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

Create a new file in content/science/updates/ using the format YYYY-MM-DD-lastname.md (e.g. 2018-10-11-chodera.md)
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"
---

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

Add an image to content/members/img/ (e.g. firstname-lastname.jpg).
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: Associate 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
twitter: jchodera
github: jchodera

where role can be Researcher, Advisor, Software Scientist, or Primary Investigator.

Adding new publications

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

- title: "Escaping atom types using direct chemical perception"
  authors: "David Mobley, Caitlin C. Bannan, Andrea Rizzi, Christopher I. Bayly, John D. Chodera, Victoria T Lim, Nathan M. Lim, Kyle A. Beauchamp, Michael R. Shirts, Michael K. Gilson, and Peter K. Eastman"
  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: smirnoff-v0.1.png
  date: 2018-10-11
  preprint:
    server: bioRxiv
    url: https://doi.org/10.1101/286542
    license: "CC BY 4.0"
    date: 2018-07-13
  published:
    doi: 10.1021/acs.jctc.8b00640
    journal: Journal of Chemical Theory and Computation
    date: 2018-10-11
    volume: 14
    pages: 6076
    year: 2018
    pmcid: PMC6245550
- 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: Here, we introduce a proof of principle for automatically sampling chemical perception compared to traditional atom typed force fields and our SMIRNOFF format.
  img: smarty.jpg
  date: 2018-12-04
  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
  published:
    doi: 10.1021/acs.jctc.8b00821
    journal: Journal of Chemical Theory and Computation
    date: 2018-12-04
    volume: 15
    pages: 402
    year: 2019
    nihmsid: 1012523
  github: openforcefield/smarty

The preprint, published, and github fields are optional, though at least one should be specified.
For preprints, server can either be bioRxiv or chemRxiv.
For published papers, the pmcid (PubMed Central PMCID) should be specified. If the article doesn't yet have a PMCID, be sure to submit it to PubMed Central and report the nihmsid instead. Failure to do so will jeopardize our NIH grants.
Each preprint block should list a url, while published blocks should report a doi (not a URL).
The license can be one of CC BY 4.0 or Public Domain. Please ensure all manuscripts are available via one of these licenses, as other licenses violate the terms of the Open Force Field Consortium.

Preview the website locally

Download and install Hugo.
In the openforcefield/ directory, run hugo server -D
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)

Paste the Web address into your browser

Building and deploying

Make sure you have downloaded and installed Hugo.
Create a new branch with git checkout -b <mybranch>, where <mybranch> is the name of your new branch.
Run ./rebuild.sh to rebuild the docs/ directory and add any missing files to git
Commit the changes (git commit .) and push the repository to your branch (git push origin <mybranch>)
Open a PR and request review

mohebifar / openforcefield.org