GIDInd: an automated indexing software for grazing-incidence X-ray diffraction data

Abstract

Grazing-incidence X-ray diffraction (GIXD) is a widely used technique for the crystallographic characterization of thin films. The identification of a specific phase or the discovery of an unknown polymorph always requires indexing of the associated diffraction pattern. However, despite the importance of this procedure, only a few approaches have been developed so far. Recently, an advanced mathematical framework for indexing of these specific diffraction patterns has been developed. Here, the successful implementation of this framework in the form of an automated indexing software, named GIDInd, is introduced. GIDInd is based on the assumption of a triclinic unit cell with six lattice constants and a distinct contact plane parallel to the substrate surface. Two approaches are chosen: (i) using only diffraction peaks of the GIXD pattern and (ii) combining the GIXD pattern with a specular diffraction peak. In the first approach the six unknown lattice parameters have to be determined by a single fitting procedure, while in the second approach two successive fitting procedures are used with three unknown parameters each. The output unit cells are reduced cells according to approved crystallographic conventions. Unit-cell solutions are additionally numerically optimized. The computational toolkit is compiled in the form of a MATLAB executable and presented within a user-friendly graphical user interface. The program is demonstrated by application on two independent examples of thin organic films.

Analysis of Crystallographic Structures and Properties of Silver Nanoparticles Synthesized Using PKL Extract and Nanoscale Characterization Techniques

“…The production of silver nanoparticles of a larger size is evident from the observation that their diffraction profiles are broadened in comparison to those of bulk silver. The standard diffraction angles (2θ) and the experimental diffraction angles (2θ) in Table S2 also agree well. − …”

From 2D to 3D: Bridging Self-Assembled Monolayers to a Substrate-Induced Polymorph in a Molecular Semiconductor

“…Calibration was performed using LaB 6 standards. GIDVis software was used to analyze the collected data, and the corresponding GIXD pattern was indexed by GIDInd software . During indexation, the lattice parameters were solved in a two-step procedure.…”

“…GIDVis software 52 was used to analyze the collected data, and the corresponding GIXD pattern was indexed by GIDInd software. 53 During indexation, the lattice parameters were solved in a two-step procedure. In step one, two Miller indices of the contact plane between the thin-film crystal and the substrate, h and k, were determined from the observed peaks, from which the lattice parameters a, b, and γ can be calculated.…”

Engineering of a kinetically driven phase of phenoxazine by surface crystallisation

“…In a first step, indexation of the GIXD pattern reveals the lattice constants of the crystallographic unit cell by applying a self-developed strategy. 32,33 The obtained unit cell was then used as the initial parameter for the molecular packing simulation using molecular dynamics (MD) based on the LAMMPS software package, 34 the CHARMM general force field version 3.0.1, 35 and the Dreiding generic force field. 36 For each simulation run, two randomly oriented phenoxazine molecules were placed into an expanded volume of the found crystallographic unit cell.…”