized beta distribution
- added skewed gaussian and exponentially modified gaussian size distribution
- added spherical-t design algorithm for integration over the surface of a sphere
- added a new form factor of PEGylated vesicle with smoothed interfaces
- added metalog size distribution as well as the Johnson's family of distributions (SN, SL, SB, SU) and its generalization
- update to FFTW 3.3.10
- supply of a piecewise constant potential for OZ solver
- moved sticky hard sphere and square well structure factors into the plugin menu folder.
The order of parameters changed slightly to be a bit more consistent - added RLCA and DLCA structure factors for aggregates, which include nearest neighbor correlations
- supply of internal multidimensional integration routines, which can be configured via GUI
- supply of internal orientation average integration routines, which can be configured via GUI
- added form factor of super-ellipsoid
- added form factor of super-egg
- update to gsl 2.7
- update to FFTW 3.3.9
- use under Widows systems a powershell script to copy a 2D image to the clipboard as the previous code does not work anymore under MSYS2. A similar solution might be available under Unix and MacOS
- added form factor for an octahedron
- added form factor for an tetrahedron
- added form factor for a cone with six-fold symmetry
- added form factor for a cone
- added form factor for a rectangular base pyramid
- added perl necklace model both with stiff rodlike connections as well as "freely connected rods"
- extended "random flight" structure model by introducing an uncertainty parameter for the step width identical to the paracrystalline model for lamellar structures
- for merging files a multiplier instead of divisor is used now
- added structure factor for a 2-Yukawa potential in MSA approximation
- added a parameter choosing for some of the wormlike micelle structure factors either a polydisperse or a monodisperse contour length
- added three more radial profiles of spherical symmetric objects showing a Porod-law different from q^-4
- added a trapezoidal peak function and its generalized as well as its symmetric variant
- added some cluster models for structure factors from [Larsen 2020]
- implemented a modified DAB model assuming a deformation and subsequent random orientation average of the standard DAB model
- implemented structure factors for multilamellar structures as plug-in function and added the monodisperse stacking case.
In earlier version only the more practically relevant case of polydisperse case was implemented. - added structure factors for one and two dimensional hard sphere potentials both for aligned structures in a certain direction as well as for random oriented 1D structures.
- the model Pcs:Plate+Chains(RW) now assumes always a non-zero surface area to avoid division by zero for zero layer thickness
- fixed a memory leak, when resolution function for single data set was used
- added form factor for ring polymer under shear flow in the approximation of Rousse modes
- successfully updated from gsl2.5 to gsl2.6 library.
- added a plugin for randomly oriented ellipsoids with a gamma-size distribution, where the integration over the size distribution can be performed analytically.
- added a generalized and lesser generalised form factor according to Fedorova describing several shapes and geometries of objects depending on only one size parameter visible in the q-range of the SAS instrument
- added a form factor describing the scaling function of a phase separating system after a quench in the miscibility gap
- added form factor for cylinders with a fuzzy interface (Pcs:Boucher cyl., Pcs:Boucher2 cyl., Pcs:fuzzy cyl., Pcs:linear shell cyl.) and the corresponding profiles in real space ("profile:Boucher cyl.", "profile:Boucher2 cyl.", "profile:fuzzy cyl.", "profile:linear shell cyl.")
- added in integral structural parameters a command for developing model-free calculations of size distributions using EM algorithms as well as Maximum Entropy methods and traditional Tikhonov regularization methods. This part is still experimental and not well documented in the manual.
- bug fix for TetraheadronDoubleShell. The double sum over the number of spheres has been corrected.
- bug fix in Porod cylinder as by moving the form factor to the plugin area the length parameter was assigned to the wrong index of the parameter array.
- supplied those models available for SESANS analysis as multiple scattering models because the projected correlation function is directly related to the intermediate function s(r) as described in the reference paper from Schelten and Schmatz, J. Appl. Cryst. (1980). 13, 385-390
- bug fix in the SESANS model of G_gDAB(z)
- added form factors of clipped random waves for 5 different two-point correlation functions
- added form factor of a stochastic model of a boolean union model of spheres with LogNorm size distribution.
- added form factor of a stochastic model of a dead-leave model of spheres with LogNorm size distribution.
- added form factors of polymers under shear flow
- added anisotropic form factor for step deformed networks according to the tube models of Warner-Edwards and a second one from Heinrich-Straube-Helmis
- added some additional azimuthal intensity distributions valid for long objects with certain orientation distribution (Maier-Saupe, Onsager)
- added some azimuthal intensity distributions based on the model of sheared cylinders and spheroids following a Maier-Saupe, Onsager, Heaviside, Gauss, or a Boltzmann orientation distribution. These functions return I(psi) instead of I(q)
- extended the reading routine for SESANS data. A common file format has been established. These data files have in their header a version information (FileFormatVersion 1.0). At the moment some old formats from Delft, where the projected correlation function still has to be calculated from the polarisation and the new format 1.0 are supported.
- removed the old entries for mass fractal structure factors which have been moved to the plug-in sub-menu.
- added some structure factors for worm-like micelles: one RPA approximation and three different PRISM approximations. For all of them an exponential length distribution is included.
v0.94.11 2018-11-15
- reduced the frequency of updating the progress bar as well as checking of pressing the interrupt button to maximal 10 times per second.
- added two additional form factors for ring polymers with excluded volume effects (RingPolymerBZ, RingPolymerBMB) and renamed the old one from FlexibleRingPolymer to RingPolymerCasassa
- bug fix in ring polymers, daisy-like ring and m-membered twisted ring.
- bug fix of GzSphere, returns wrong value for z>2R
- bug fix of GzgDAB for extrapolation to z->0
- added two more models for P'(Q) of thin cylindrical objects describing wormlike structure: "Koyama worm" and "fre 10000 ely joined chain of rods"
- Some form factors for polymers like Gaussian chains, star polymers and ring polymers have been moved to the plug-in area.
- As all peak functions are now available as plug-ins the obsolete old code has been deleted
- The Lorenz-Mie form factors for static light scattering are now made available as plug-in form factors
- SASfit now tries to avoids starting a new fit or simulation before the previous one is finished
- Successfully updated from gsl2.4 to gsl2.5 library.
- The new 2D/3D hard sphere structure factors are now available in the structure factor plug-in folder named "Hard Sphere 2D/3D"
- update to FFTW 3.3.8 worked after disabling threads however on Windows McAfee had to switched off during configure process.
- implemented some thermodynamic self-consistent hard sphere structure factors based on the rational function approximation method
- tried to avoid overflow of sinh-function in the model "Khodolenko-Worm"
- now between thin objects (local planar and local cylindrical approximation) and anisotropic shapes is distinguished.
- started to implement a 2D fit routine, which can fit data of a single detector position
- new plug-in folder for azimuthal data
- new plug-in folder for deformed or sheared objects
- new form factors for partly aligned cylinders and ellipsoids following a Maier-Saupe, Onsager, Heaviside, Gauss, or a Boltzmann orientation distribution
- new factor of a reptating chain after a deformation step
- new plug-in structure factors for 2-dimensional fluids of monodisperse hard spheres, "2D hard disks (Rosenfeld)" and "2D hard disks (Guo)"
v0.94.10 2018-03-20
- The form factors "Ellipsoid i" "Ellipsoid ii" "EllipsoidalCoreShell", and "triaxEllShell1" have been disabled and replaced by a series of plug-in functions. Those replacements make use of a faster routine for multidimensional integrals (pcubature). Because of this an optional size distribution became part of the supplied plug-in form factors.
- bug fix of unit conversion via clipboard
- added a plug-in for a random flight structure factor
- bug fix in the algorithm for calculating the resolution parameter in case of averaging neighboring data points
- plug-in implementation of several variants of helices
- plug-in for rectangular parallelepipeds have been extended so that it can have a size distribution of one, two or all three axis. The multiple integration is done by using the pcubature code from Steven G. Johnson
- multi dimensional integration package "cubature" from Steven G. Johnson becomes generally available also in plug-ins (https://github.com/stevengj/cubature)
0.94.9 2017-08-16
- changed scaling of SESANS correlation functions by factor 1/(2pi)^2
- unit conversion for reading ASCII files corrected and extended
- update to FFTW 3.3.6-pl2 did not work, went back to 3.3.5
- update to gsl 2.4
- bug fix: resolution bar was not plotted properly
- Uncertainties on x and y axis are now plotted symmetrically from x+-Delta_x and y+-Delta_y.
Before they were plotted from x+-0.5Delta_x and y+-0.5Delta_y.
v0.94.8 2016-12-16
- moved all peak functions into the plugin area.
- Added the possibility to apply after the summation of all scattering contributions a final operator.
At the moment between three operator can be chosen:- Unit operator which does not do anything with the data
- Taking the Hankel transform 2pi*H[I(Q)] for converting SAS model into a projected correlation function G(delta),
which defines the SESANS signal - Applying the operator from 2) and taking the exponetial function of it exp(2pi*H[I(Q)]) to get SESANS signal
- For the extension to SESANS also an option for reading SESANS data has been supplied.
The format has been defined by TU Delft and has the default extension *.ses. - added a model for of a self-fine random density distribution (gDAB) both under non-particular
structures as well as under SESANS as a correlation function. - added a SESANS correlation function for a generalized Gaussian chain for Flory exponents between nu ϵ (0,1/2)
- updated to FFTW 3.3.5
- updated to sundials 2.7.0
- updated to gsl 2.3
- supplying some alternative integration routines for integrating over the size distribution
- bug fix of sasfit_integrate routine, which caused a crash when called from plugin functions
- first minimal routine for reading simple ascii data from ALV-5000 with single correlation function for DLS-analysis
- adding the PLHNC and RMSA closure to the OZ solver
- fixed a bug in the scaling parameter of the Teubner-Strey model
- bugfix in routine for reading data in BerSANS format
MacOS version requires X11 like xquartz
0.94.7 2016-04-25
- implementation of another cumulant formula for DLS
- Bug-fix in the unit conversion routine
- implementation of GMRES, Bi-CGStab, TFQMR and Andersen Accelarion
for solving efficiently the Ornstein Zernicke fixpoint problem - bug fix: since version 0.94.4 the new interrupt option suppressed
a proper error reporting to the GUI for undefined input values - removed some old structure factors,
which were rarely used and theoretically not up to date - a first version of a plugin for ordered mesoscopic and nano structures.
The plugin is providing a part of the structure factors available
in the software package "scatter" from S. Förster. - plugin of a radial profile for a sphere resulting in a Porod law both below and above Q^-4
0.94.6
- improved analysis of confidence intervals of fit parameters:
- clickable correlation coefficients in the matrix highlight associated
pair of fit parameters - covariance matrix elements are highlighted according to their correlation
coefficient - highlighting and selection of correlated params improved
- clickable correlation coefficients in the matrix highlight associated
0.94.5
- storing intensity and size distribution in batch processing routine
- changed the width of the error bar, assuming that the supplied error is FWHM
- changed the internal procedure for plotting error bars
- resolution parameter can now also be plotted
- changed the order of plotting the fit results
in "integral structural parameters" - interruption of batch processing or series analysis implemented
0.94.4
- a new interrupt button can stop now the intensity evaluation of fitting
procedure after each q-value. Before the whole scattering curve needed to be
calculated. - progress bar has been added to the GUI
- bug fix in plotting error bars of multiple data sets.
- implementation of another method for thinning out oversampled data sets. The
new methods is performing an averaging of data points depending on a
user-defined maximum allowed q-smearing and a user-defined maximum distance
in intensity in units of the error bar of the data points, i.e. an averaging is
only performed, if the intensities look similar with n-times the intensity
error bars. - bug fix in GUI if one wants to forget old data and load a new data sets.