https://github.com/klarh/flowws-examples

Example workflows using the flowws library
https://github.com/klarh/flowws-examples

examples molecular-dynamics molecular-simulation notebook python simulation visualization workflows

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Example workflows using the flowws library

• Host: GitHub
• URL: https://github.com/klarh/flowws-examples
• Owner: klarh
• License: mit
• Created: 2020-02-13T13:46:13.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2020-06-22T14:45:28.000Z (over 4 years ago)
• Last Synced: 2024-11-06T17:57:50.591Z (2 months ago)
• Topics: examples, molecular-dynamics, molecular-simulation, notebook, python, simulation, visualization, workflows
• Language: Jupyter Notebook
• Size: 13.7 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/klarh/flowws-examples/master)

[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/klarh/flowws-examples/blob/master/)

# Introduction

This repository demonstrates several workflows for simulation,

visualization, and analysis using

[flowws](https://github.com/klarh/flowws).

To launch an interactive notebook server using mybinder.org, use the

link above; otherwise, install the prerequisites below to run

locally. Google colab is also supported somewhat, but see the caveats

in the section below.

# Prerequisites

Note that not all of these are required for all notebooks. Everything

except for hoomd is available on the PyPI and is available using `pip

install -r requirements.txt`:

- flowws

- flowws-analysis

- flowws-freud

- freud-analysis

- gtar

- [hoomd-blue](https://hoomd-blue.readthedocs.io/en/stable/installation.html)

- hoomd_flowws

- matplotlib

- plato-draw

- pyriodic-aflow

- pyside2

- vispy (if using a notebook, make sure to follow the [installation instructions](http://vispy.org/installation.html))

# Running on Google Colab

Example notebooks can also run in [Google

Colab](https://colab.research.google.com), although it can be annoying

to install prerequisites like HOOMD on a colab notebook. Note that

interactive plato backends are unlikely to work in colab. You can use

the following code in each notebook to install prerequisites:

```

!pip install -U -q PyDrive

# download compiled hoomd release

from pydrive.auth import GoogleAuth

from pydrive.drive import GoogleDrive

from google.colab import auth

from oauth2client.client import GoogleCredentials

auth.authenticate_user()

gauth = GoogleAuth()

gauth.credentials = GoogleCredentials.get_application_default()

drive = GoogleDrive(gauth)

fileId = '1sbyj-ruKLtEK-9qVlsXSJU0hxCHf_blD'

downloaded = drive.CreateFile({'id': fileId})

downloaded.GetContentFile('hoomd.tar.gz')

# extract hoomd

!mkdir -p "$(python -c 'import site;print(site.USER_SITE)')"

!tar xC "$(python -c 'import site;print(site.USER_SITE)')" -f hoomd.tar.gz

# install other dependencies

!apt-get install povray

!pip install flowws-analysis flowws-freud freud-analysis gtar hoomd-flowws matplotlib plato-draw pyriodic-aflow

# hoomd won't be able to be imported the first time this cell is run, so

# restart the process.

try:

    import hoomd

except ImportError:

    exit()

```

**Note:** The hoomd package is compiled with GPU support; select a GPU

runtime ("Runtime -> Change runtime type") to be able to correctly import it.