Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/smutao/PyVibMS

A PyMOL plugin for visualizing vibrations in molecules and solids
https://github.com/smutao/PyVibMS

computational-chemistry computational-physics pymol pymol-plugin quantum-chemistry theoretical-chemistry vibrational-spectroscopy

Last synced: 3 months ago
JSON representation

A PyMOL plugin for visualizing vibrations in molecules and solids

Awesome Lists containing this project

README 

        

![](https://raw.github.com/smutao/PyVibMS/master/for-readme/logo.png)



PyVibMS

=========================

A PyMOL plugin for visualizing vibrations in molecules and solids



Updates

-----

Oct 22, 2021 - [Bug fix](https://github.com/smutao/PyVibMS/commit/896fdf0123e50fc180b4de98caa49dfd4a515ece) 



May 8, 2021 - Add example for [BDF](http://182.92.69.169:7226)



May 5, 2021 - Add examples for [UniMoVib](https://github.com/zorkzou/UniMoVib/) which can generate XYZ and mode files for PyVibMS



May 3, 2021 - Add support for ORCA 4 and Q-Chem 4/5



May 2, 2021 - Add support for Prof. Grimme's xtb program  



User Guide

------



介绍PyVibMS使用的中文文章 请前往 http://bbs.keinsci.com/thread-22835-1-1.html



Our paper on PyVibMS is now published. 🎉 



PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids,

**Journal of Molecular Modeling**, 2020, 26, 290. (full text also available at https://sites.smu.edu/dedman/catco/publications/pdf/434.pdf)



This paper serves as a detailed manual of PyVibMS and a few typographical errors need to be corrected:

1) Page 2






2) Page 3






3) Page 5






Installation

=========================

1) Please install PyMOL 2.x and download the zip file of this repository



2) Open PyMOL 2.x 



3) Click "Plugin" -> "plugin manager" -> "Install New Plugin" -> "Choose", then choose the "src/\_\_init\_\_.py" file



4) The "PyVibMS" will be installed to PyMOL and show up in the "Plugin" drop-in menu



PyVibMS runs on various operating systems.



Windows






Linux






Mac OS






Supported quantum chemistry programs 

=========



Natively supported

----



* Gaussian 09/16

* ORCA 4

* xtb 

* Q-Chem

* CRYSTAL17

* VASP 



Generically supported

----



The following packages are supported with the help of [UniMoVib](https://github.com/zorkzou/UniMoVib/).



* [Adf](http://www.scm.com/)

* [BDF](http://182.92.69.169:7226)

* [CFour](http://www.cfour.de/)

* [Columbus](http://www.univie.ac.at/columbus/)

* [CP2k](http://www.cp2k.org/)

* [Dalton](http://daltonprogram.org/)

* [deMon2k](http://www.demon-software.com/public_html/)

* [Dmol3](http://accelrys.com/)

* [Firefly](http://classic.chem.msu.su/gran/gamess/)

* [Gamess](http://www.msg.chem.iastate.edu/gamess/)

* [Gamess-UK](http://www.cfs.dl.ac.uk/)

* [Molcas](http://www.molcas.org/) and [OpenMolcas](https://gitlab.com/Molcas/OpenMolcas)

* [Molpro](http://www.molpro.net/)

* [Mopac](http://openmopac.net/)

* [NWChem](http://www.nwchem-sw.org/index.php/Main_Page)

* [Pqs](http://www.pqs-chem.com/)

* [Psi4](http://www.psicode.org/)

* [Turbomole](http://www.cosmologic.de/)

* [Quantum ESPRESSO](https://www.quantum-espresso.org/)

* [DFTB+](https://dftbplus.org/)

* and more



Other analysis tools

------

* [LModeA](https://onlinelibrary.wiley.com/doi/full/10.1002/wcms.1480)

* [Phonopy](https://phonopy.github.io/phonopy/)



Tips

========

* When using the open-source version of PyMOL, one may find it difficult to export the vibration animation directly as a GIF or QuickTime movie due to the missing encoder, a work-around is to export the animation as "PNG images" (by clicking "File"->"Export Movie As"->"PNG Images..."). Then one can use a third-party tool like [ezgif](https://ezgif.com/apng-to-gif) to combine these PNG images as animated GIF image.  

Here is an example