crystallography – crystal viewers
Visualizing crystals and rotating them on your screen to watch them from any point of view, that’s a useful feature. There are many tools available that can do that for you. A few of them are listed here:
One of the more popular free crystal viewers, is VESTA. You can download and install VESTA on your computer (Windows, Linux, Mac), and learn to use it by this short tour. The full documentation of VESTA is here. VESTA can visualize crystals that are supplied in cif format, as well as in many other code-specific formats.
Execute these commands in a terminal window inside the Quantum Mobile virtual machine:
cd
wget https://jp-minerals.org/vesta/archives/3.4.6/VESTA-x86_64.tar.bz2
tar ‐xvjf VESTA-x86_64.tar.bz2
cd VESTA-x86_64
./VESTA
Using the ‘file’ menu, you can open cif files on your computer.
In order to start VESTA later from within any other folder in the virtual machine, to display for instance the file halite.cif, do:
~/VESTA-x86_64/VESTA halite.cif
Once you have opened a crystal in VESTA, go through this short tour document to learn the basics of working with VESTA.
Jmol is already available in the Quantum Mobile virtual machine. No installation required. Navigate to a folder where you have a cif file (e.g. halite.cif), and visualize it as follows:
jmol
File ==> Open ==> select cif file ==> Open
right-click ==> Symmetry ==> Reload { 444 666 1 } + Display 555
keep pressing the left mouse button and drag to rotate
- If you use the QuantumATK GUI to prepare input files for your DFT code, then you will have seen it displays crystals too.
- Another freeware tool is SageMD (not thoroughly tested by us, but it looks OK).
We recommend you install at least VESTA to use throughout this course and follow this short tour through the code. Then tell us how it went for you :