Atomic Modeling with GAMGI

For this article, I'm moving back into the realm of chemistry software—specifically, the General Atomistic Modelling Graphic Interface, or GAMGI. GAMGI provides a very complete set of tools that allows you to design and visualize fairly complex molecules.

GAMGI has the special ability to make creating repeating structures much easier, which is handy when you're trying to create crystalline structures.

GAMGI should be available in the package repositories of most Linux distributions. For example, on Debian-based distros, you can install GAMGI with the following command:


sudo apt-get install gamgi

There are also data and documentation packages (gamgi-data and gamgi-doc), and when you first start to use GAMGI, it's a good idea to install those packages as well.

Once the packages are installed, you can start GAMGI from the command line or from your desktop environment's menu system. When it starts up, you get a blank canvas to begin your work.

Figure 1. When you start GAMGI, you get a minimal set of tools to help begin your project.

This interface is probably one of the more minimal ones of the chemistry packages that you are likely to use, but it hides all of the functionality that is present within GAMGI. It is object-oriented, in that all of the main elements are treated as independent objects, with properties and relationships to other objects. These elements include atoms, bonds, molecules and crystal planes. Each of them are built up of a number of the earlier ones. One extra piece that GAMGI has is the ability to work with orbitals. Let's walk through an example of a salt crystal (NaCl) to show how you can use GAMGI to do graphical analysis.

When looking at a crystalline structure, you'll want to start by creating a cell in the window. You do this by clicking the Cell→Create menu item. Then you'll get a pop-up window where you can set several properties of the new cell.

Figure 2. When you create a new cell for crystal structures, you can set several different properties on how it will be constructed.

Since salt is a cubic crystal, you'll want to set the system value to c (for cubic), and set the lattice value to F (for face-centered). For each of these, you can get a full set of allowed values by clicking the associated "List" button. Clicking Ok creates the cell.