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License DOI

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

Have a look at our project website for the calculation of thermal ellipsoids: www.ellipsoids.de!