Tal

AL v1.beta – A New Step in Crystallography (and Faster Than Cooking Stuffed Cabbage!)

When Tolkien wanted to introduce his new language to the world, he wrote The Hobbit and The Lord of the Rings. I had a slightly more modest starting point – the program was written in a week, in between cooking stuffed cabbage (gołąbki) and my regular work. That is how TAL was born.

Where does the name come from? Well, quite perversely: Thallium (TAL) comes right after Mercury in the periodic table (Hg -> Tl)!

Mercury has over 20 years of development behind it, so please look at TAL with a bit of understanding – this is version 1.beta, which means not everything has been tested as thoroughly as it should be. Nevertheless, the program already offers most of Mercury’s basic functions, and in many ways, it can do quite a bit more.

What’s New in TAL? (A Few Jabs at the Competition)

  1. Overlaying molecules from different crystals (Killer feature): In Mercury, this feature is often paid or overly complicated. Since I use it often myself, I wrote it my way – exactly how it should work. It’s dead simple: select any 3 atoms from one structure, click the „Add molecule” button, do the same for any other structure (or the same one, if you prefer), and you’re done!
  2. Modern technology under the hood: TAL was built using .NET 8 (C#) and MonoGame, supported by an absolutely fantastic window manager modeled after Visual Studio 2022 – weifenluo WinForms Docking. This solution literally „buries” Mercury’s older architecture. The interface is extremely flexible and a joy to work with.

The Main Event: The Cavity Module

Although TAL was supposed to be just a pretty wrapper, its beating heart is my proprietary free-space calculation function (Cavity).

Traditional approaches (like spherical voids in older programs) often fail when dealing with irregular, elongated pores or channels. Cavity in TAL calculates free spaces in crystals with incredible precision – it is currently the best available method on the market.

I’ve described the technical details of how this algorithm works in a separate paper: Cavity Detector in CIF. You can also take a look at the CIF project.

Download and Test

The program is fresh, raw, and waiting for your feedback. If you notice anything, encounter a bug, or have an idea for improvement – feel free to drop me a message!