Brian H. Toby

GSAS-II: the genesis of a modern open-source all purpose crystallography software package

The newly developed GSAS-II software is a general purpose package for data reduction, structure solution and structure refinement that can be used with both single-crystal and powder diffraction data from both neutron and X-ray sources, including laboratory and synchrotron sources, collected on both two- and one-dimensional detectors. It is intended that GSAS-II will eventually replace both the GSAS and the EXPGUI packages, as well as many other utilities. GSAS-II is open source and is written largely in object-oriented Python but offers speeds comparable to compiled code because of its reliance on the Python NumPy and SciPy packages for computation. It runs on all common computer platforms and offers highly integrated graphics, both for a user interface and for interpretation of parameters. The package can be applied to all stages of crystallographic analysis for constant-wavelength X-ray and neutron data. Plans for considerable additional development are discussed.

A dedicated powder diffraction beamline at the Advanced Photon Source: Commissioning and early operational results

A new dedicated high-resolution high-throughput powder diffraction beamline has been built, fully commissioned, and opened to general users at the Advanced Photon Source. The optical design and commissioning results are presented. Beamline performance was examined using a mixture of the NIST Si and Al(2)O(3) standard reference materials, as well as the LaB6 line-shape standard. Instrumental resolution as high as 1.7 x 10(-4) (DeltaQQ) was observed.

A twelve-analyzer detector system for high-resolution powder diffraction.

A dedicated high-resolution high-throughput X-ray powder diffraction beamline has been constructed at the Advanced Photon Source (APS). In order to achieve the goals of both high resolution and high throughput in a powder instrument, a multi-analyzer detector system is required. The design and performance of the 12-analyzer detector system installed on the powder diffractometer at the 11-BM beamline of APS are presented.

DRAWxtl, an open-source computer program to produce crystal structure drawings

The computer program DRAWxtl produces crystal structure drawings in the form of an interactive screen representation, as well as VRML files for use on web pages and in classroom teaching, and creates input files for the popular Persistence of Vision Raytracer (POV-Ray) rendering program for publication-quality graphics, including generation of stereo pairs. DRAWxtl output produces the standard kinds of graphical representations: spheres, ellipsoids, bonds and polyhedra of any complexity. In addition, it can draw arrows to represent magnetic moments, show capped cones to indicate the location of lone-pair electrons and display Fourier contours in three dimensions. A unique feature of this program is the ability to plot incommensurately modulated and composite structures. This open-source program can be used with operating systems as diverse as Windows (9X, NT, 2000 and XP), Mac OS X, Linux and most other varieties of Unix.

Magnetic structure refinement with neutron powder diffraction data using GSAS: A tutorial

Neutron diffraction provides a direct probe for the ordering of spins from unpaired electrons in materials with magnetic properties. The ordering of the spins can be modeled in many cases by adding spin directions to standard crystallographic models. This requires, however, that crystallographic space groups be extended by addition of a “color” attribute to symmetry operations, which determines if the operation maintains or flips the direction of a magnetic spin. Rietveld analysis provides a mechanism for fitting magnetic structure models to powder diffraction data. The general structure and analysis system (GSAS) software suite is commonly used for Rietveld analysis and includes the ability to compute magnetic scattering. Different approaches are commonly used within GSAS to create models that include magnetism. Three equivalent but different approaches are presented to provide a tutorial on how magnetic scattering data may be modeled using differing treatment of symmetry. Also discussed is how magnetic models may be visualized. The commands used to run the GSAS programs are summarized within, but are shown in great detail in supplementary web pages.

Management of metadata and automation for mail‐in measurements with the APS 11‐BM high‐throughput, high‐resolution synchrotron powder diffractometer

A high-resolution and high-throughput synchrotron powder diffractometer has been automated for use with samples that are mailed in by Advanced Photon Source users. Implementation of a relational database with web interfaces for both outside users and beamline staff, which is integrated into the facility-wide proposal and safety system, allows all aspects of beamline management to be integrated. This system permits users to request kits for mounting samples, to provide sample safety information, to obtain their collected data and to provide usage information upon project completion in a quick and simple manner. Beamline staff use a separate interface to note receipt of samples, schedule and collect diffraction data, post-process and quality-check data, and dispose of samples. The design of the software and database are discussed in detail.

Rigid body refinements in GSAS / EXPGUI

Rigid bodies provide a way to simplify the model used in a crystallographic refinement by removing parameters that describe degrees of freedom that are unlikely to change based on chemical experience. The GSAS software package provides a powerful implementation of rigid bodies that allows for refinement of classes of bond lengths, grouping of bodies to further reduce parameterization and where atomic motion can be described from group displacement parameters (TLS) representation. However, use of rigid bodies in GSAS is complex to learn and time-consuming to perform. This paper describes how the rigid body definition process has been simplified and extended through implementation in the EXPGUI interface to GSAS .

Why scientists should learn to program in Python

The importance of software continues to grow for all areas of scientific research, no less for powder diffraction. Knowing how to program a computer is a basic and useful skill for scientists. This paper explains the three approaches for programming languages and why scripting languages are preferred for non-expert programmers. The Python-scripting language is extremely efficient for science and its use by scientists is growing. Python is also one of the easiest languages to learn. The language is introduced, as well as a few of the many add-on packages available that extend its capabilities, for example, for numerical computations, scientific graphics, and graphical user interface programming. Resources for learning Python are also provided.

Xclaim: A graphical interface for the calculation of core-hole spectroscopies

Abstract Xclaim (X-ray core level atomic multiplets) is a graphical interface for the calculation of core-hole spectroscopy and ground state properties within a charge-transfer multiplet model taking into account a many-body Hamiltonian with Coulomb, spin–orbit, crystal-field, and hybridization interactions. Using Coulomb and spin–orbit parameters calculated in the Hartree–Fock limit and ligand field parameters (crystal-field, hybridization and charge-transfer energy) the program calculates X-ray absorption spectroscopy (XAS), X-ray photoemission spectroscopy (XPS), photoemission spectroscopy (PES) and inverse photoemission (IPES). The program runs on Linux, Windows and MacOS platforms.

What's new in GSAS-II

The General Structure and Analysis Software II (GSAS-II) package is an all-new crystallographic analysis package written to replace and extend the capabilities of the universal and widely used GSAS and EXPGUI packages. GSAS-II was described in a 2013 article, but considerable work has been completed since then. This paper describes the advances, which include: rigid body fitting and structure solution modules; improved treatment for parametric refinements and equation of state fitting; and small-angle scattering data reduction and analysis. GSAS-II offers versatile and extensible modules for import and export of data and results. Capabilities are provided for users to select any version of the code. Code documentation has reached 150 pages and 17 web-tutorials are offered.