Kabsch interpolation for hybrid materials

⚠️ Warning: Always check that the interpolated structures are correct - you can visualise the generated structures using vesta or similar.

If you use this code please consider:

• citing the associated paper)
• Citing the Atomic Simulation Environment
• letting me know so that I can start a list of where it has been used successfully. I'll link to your project from this page.

If you have any questions or comments about this code please contact l.whalley@northumbria.ac.uk or (preferably) raise an issue on the repository issue tracker.

This has only been tested on a small family of materials (hybrid perovskites). If you want to apply this to another system and have problems transferring the code across, please let me know, I may be able to help.

What does this code do? 🖥️

• this code interpolates between two crystal structures
• for isolated atoms it linearly interpolates along the translation vector mapping between the atom start position and atom end position.
• for molecules it linearly interpolates along the translation vector mapping between the molecule start centre-of-mass and molecule end centre-of-mass, and combines this with a linear interpolation along the rotation vector mapping between the molecule start orientation and molecule end orientation. To do so it uses the Kabsch algorithm.

Why was this code developed? ⚛️

• this code was developed to study hybrid organic-inorganic materials where distortions to the inorganic framework can be accurately described using translational interpolation, whereas molecular species require a description of translation and rotation.

What does this code assume? ✍🏽

• any molecular distortion can be ignored; the molecules are treated as rigid bodies.
• molecules can be identified using natural cutoffs. Please see the following link for more information. Alternatively, a neighbours list can be explicitly provided.
• atoms in the start Atoms object and end Atoms object are listed in the same order.

How do I use this code for my own research? 🔬

• you need to have the ASE, scipy and numpy Python libraries installed. If you are new to Python, Anaconda is recommended.
• you can generate interpolated structures using the Jupyter Notebook or the the script.
• if you are using the script, you can call it from the command line e.g. python kabsch_interpolation.py POSCAR_start.vasp POSCAR_end.vasp -m "CNH6". You can access information about the commnand line arguments using python kabsch_interpolation.py --help.

Which simulation packages does this code interface with? ⚙️

• this code makes extensive use of the Atomic Simulation Environment and so can read-in/generate crystal structures for various atomistic simulation codes.
• the script currently assumes that you are reading in VASP POSCAR files, however it can be easily adapted for use with other codes. If you don't know how to do this yourself, please raise an issue on the repository issue tracker and someone else may be able to help.

Something isn't quite right...🙋

• If your molecules are not interpolating as expected you may need to vary the mic_cutoff parameter. Too large or too small values for mic_cutoff can lead to unexpected output!
• ASE can also be used to identify unusual changes in bond lengths. There is example code for this in the final cell of the notebook.
• If you have any questions about this code please contact l.whalley@northumbria.ac.uk or (preferably) raise an issue on the repository issue tracker.