MolecularToolbox

Features of the Toolbox

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.

How to install the MATLAB Toolbox

• 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

How to use the scripts

• 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.

What to cite

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)

Versions

• 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

Todo

• Make choice of temperatures in ADP conversion more freely

Information about the Author

• 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!