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topasavogadrozmatrixconverter

Script to convert Gaussian ZMatrix to Topas format ZMatrix. This way u can create rigid bodies in Avogadro, save it as Gaussian ZMatrix and then load it into Topas thanks to this script

https://github.com/marcovando/topasavogadrozmatrixconverter

Science Score: 67.0%

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    Links to: zenodo.org
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Repository

Script to convert Gaussian ZMatrix to Topas format ZMatrix. This way u can create rigid bodies in Avogadro, save it as Gaussian ZMatrix and then load it into Topas thanks to this script

Basic Info
  • Host: GitHub
  • Owner: MarcoVando
  • License: bsd-3-clause
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 3.96 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created almost 2 years ago · Last pushed 11 months ago
Metadata Files
Readme License Citation

README.md

TopasAvogadroZmatrixConverter

Script to convert Gaussian ZMatrix to Topas format ZMatrix. This way u can create a rigid body in Avogadro, save it as Gaussian ZMatrix and then load it into Topas.
Don't worry too much about drawing your molecule very precisely. You can always use the Geometry Optimization tool! U can exclude atoms from the optimization using "Ignore selection" and "Fix selected atoms". Check the following GIF.
When saving in .gzmat format, Avogadro saves the molecules you draw placing the atoms in the order you drew them! When you want some atoms to be defined in specific positions keep in mind this detail! (Like dummy atoms in the middle of benzene rings or two dummy atoms in a line to be placed on an axis should be drawn first!)

Instructions

To use the script simply run the .py file.
You just need to change the path to the gzmat file and the start_matrix variable from the .py file.
- start_matrix: the line number in which first atom is written - path: the file path

.pynb file (Jupyter Notebook) provides a step-by-step conversion tutorial.

Citation

If you find this useful, please cite the repository using the dedicated button on the right.
DOI

Owner

  • Name: Marco Vandone
  • Login: MarcoVando
  • Kind: user
  • Location: Milan
  • Company: University of Milan

Italian PhD student in Chemistry.🧑‍🔬 Learning crystallography and XAS.💎 Interested in python application for data analysis.🐍📈 3D printing enthusiast.

Citation (citation.cff) 

cff-version: 1.0.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Vandone"
  given-names: "Marco"
  orcid: "https://orcid.org/0000-0003-2835-4663"
title: "TopasAvogadroZmatrixConverter"
version: 1.0.0
doi: 10.5281/zenodo.14996718
date-released: 2024-30-08
url: "https://github.com/MarcoVando/TopasAvogadroZmatrixConverter"

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