1. Conversion of Anisotropic Displacement Parameters to Different Parametrizations
This toolbox can convert anisotropic displacement parameters calculated with Phonopy referring to a Cartesian coordinate system (Ucart) to Ucif, B, U*, Beta, Ui and Ueq. Moreover, Ucart, Ucif, B, U* and Beta from literature can be converted to Ucif, B, U* and Beta.
This is all done according to: R. W. Grosse-Kunstleve and P. D. Adams, J. Appl. Crystallogr., 2002, 35, 477–480. This article also includes the nomenclature of the different parametrizations.
2. Calculation of the Root-Mean-Square of the Cartesian Displacements
Moreover, this toolbox can also calculate the root-mean-square of the Cartesian displacements as defined in
- J. George, V. L. Deringer, R. Dronskowski, Inorg. Chem., 2015, 54, 956–962.
- J. van de Streek, M. A. Neumann, Acta Cryst. B, 2010, 66, 544–558.
- Download the Molecular-Toolbox.mltbx-file
- Open your MATLAB. Please use version 2015a or newer.
- Browse with MATLAB's explorer to the folder with the Molecular-Toolbox files.
- Double click on the Molecular-Toolbox.mltbx-file.
- Click Install.
- Check whether the Molecular-Toolbox is correctly installed: this is done by going to the Home tab, then switching to the Environment section, clicking on the Add-Ons icon and finally selecting Manage Add-Ons.
- Run the scripts within the Matlab GUI or in the shell by typing:
matlab -nodisplay < NameOfTheScript.m
- Download a script from the Example folder (choose according to task)
- Adapt the filenames and temperatures in the scripts (names for POSCAR files and thermal_displacement_matrices.yaml)
- Run the scripts within the Matlab GUI or in the shell by typing:
matlab -nodisplay < NameOfTheScript.m - Have a look at Doc/Documentation.pdf for more details.
If you use the program to convert ADPs, please cite:
- R. W. Grosse-Kunstleve and P. D. Adams, J. Appl. Crystallogr., 2002, 35, 477–480.
- J. George, A. Wang, V. L. Deringer, R. Wang, R. Dronskowski, U. Englert, CrystEngComm, 2015, 17, 7414–7422.
And please, don’t forget to cite Phonopy
- A. Togo, I. Tanaka, Scr. Mater. 2015, 108, 1–5.
and the ADP calculation with Phonopy, if you have performed it:
- V. L. Deringer, R. P. Stoffel, A. Togo, B. Eck, M. Meven, R. Dronskowski, CrystEngComm, 2014, 16, 10907–10915.
- J. George, A. Wang, V. L. Deringer, R. Wang, R. Dronskowski, U. Englert, CrystEngComm, 2015, 17, 7414–7422.
If you use the program to calculate the root-mean-square of the Cartesian displacements, please cite:
- J. George, V. L. Deringer, R. Dronskowski, Inorg. Chem., 2015, 54, 956–962.
If you use the program to calculate the root-mean-square of the Cartesian displacements as defined by van de Streek and Neumann, please cite:
- J. van de Streek, M. A. Neumann, Acta Cryst. B, 2010, 66, 544–558.
- J. George, V. L. Deringer, R. Dronskowski, Inorg. Chem., 2015, 54, 956–962.
If you use the program, please always cite: Janine George, & Richard Dronskowski. (2017, November 30). Molecular Toolbox (Version 1.0.2). Zenodo. http://doi.org/10.5281/zenodo.1069052 (BibTeX)
- 1.0.0 (February 2016): First Molecular-Toolbox version is released!
- 1.0.1 (September 2016): Compatible with Phonopy 1.11.2.
- 1.0.2 (April 2017):
- RMS of van de Streek and Neumann is included
- Further safety checks are included in the RMS calculation
- ADP transformation starting from Ucart is included
- Make choice of temperatures in ADP conversion more freely
- J. George (RWTH Aachen University, now: Université catholique de Louvain)
- PI during the development of the code: R. Dronskowski, RWTH Aachen University
Have a look at our project website for the calculation of thermal ellipsoids: www.ellipsoids.de!