A new tool for validating theoretically derived anisotropic displacement parameters with experiment.
This python program is used to determine the angles and therefore the agreement between the eigenvectors of theoretical and experimental thermal ellipsoids. The ADPs (anisotropic displacement parameters) are an important quantity during the refinement of crystal structures. For this you will need DFT-programs, such as VASP and a phonon-code, such as Phonopy.
Please cite this repository: Damian Mroz, Janine George,& Richard Dronskowski. (2019, April 08). Angle (Version 1.0). If used, please also cite VASP and Phonopy. In addition to this, you should cite MolecularToolbox if used. Please follow the citation guidelines on this repository.
You will need to export the python path of the folder including the "Angle.py" file or copy it to the folder where you run the script. Furthermore, you will need numpy and math.
You have to perform DFT calculations for example with VASP first, followed by phonon evaluation (e.g. Phonopy). Furthermore, you need to transform the thermal displacement matrices (Phonopy output) to the "Ustar" format. You can use the MolecularToolbox to obtain the Ustar values directly from Phonopy.
Then you just need to prepare the input files "inpex.txt" and "inpth.txt" as shown in the Example folder. These files include the matrix components of Ustar which can be derived with the help of the MolecularToolbox. Please make sure that the Ustar parameters are sorted in the correct way: E11 E22 E33 E23 E13 E12.
You will get three output files: Two of them will give you the main axis components of the ADPs. The other one will give you a quantities related to the length of the semi principal axes and angles between the theoretical and experimental main axes.
- D. Mroz (RWTH Aachen University)
- Refactoring and changes to the code by J. George (Université Catholique de Louvain)
- PI during the development of the code: R. Dronskowski, RWTH Aachen University