https://github.com/jageo/moleculartoolbox
Converts anisotropic displacement parameters to different parametrizations and can also handle Phonopy output.
https://github.com/jageo/moleculartoolbox
adps phonons phonopy thermal-motion vasp
Last synced: about 2 months ago
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Converts anisotropic displacement parameters to different parametrizations and can also handle Phonopy output.
- Host: GitHub
- URL: https://github.com/jageo/moleculartoolbox
- Owner: JaGeo
- License: bsd-3-clause
- Created: 2017-11-29T13:32:53.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2019-01-14T10:25:41.000Z (over 6 years ago)
- Last Synced: 2025-03-25T09:49:47.572Z (7 months ago)
- Topics: adps, phonons, phonopy, thermal-motion, vasp
- Language: MATLAB
- Homepage: http://www.ellipsoids.de
- Size: 49.9 MB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://github.com/JaGeo/AtomicContributions/blob/master/LICENSE) [](https://zenodo.org/badge/latestdoi/112479183)
# MolecularToolbox
Features of the Toolbox
----------
**1. Conversion of Anisotropic Displacement Parameters to Different Parametrizations**
This toolbox can convert anisotropic displacement parameters calculated with [Phonopy](https://atztogo.github.io/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](https://github.com/JaGeo/MolecularToolbox/blob/master/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](http://doi.org/10.5281/zenodo.1069052) ([BibTeX](https://zenodo.org/record/1069052/export/hx))
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](http://www.ssc.rwth-aachen.de/)
Have a look at our project website for the calculation of thermal ellipsoids: [www.ellipsoids.de](http://www.ellipsoids.de)!