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Open Source Science

https://github.com/cmelab/cg-tutorial

https://github.com/cmelab/cg-tutorial

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 4 DOI reference(s) in README
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    Scientific vocabulary similarity
    Low similarity (5.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: cmelab
  • Language: Python
  • Default Branch: master
  • Size: 575 KB
Statistics
  • Stars: 3
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created almost 7 years ago · Last pushed over 6 years ago

https://github.com/cmelab/CG-Tutorial/blob/master/ 

# Coarse-graining tutorial
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cmelab/CG-Tutorial/master)

This tutorial demonstrates code which ties together [mbuild](https://mosdef.org/mbuild/index.html) and [openbabel](http://openbabel.org/docs/current/)'s [SMILES/SMARTS](https://www.daylight.com/dayhtml/doc/theory/index.html) matching to help create coarse-grain chemical structures. 
The tutorial also demonstrates how to initialize these coarse-grain structures in a [HOOMD](https://hoomd-blue.readthedocs.io/en/stable/) simulation using [foyer](https://mosdef.org/foyer/) and analyze the output of the simulation using [freud](https://freud.readthedocs.io/en/stable/).

To read more about how using simple models and community-driven, open-source tools can help lower cognitive load, increase simulation transferability, reproducibility, usability, and extensibility ([TRUE](https://doi.org/10.6084/m9.figshare.8966312)), and make the world a better place, please read our [perspective paper](https://doi.org/10.1016/j.commatsci.2019.109129).

This tutorial depends heavily on tools from [MoSDeF](https://mosdef.org/) and the [Glotzer group](https://github.com/glotzerlab).

Owner

  • Name: Computational Materials Engineering Laboratory
  • Login: cmelab
  • Kind: organization
  • Location: Boise, ID

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