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The software ReciPro makes various crystallographic calculations, visualizes a crystal structure, simulates diffraction patterns and TEM image, indexes diffraction spots, plots stereographic projection, and so on.
SHRY (Suite for High-throughput generation of models with atomic substitutions implemented by python) is a tool for generating unique ordered structures corresponding to a given disordered structure.
CSManager is a Windows application for browsing, searching, and editing crystal structure databases: AMCSD is bundled, COD is downloaded on demand, CIF/AMC files can be imported and exported, and crystals can be sent to ReciPro and PDIndexer.