Introduction

This repository demonstrates several workflows for simulation, visualization, and analysis using 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
• hoomd_flowws
• matplotlib
• plato-draw
• pyriodic-aflow
• pyside2
• vispy (if using a notebook, make sure to follow the installation instructions)

Running on Google Colab

Example notebooks can also run in Google Colab, 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.