Gixstapose: Interactive and Reproducible Scattering Analysis of Simulation Snapshots

We develop a tool for solving common problems in structural analysis at nanometer length scales. Molecular simulations typically employ periodic boundary conditions to represent conditions in bulk materials, but this places constraints on observable structural features. Analyzing material structure in the frequency domain quantifies the degree to which repeating structural features exist, but can be difficult to implement, interpret, and reproduce. Furthermore, the generation of simulated diffraction patterns from molecular simulation plays a crucial role in validating simulation results against experiments that rely on diffraction patterns to quantify structure.

In this work we develop GIXStapose, a new interactive analysis software for studying crystalline and amorphous materials structures. It enables grazing incidence X-ray scattering (GIXS) patterns to be visualized while interactively rotating chemical structures, especially periodic simulation volumes generated from molecular simulations. This functionality is useful for interactively identifying real-space chemical features that correspond to bright diffraction peaks and the rotation matrices that generate them. As such, this tool has potential to aid in the reproducible generation of publication quality figures which connect both GIXS and structural data, and it has pedagogical potential for students learning about crystal structures and diffraction.

GIXStapose is made possible by open-source packages, including the high-quality rendering of the Fresnel ray-tracer, the chemical file formats parsing of MBuild, and numpy's fast Fourier implementations used in interactive diffraction analysis, and by funding from the National Science Foundation (#1835593)