automekin

Automated discovery of reaction Mechanisms and Kinetics

https://github.com/emartineznunez/automekin

Science Score: 67.0%

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Repository

Automated discovery of reaction Mechanisms and Kinetics

Basic Info

Host: GitHub
Owner: emartineznunez
License: mit
Language: Shell
Default Branch: main
Homepage: https://emartineznunez.github.io/AutoMeKin/
Size: 76.9 MB

Statistics

Stars: 22
Watchers: 3
Forks: 4
Open Issues: 2
Releases: 1

Created about 4 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog License Citation Authors

Automated Mechanisms and Kinetics (AutoMeKin)

This is the official repository of the automated reaction discovery program AutoMeKin.

AutoMeKin (formerly tsscds) has been designed to discover reaction mechanisms in an automated fashion. Transition states are located using MD simulations and Graph Theory algorithms. Monte Carlo simulations afford kinetic results. The only input is a starting structure in XYZ format. The method is described in these two publications: 1 2.

Our custom version of MOPAC is built-in, and the following quantum engines are interfaced with AutoMeKin: Entos Qcore and Gaussian (G09/G16).

Installation and documentation

Verify if your version is up to date here
The installation instructions and much more are detailed here

Simple example in Colab

You can have a look at this Notebook to install it, test a simple example and more...

This second Notebook can be used to try some further tests.

Web site for submitting simple examples

You can also test our web site, where you can submit a simple example.

Owner

Name: Emilio Martínez Núñez
Login: emartineznunez
Kind: user
Location: Spain
Company: Universidade de Santiago de Compostela

Website: http://webspersoais.usc.es/persoais/emilio.nunez/
Repositories: 1
Profile: https://github.com/emartineznunez

Developer of AutoMeKin, (formerly known as tsscds) a computer program designed to discover reaction mechanisms and solve the kinetics in an automated manner

Citation (CITATION.cff)

cff-version: 1.2.0
authors:
- family-names: "Martinez-Nunez"
  given-names: "Emilio"
- family-names: "Barnes"
  given-names: "George L."
- family-names: "Bo"
  given-names: "Carles"
- family-names: "Fernández-Ramos"
  given-names: "Antonio"
- family-names: "Ferro-Costas"
  given-names: "David"
- family-names: "Garay-Ruiz"
  given-names: "Diego"
- family-names: "Glowacki"
  given-names: "David R."
- family-names: "Kopec"
  given-names: "Sabine"
- family-names: "Pelaez-Ruiz"
  given-names: "Daniel"
- family-names: "Rodriguez"
  given-names: "Aurelio"
- family-names: "Rodriguez-Fernandez"
  given-names: "Roberto"
- family-names: "Shannon"
  given-names: "Robin J."
- family-names: "Stewart"
  given-names: "Jameas J.P."
- family-names: "Tahoces"
  given-names: "Pablo G."
- family-names: "Vazquez"
  given-names: "Saulo A."
title: "AutoMeKin"
version: 2021rev1137
url: "https://github.com/emartineznunez/AutoMeKin"
date-released: 2024-02-17
doi: 10.5281/zenodo.10674958

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