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https://github.com/andeplane/atomify-examples-template
An example on how to customize Atomify examples
https://github.com/andeplane/atomify-examples-template
Last synced: 16 days ago
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An example on how to customize Atomify examples
- Host: GitHub
- URL: https://github.com/andeplane/atomify-examples-template
- Owner: andeplane
- Created: 2022-10-19T08:03:49.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-09-15T11:39:49.000Z (4 months ago)
- Last Synced: 2024-09-15T13:21:25.236Z (4 months ago)
- Language: Jupyter Notebook
- Size: 3.21 MB
- Stars: 5
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 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](https://github.com/andeplane/atomify-examples-template/blob/main/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