Visualizing the atomic-scale structure from the output of a calculation is critical, both for understanding your system and disseminating the results. There are many available tools, but some useful suggestions are below.
When you make a PowerPoint with a given structure visualization, you should always provide an atom label color key!
Visualization of Solid-State Systems:
Andrew's Recommendations: For solid-state materials, use VESTA for casual viewing. For more involved editing (e.g. adding adsorbates) and making production-quality figures, use CrystalMaker or Virtual NanoLab.
VESTA: Visualizing crystalline systems (e.g. CIF) and volumetric outputs from solid-state DFT calculations. It's free and fast but not the most beautiful.
CrystalMaker: Publication-quality figures for solid-state systems. Check out their YouTube channel for tutorials
We have a Windows license for v11 on the group Dropbox.
Quantum ATK Virtual NanoLab: Publication-quality figures for solid-state systems and can visualize the outputs of periodic DFT calculations. Can also visualize VASP output data. When registering, use 16183 as the Site ID.
To activate the Princeton site license, VPN into the Princeton network, set the host as license.rc.princeton.edu, and the port as 27020. The program can only be used when VPN'd or on the Princeton network.
Visualization of Molecular Systems:
Andrew's Recommendations: For molecular systems, use ChemCraft for casual visualizing/editing. For production-quality figures, use SAMSON.
ChemCraft: Visualizing molecular systems (e.g. XYZ) and the outputs of molecular DFT calculations. The default style is ugly. Prettier templates are below, which you can add to /Chemcraft/schemes3.
There is a 150-day free trial, after which Andreew can purchase a license for you.
If you are looking to make professional (cover art-quality) visualizations, the following tools are worth considering. Nobody in the group needs to do this, but if you are feeling artsy and ambitious by all means go ahead:
Blender: A CGI library (not for routine visualizations). See CGFigures for a tutorial for scientists.
Oftentimes, when you download a crystal structure it may be missing hydrogen atoms, which are difficult to resolve crystallographically. You can automatically add hydrogen atoms to a structure using the CCDC suite's Mercury tool (💠Material/Property DBs ). For this easy task though, simply install the software program and follow these steps:
Import the CIF
Edit > Auto Edit Structure and then press Apply. You will likely need to modify the results slightly.
Alternatively, for manual edits, do Edit > Edit Structure and then Add > Hydrogen Atoms