HipGISAXS: a high-performance computing code for simulating grazing-incidence X-ray scattering data

2013 ◽  
Vol 46 (6) ◽  
pp. 1781-1795 ◽  
Author(s):  
Slim T. Chourou ◽  
Abhinav Sarje ◽  
Xiaoye S. Li ◽  
Elaine R. Chan ◽  
Alexander Hexemer
Keyword(s):  
Refractive Index ◽  
High Performance ◽  
Multicore Processors ◽  
Grazing Incidence ◽  
Scattering Data ◽  
Simulation Code ◽  
X Ray ◽  
X Ray Scattering ◽  
Wide Range ◽  
Ray Scattering

This article describes the development of a flexible grazing-incidence small-angle X-ray scattering (GISAXS) simulation code in the framework of the distorted wave Born approximation that effectively utilizes the parallel processing power provided by graphics processors and multicore processors. The code, entitledHigh-Performance GISAXS, computes the GISAXS image for any given superposition of user-defined custom shapes or morphologies in a material and for various grazing-incidence angles and sample orientations. These capabilities permit treatment of a wide range of possible sample structures, including multilayered polymer films and nanoparticles on top of or embedded in a substrate or polymer film layers. In cases where the material displays regions of significant refractive index contrast, an algorithm has been implemented to perform a slicing of the sample and compute the averaged refractive index profile to be used as the reference geometry of the unperturbed system. A number of case studies are presented, which demonstrate good agreement with the experimental data for a variety of polymer and hybrid polymer/nanoparticle composite materials. The parallelized simulation code is well suited for addressing the analysis efforts required by the increasing amounts of GISAXS data being produced by high-speed detectors and ultrafast light sources.

Silver behenate as a calibration standard of grazing-incidence small-angle X-ray scattering

2006 ◽  
Vol 39 (5) ◽  
pp. 749-751 ◽  
Author(s):  
Byeongdu Lee ◽  
Chieh-Tsung Lo ◽  
Soenke Seifert ◽  
Randall E. Winans
Keyword(s):  
Refractive Index ◽  
Sample Preparation ◽  
Small Angle ◽  
Incident Angle ◽  
Grazing Incidence ◽  
Peak Position ◽  
Calibration Standard ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Grazing-incidence small-angle X-ray scattering (GISAXS) patterns of a silver behenate composite film, which has a typical layered structure, are described. The peak position of the film in the GISAXS pattern was varied depending on the incident angle, which was well described by taking into account the refraction and the reflection effects. Since the refractive index of samples depends on sample preparation, it is recommended that the measurement of silver behenate as a standard be done in conventional transmission mode to avoid any complexity.

scholarly journals A customizable software for fast reduction and analysis of large X-ray scattering data sets: applications of the newDPDAKpackage to small-angle X-ray scattering and grazing-incidence small-angle X-ray scattering

2014 ◽  
Vol 47 (5) ◽  
pp. 1797-1803 ◽  
Author(s):  
Gunthard Benecke ◽  
Wolfgang Wagermaier ◽  
Chenghao Li ◽  
Matthias Schwartzkopf ◽  
Gero Flucke ◽  
...  
Keyword(s):  
Small Angle ◽  
Data Reduction ◽  
Grazing Incidence ◽  
Scattering Data ◽  
Limiting Factor ◽  
Online Data ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

X-ray scattering experiments at synchrotron sources are characterized by large and constantly increasing amounts of data. The great number of files generated during a synchrotron experiment is often a limiting factor in the analysis of the data, since appropriate software is rarely available to perform fast and tailored data processing. Furthermore, it is often necessary to perform online data reduction and analysis during the experiment in order to interactively optimize experimental design. This article presents an open-source software package developed to process large amounts of data from synchrotron scattering experiments. These data reduction processes involve calibration and correction of raw data, one- or two-dimensional integration, as well as fitting and further analysis of the data, including the extraction of certain parameters. The software,DPDAK(directly programmable data analysis kit), is based on a plug-in structure and allows individual extension in accordance with the requirements of the user. The article demonstrates the use ofDPDAKfor on- and offline analysis of scanning small-angle X-ray scattering (SAXS) data on biological samples and microfluidic systems, as well as for a comprehensive analysis of grazing-incidence SAXS data. In addition to a comparison with existing software packages, the structure ofDPDAKand the possibilities and limitations are discussed.

scholarly journals The Diffraction Pattern Calculator(DPC) toolkit: a user-friendly approach to unit-cell lattice parameter identification of two-dimensional grazing-incidence wide-angle X-ray scattering data

2014 ◽  
Vol 47 (6) ◽  
pp. 2090-2099 ◽  
Author(s):  
Anna K. Hailey ◽  
Anna M. Hiszpanski ◽  
Detlef-M. Smilgies ◽  
Yueh-Lin Loo
Keyword(s):  
Crystal Structure ◽  
Grazing Incidence ◽  
Unit Cell ◽  
Lattice Parameters ◽  
Scattering Data ◽  
Wide Angle ◽  
Two Dimensional ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

TheDPCtoolkit is a simple-to-use computational tool that helps users identify the unit-cell lattice parameters of a crystal structure that are consistent with a set of two-dimensional grazing-incidence wide-angle X-ray scattering data. The input data requirements are minimal and easy to assemble from data sets collected with any position-sensitive detector, and the user is required to make as few initial assumptions about the crystal structure as possible. By selecting manual or automatic modes of operation, the user can either visually match the positions of the experimental and calculated reflections by individually tuning the unit-cell parameters or have the program perform this process for them. Examples that demonstrate the utility of this program include determining the lattice parameters of a polymorph of a fluorinated contorted hexabenzocoronene in a blind test and refining the lattice parameters of the thin-film phase of 5,11-bis(triethylsilylethynyl)anthradithiophene with the unit-cell dimensions of its bulk crystal structure being the initial inputs.

scholarly journals The modular small-angle X-ray scattering data correction sequence

2017 ◽  
Vol 50 (6) ◽  
pp. 1800-1811 ◽  
Author(s):  
B. R. Pauw ◽  
A. J. Smith ◽  
T. Snow ◽  
N. J. Terrill ◽  
A. F. Thünemann
Keyword(s):  
Small Angle ◽  
Direct Detection ◽  
Photon Counting ◽  
Scattering Data ◽  
X Ray ◽  
Data Correction ◽  
X Ray Scattering ◽  
Uncertainty Estimates ◽  
Wide Range ◽  
Ray Scattering

Data correction is probably the least favourite activity amongst users experimenting with small-angle X-ray scattering: if it is not done sufficiently well, this may become evident only during the data analysis stage, necessitating the repetition of the data corrections from scratch. A recommended comprehensive sequence of elementary data correction steps is presented here to alleviate the difficulties associated with data correction, both in the laboratory and at the synchrotron. When applied in the proposed order to the raw signals, the resulting absolute scattering cross section will provide a high degree of accuracy for a very wide range of samples, with its values accompanied by uncertainty estimates. The method can be applied without modification to any pinhole-collimated instruments with photon-counting direct-detection area detectors.

scholarly journals Comprehensive synchrotron grazing-incidence X-ray scattering analysis of nanostructures in porous polymethylsilsesquioxane dielectric thin films

2013 ◽  
Vol 46 (2) ◽  
pp. 466-475 ◽  
Author(s):  
Yecheol Rho ◽  
Byungcheol Ahn ◽  
Jinhwan Yoon ◽  
Moonhor Ree
Keyword(s):  
Thin Films ◽  
Grazing Angle ◽  
Grazing Incidence ◽  
Scattering Data ◽  
Small Contribution ◽  
Dielectric Thin Films ◽  
Dielectric Thin Film ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

A complete grazing-incidence X-ray scattering (GIXS) formula has been derived for nanopores buried in a polymer dielectric thin film supported by a substrate. Using the full power of the scattering formula, GIXS data from nanoporous polymethylsilsesquioxane dielectric thin films, a model nanoporous system, have successfully been analysed. The nanopores were found to be spherical and to have a certain degree of size distribution but were randomly dispersed in the film. In the film, GIXS was confirmed to arise predominantlyviathe first scattering process in which the incident X-ray beam scatters without reflection; the other scattering processes and their contributions were significantly dependent on the grazing angle. This study also confirmed that GIXS scattering can be analysed using only independent scattering terms, but this simple approach can only provide structural parameters. The cross terms were found to make a relatively small contribution to the intensity of the overall scattering but were required for the complete characterization of the measured two-dimensional scattering data, in particular the extracted out-of-plane scattering data, and their inclusion in the analysis enabled film properties such as film thickness, critical angle (i.e.electron density), refractive index and the absorption term to be determined.

scholarly journals Beamline B21: high-throughput small-angle X-ray scattering at Diamond Light Source

2020 ◽  
Vol 27 (5) ◽  
pp. 1438-1446
Author(s):  
Nathan P. Cowieson ◽  
Charlotte J. C. Edwards-Gayle ◽  
Katsuaki Inoue ◽  
Nikul S. Khunti ◽  
James Doutch ◽  
...  
Keyword(s):  
Light Source ◽  
Small Angle ◽  
High Performance ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Scattering ◽  
Wide Range ◽  
The Uk ◽  
High Level ◽  
Ray Scattering

B21 is a small-angle X-ray scattering (SAXS) beamline with a bending magnet source in the 3 GeV storage ring at the Diamond Light Source Ltd synchrotron in the UK. The beamline utilizes a double multi-layer monochromator and a toroidal focusing optic to deliver 2 × 1012 photons per second to a 34 × 40 µm (FWHM) focal spot at the in-vacuum Eiger 4M (Dectris) detector. A high-performance liquid chromatography system and a liquid-handling robot make it possible to load solution samples into a temperature-controlled in-vacuum sample cell with a high level of automation. Alternatively, a range of viscous or solid materials may be loaded manually using a range of custom sample cells. A default scattering vector range from 0.0026 to 0.34 Å−1 and low instrument background make B21 convenient for measuring a wide range of biological macromolecules. The beamline has run a full user programme since 2013.

Treatment of grazing-incidence small-angle X-ray scattering data taken above the critical angle

2001 ◽  
Vol 34 (2) ◽  
pp. 152-156 ◽  
Author(s):  
A. Martorana ◽  
A Longo ◽  
F. d'Acapito ◽  
C. Maurizio ◽  
E. Cattaruzza ◽  
...  
Keyword(s):  
Small Angle ◽  
Critical Angle ◽  
Hard Spheres ◽  
Grazing Incidence ◽  
Sample Surface ◽  
Scattering Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Incoming Beam ◽  
Ray Scattering

The equations taking into account refraction at the sample surface in grazing-incidence small-angle X-ray scattering (GISAXS) when the angle between the incoming beam and the sample surface is slightly larger than the critical angle are derived and discussed. It is demonstrated that the refraction of both the incoming and the scattered beam at the sample surface affects the GISAXS pattern and that, when a planar bidimensional detector perpendicular to the incoming beam is used, the effect depends on the azimuthal detector angle. The smearing of the pattern depending on the size of the illuminated sample area in grazing incidence is estimated by simulations with Cauchy functions of different widths. The possibility of integrating the recorded intensities over a suitable azimuthal angular range and then of making the correction for refraction is also analysed, employing simulations involving the intensity function of monodisperse interacting hard spheres. As a case study, the refraction correction is applied to the investigation of a Cu–Ni implant on silica glass.

GIXSGUI: a MATLAB toolbox for grazing-incidence X-ray scattering data visualization and reduction, and indexing of buried three-dimensional periodic nanostructured films

2015 ◽  
Vol 48 (3) ◽  
pp. 917-926 ◽  
Author(s):  
Zhang Jiang
Keyword(s):  
Thin Films ◽  
Three Dimensional ◽  
Grazing Incidence ◽  
Surface Scattering ◽  
Scattering Data ◽  
Matlab Toolbox ◽  
X Ray ◽  
X Ray Scattering ◽  
Reduction Methods ◽  
Ray Scattering

GIXSGUIis a MATLAB toolbox that offers both a graphical user interface and script-based access to visualize and process grazing-incidence X-ray scattering data from nanostructures on surfaces and in thin films. It provides routine surface scattering data reduction methods such as geometric correction, one-dimensional intensity linecut, two-dimensional intensity reshapingetc. Three-dimensional indexing is also implemented to determine the space group and lattice parameters of buried organized nanoscopic structures in supported thin films.

Sign in / Sign up

Export Citation Format

Share Document