Atomify examples template

➡️ https://andeplane.github.io/atomify?examplesUrl=https://raw.githubusercontent.com/andeplane/atomify-examples-template/main/examples.json

If you want customize the examples in Atomify for e.g. teaching, you can use this GitHub template (Click the green Use this template button in the top of the repository). You can specify simulations and Python notebooks to perform analysis of the simulations.

The configuration is a file (examples.json) that you can provide in the Atomify URL. The examples page in Atomify will then show your examples. The format of this file is

{
  "baseUrl": "https://raw.githubusercontent.com/andeplane/atomify-examples-template/main",
  "title": "Examples",
  "descriptionFile": "diffusion.md",
  "examples": [
    {
      "id": "diffusion",
      "title": "2D diffusion",
      "description": "We measure the diffusion coefficient",
      "analysisDescription": "This markdown formatted text appears in the default analyze notebook.",
      "imageUrl": "2d-msd-diffusion/2d-msd-diffusion.png",
      "inputScript": "2d-msd-diffusion.in",
      "analysisScript": "2d-msd-diffusion.ipynb",
      "keywords": [
        "lennard jones",
        "diffusion"
      ],
      "files": [
        {
            "fileName": "2d-msd-diffusion.in",
            "url": "2d-msd-diffusion/2d-msd-diffusion.in"
        },
        {
          "fileName": "2d-msd-diffusion.ipynb",
          "url": "2d-msd-diffusion/2d-msd-diffusion.ipynb"
        }
      ]
    }
  ]
}

• baseUrl is the prefix of all the file url's. This is typically on the format https://raw.githubusercontent.com/{user}/{repository}/main. When you are creating examples locally, you can put http://localhost:8000 and run python server.py to test.
• title is the title that appears on top of the examples page in Atomify
• descriptionFile is the filename of an (optional) markdown formatted file that appears on top of the examples. Use this to e.g. tell your students what this is about.
• examples is an array of the examples.

The examples are on the format

• id id of a simulation. This will be used as folder name for both LAMMPS the Jupyter notebook.
• title title of the simulation
• description description of the simulation
• analysisDescription (optional) markdown formatted string that appears in the default analysis notebook
• imageUrl url to the image. Full url becomes {baseUrl}/{imageUrl}
• inputScript file name of the input script
• analysisScript file name of a notebook that is the entry point of simulation analysis
• keywords list of keywords that can be used to filter a larger set of simulations
• files list of files needed for simulation and analysis. A file is an object with the two properties fileName and url. Full url becomes {baseUrl}/{url}

Local development

When you are creating a new set of examples, you can point Atomify to a local server. You need to update the baseUrl to be http://localhost:8000 in examples.json. Run the server with

python server.py

and open https://andeplane.github.io/atomify?examplesUrl=http://localhost:8000/examples.json