What Happens When Atoms Go Missing in Crystals?

Crystal structures are often taught as perfect, repetitive lattices. But in actual materials, atoms are not always perfectly placed. Defects—such as missing atoms or substitutions—can significantly change the properties of a material, from conductivity to hardness. For molecular modelers trying to simulate realistic materials, accounting for such imperfections is essential — yet not always straightforward.

In this post, we explore how to introduce and visualize atomic defects using the Crystal Creator Extension in SAMSON. Specifically, we’ll look at the case of missing atoms (occupancy less than 1) in diamond structures. This can help researchers simulate real crystal behavior more accurately, improving the fidelity of mechanical, thermal, or electronic property predictions.

Step-by-step: Introducing defects into diamond

To simulate defects in a diamond crystal, you’ll want to modify the .cif (Crystallographic Information File) file in a specific way. Here’s how:

1. First, load a clean diamond crystal (you can find one at https://rruff.info/) in SAMSON and create the bonds using the Crystal Creator Extension.
2. Use the Brenner interaction model to minimize the energy of the pristine structure, giving you a relaxed reference state.
3. Now make a copy of the diamond’s .cif file. Open this copy in a text editor. At the part of the file that lists atomic positions, change it as shown below:

That final number—0.95—means there’s a 95% chance for that site to actually contain a carbon atom. When the file is loaded in SAMSON, this probability will be taken into account, reflecting the stochastic nature of such defects.

Then:

• Load the modified defect-containing crystal in SAMSON.
• Create bonds again and observe the structural differences compared to the original.

This allows you to probe how defects affect geometries, stress distributions, or even reactivity in materials. You can build multiple variations with different defect rates, run energy minimizations, and observe the resulting differences in structure. Defects can lead to lattice distortions, dangling bonds, or even the emergence of new material properties that wouldn’t exist in the perfect lattice.

Visualizing changes

The Crystal Creator Extension even includes a tool to check atom presence ratios based on the CIF file definitions. This can be a valuable way to confirm that the statistical nature of occupancy values is respected in your model. Particularly helpful if you’re validating structures with partial substitution or randomly distributed imperfections.

Whether you’re studying semiconductors, minerals, or designing new materials, simulating defects is often necessary to understand and replicate real situations. With the tools provided in SAMSON, this becomes simpler and more controllable—even if you’re just getting started with crystal modeling.

Want to dive deeper into creating and manipulating crystals in SAMSON? Read the full documentation here.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.