Open Force Field Initiative website source

This website is hosted by GitHub Pages at http://openforcefield.org

Making changes

Changes should be contributed as pull requests.

Only the source files in openforcefield/ should be changed.

You will primarily want to focus on changing the following Markdown files in openforcefield/content/:

• _index.md: main landing page content (some detail is in themes/kube/layouts/index.html)
• news/: Add new news posts here as separate Markdown files, using a header like

---
date: "2017-04-10T16:42:50+01:00"
draft: false
weight: 180
description: "Smoothly and reliably collapse elements for extra convenience"
title: "Collapse"
bref: "A demo to collapsable elements"
---

with the fields replaced with their equivalents.

• forcefields/_index.md: information about available force field releases
• datasets/_index.md: information about available datasets
• science/_index.md: overview of planned science, timelines, science updates, etc.
• data/publications/publications.yaml: publications and white papers
  • content/publications/img/: thumbnail images for publications and white papers
• consortium/_index.md: information about the Open Force Field Consortium and other federal funding sources
• faq/_index.md: frequently asked questions

See the Kube for Hugo GitHub repo for more examples of Markdown content.

Adding Science Updates

1. Create a new file in content/science/updates/ using the format YYYY-MM-DD-lastname.md (e.g. 2018-10-11-chodera.md)
2. Populate the file in Markdown with the following header style:

---
date: "2018-10-11T00:00:00+00:00"
title: "Introducing Open Force Field Science Updates"
tags: ["general"]
categories: ["science"]
draft: false
description: "Open Force Field Science Updates will help you keep track of research and engineering activities from the Open Force Field Initiative"
weight: 10
author: "John D. Chodera"
---

3. If you have images to post, create a subdirectory in content/science/updates/ using the format YYYY-MM-DD-lastname/ (e.g. 2018-10-11-chodera/) and put your images there. You can reference them with

![GAFF densities](gaff-densities.jpg "GAFF densities")

where the file gaff-densities.jpg is located in content/science/updates/YYYY-MM-DD-lastname/gaff-densities.jpg

Adding new members

1. Add an image to content/members/img/ (e.g. firstname-lastname.jpg).
2. Add a YAML file firstname-lastname.yaml to openforcefield/data/members/ in the following format:

name: John D. Chodera
role: Primary Investigator
lab: Chodera lab
title: Assistant Member
institution: Sloan Kettering Institute
img: john-chodera.jpg
webpage: "http://choderalab.org"
description: Automated Bayesian force field fitting and prediction of systematic error
google_scholar: http://goo.gl/qO0JW
ORCID: 0000-0003-0542-119X

where role can be Researcher or Primary Investigator.

Adding new publications

1. Add a thumbnail image to content/publications/img
2. Add an entry to the YAML file data/publications/publications.yaml in the following format:

- title: "Toward learned chemical perception of force field typing rules"
  authors: "Camila Zanette, Caitlin C. Bannan, Christopher I. Bayly, Josh Fass, Michael K. Gilson, Michael R. Shirts, John Chodera, and David L. Mobley"
  summary: This paper introduces the SMIRNOFF format in the context of traditional force fields, explains the development and validation of our new small molecule force field smirnoff99Frosst, and highlights some directions the initiative is headed.
  img: smarty.jpg
  preprint:
    server: chemRxiv
    url: https://chemrxiv.org/articles/Toward_Learned_Chemical_Perception_of_Force_Field_Typing_Rules/6230627
    license: "CC-BY 4.0"
    date: 2018-08-06
  github:
    url: https://github.com/openforcefield/smarty
- title: "Uncertainty quantification confirms unreliable extrapolation toward high pressures for united-atom Mie $\\lambda$-6 force field"
  authors: "Richard A. Messerly, Michael R. Shirts, and Andrei F. Kazakov"
  summary: We demonstrate how Bayesian approaches can be used to estimate the reliability of predictions made with molecular mechanics force fields.
  img: mie-potential.png
  published:
    doi: https://doi.org/10.1063/1.5039504
    journal: The Journal of Chemical Physics
    volume: 149
    pages: 114109
    year: 2018
    license: "Public Domain"
    date: 2018-09-21

The preprint, published, and github fields are optional, though at least one should be specified.

Preview the website locally

0. Download and install Hugo.
1. In the openforcefield/ directory, run hugo server -D
2. Copy the Web address from this line (in this example, it is localhost:1313):

Web Server is available at //localhost:1313/ (bind address 127.0.0.1)

3. Paste the Web address into your browser

Building and deploying

0. Download and install Hugo.
1. In the openforcefield/ directory, run hugo to rebuild the static site
2. Make sure any new files in docs/ are added to the commit:

cp CNAME docs/
git add docs/*

3. Commit the changes and push the repository to master