pymatgen tutorial #4: Structure transformations, symmetry analysis, & local environments

One of the major capabilities of the pymatgen software is its ability to manipulate and analyze crystal structures. This tutorials walks through those capabilities, including generating surfaces, doping structures, analyzing space group and Wyckoff positions, and assessing local environments and coordination polyhedra.

Links:
Jupyter notebook used in this tutorial: https://github.com/computron/pymatgen...
pymatgen: https://pymatgen.org

00:00 Introduction
00:43 Transformations package intro - perturb structure, supercell, add oxidation states, surfaces / slabs
06:57 Transformations using enumlib - order / disorder, add dopant
12:50 Analyzing symmetry and spacegroup of crystal structures with SpaceGroupAnalyzer
16:16 Crystal structure setting / representation conversion using SpaceGroupAnalyzer, Wyckoff position, and “symmetrizing” imperfect crystals
20:22 Local environment analysis - intro and coordination number algorithms (Minimum Distance, Voronoi neighbors, CrystalNN)
24:24 Coordination polyhedra using the Chemenv package (detecting octahedral, tetrahedral, square planar, etc. environments in crystals)
30:11 Conclusion