{"id":17204215,"url":"https://github.com/jageo/moleculartoolbox","last_synced_at":"2025-08-16T23:42:23.523Z","repository":{"id":103427117,"uuid":"112479183","full_name":"JaGeo/MolecularToolbox","owner":"JaGeo","description":"Converts anisotropic displacement parameters to different parametrizations and can also handle Phonopy output.","archived":false,"fork":false,"pushed_at":"2019-01-14T10:25:41.000Z","size":52297,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-25T09:49:47.572Z","etag":null,"topics":["adps","phonons","phonopy","thermal-motion","vasp"],"latest_commit_sha":null,"homepage":"http://www.ellipsoids.de","language":"MATLAB","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/JaGeo.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-11-29T13:32:53.000Z","updated_at":"2021-03-15T17:36:27.000Z","dependencies_parsed_at":null,"dependency_job_id":"ea4a4c14-61cd-4a35-b865-cb1d39015313","html_url":"https://github.com/JaGeo/MolecularToolbox","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/JaGeo/MolecularToolbox","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaGeo%2FMolecularToolbox","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaGeo%2FMolecularToolbox/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaGeo%2FMolecularToolbox/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaGeo%2FMolecularToolbox/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JaGeo","download_url":"https://codeload.github.com/JaGeo/MolecularToolbox/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaGeo%2FMolecularToolbox/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":260546110,"owners_count":23025875,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["adps","phonons","phonopy","thermal-motion","vasp"],"created_at":"2024-10-15T02:21:02.310Z","updated_at":"2025-08-16T23:42:23.493Z","avatar_url":"https://github.com/JaGeo.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://github.com/JaGeo/AtomicContributions/blob/master/LICENSE) [![DOI](https://zenodo.org/badge/112479183.svg)](https://zenodo.org/badge/latestdoi/112479183)\n\n# MolecularToolbox\n\nFeatures of the Toolbox\n----------\n**1. Conversion of Anisotropic Displacement Parameters to Different Parametrizations**\n\n\u003cimg src=\"https://github.com/JaGeo/MolecularToolbox/blob/master/Doc/Piktogramm-01.png\" width=\"40%\" height=\"40%\"\u003e\n\nThis 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. \n\nThis 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.\n\n\n**2. Calculation of the Root-Mean-Square of the Cartesian Displacements**\n\n\u003cimg src=\"https://github.com/JaGeo/MolecularToolbox/blob/master/Doc/Piktogramm-02.png\" width=\"40%\" height=\"40%\"\u003e\n\nMoreover, this toolbox can also calculate the root-mean-square of the Cartesian displacements as defined in\n- J. George, V. L. Deringer, R. Dronskowski, *Inorg. Chem.*, **2015**, *54*, 956–962.\n- J. van de Streek, M. A. Neumann,  *Acta Cryst. B*, **2010**, *66*,  544–558.\n\n\n\nHow to install the MATLAB Toolbox\n-------------\n- Download the **Molecular-Toolbox.mltbx**-file\n- Open your MATLAB. Please use version 2015a or newer.\n- Browse with MATLAB's explorer to the folder with the Molecular-Toolbox files.\n- Double click on the **Molecular-Toolbox.mltbx**-file.\n- Click **Install**.\n- 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**.\n- Run the scripts within the Matlab GUI or in the shell by typing:\n  `matlab -nodisplay \u003c NameOfTheScript.m`\n\nHow to use the scripts\n----------------------\n- Download a script from the **Example** folder (choose according to task)\n- Adapt the filenames and temperatures in the scripts (names for **POSCAR** files and **thermal_displacement_matrices.yaml**)\n- Run the scripts within the Matlab GUI or in the shell by typing:\n  `matlab -nodisplay \u003c NameOfTheScript.m`\n- Have a look at [Doc/Documentation.pdf](https://github.com/JaGeo/MolecularToolbox/blob/master/Doc/Documentation.pdf) for more details.\n\nWhat to cite\n----------\nIf you use the program to convert ADPs, please cite:\n- R. W. Grosse-Kunstleve and P. D. Adams, *J. Appl. Crystallogr.*, **2002**, *35*, 477–480.\n- J. George, A. Wang, V. L. Deringer, R. Wang, R. Dronskowski, U. Englert, *CrystEngComm*, **2015**, *17*, 7414–7422.\n\nAnd please, don’t forget to cite Phonopy\n\n- A. Togo, I. Tanaka, *Scr. Mater.* **2015**, *108*, 1–5.\n\nand the ADP calculation with Phonopy, if you have performed it:\n\n- V. L. Deringer, R. P. Stoffel, A. Togo, B. Eck, M. Meven, R. Dronskowski, *CrystEngComm*, **2014**, *16*, 10907–10915.\n- J. George, A. Wang, V. L. Deringer, R. Wang, R. Dronskowski, U. Englert, *CrystEngComm*, **2015**, *17*, 7414–7422.\n\nIf you use the program to calculate the root-mean-square of the Cartesian displacements, please cite:\n\n- J. George, V. L. Deringer, R. Dronskowski, *Inorg. Chem.*, **2015**, *54*, 956–962.\n\nIf you use the program to calculate the root-mean-square of the Cartesian displacements as defined by van de Streek and Neumann, please cite:\n\n- J. van de Streek, M. A. Neumann, *Acta Cryst. B*, **2010**, *66*, 544–558.\n- J. George, V. L. Deringer, R. Dronskowski, *Inorg. Chem.*, **2015**, *54*, 956–962.\n\nIf you use the program, please always cite: Janine George, \u0026 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))\n\n\nVersions \n-------\n- 1.0.0 (February 2016): First Molecular-Toolbox version is released! \n- 1.0.1 (September 2016): Compatible with Phonopy 1.11.2.\n- 1.0.2 (April 2017): \n  * RMS of van de Streek and Neumann is included \n  * Further safety checks are included in the RMS calculation \n  * ADP transformation starting from Ucart is included    \n\n\nTodo\n----\n- Make choice of temperatures in ADP conversion more freely\n\n\nInformation about the Author\n--------\n\n- J. George (RWTH Aachen University, now: Université catholique de Louvain)\n- PI during the development of the code: [R. Dronskowski, RWTH Aachen University](http://www.ssc.rwth-aachen.de/)\n\nHave a look at our project website for the calculation of thermal ellipsoids: [www.ellipsoids.de](http://www.ellipsoids.de)!\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjageo%2Fmoleculartoolbox","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjageo%2Fmoleculartoolbox","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjageo%2Fmoleculartoolbox/lists"}