Tess

A 3D cell-based Voronoi library based on voro++

This library includes Python bindings, using Cython.

Documentation available at Read the Docs.

Description

Tess is a library to calculate Voronoi (and Laguerre) tessellations in 3D and analyze their structure. The tessellation is calculated as a list of :class:`~tess.Cell` objects, each of which can give information on its volume, centroid, number of faces, surface area, etc. The library is made with packings of spherical particles in mind, possibly with variable sizes.

voro++

The Tess library is a set of Python bindings to the Voro++ library. Voro++ provides all the algorithms, and Tess provides an easy to use interface to the voro++ library for Python, using Cython to do so.

Original work on voro++ by Chris H. Rycroft (UC Berkeley / Lawrence Berkeley Laboratory).

Quick Start

Installation

To install, use pip (or easy_install):

pip install --user tess

Or to install from Github:

pip install --user git+git://github.com/wackywendell/tess@master

Usage

The first step is to create a :class:`~tess.Container`:

>>> from tess import Container
>>> cntr = Container([[1,1,1], [2,2,2]], limits=(3,3,3), periodic=False)

A container is a list of :class:`~tess.Cell` objects, representing Voronoi cells:

.. testsetup:: *

    from tess import Container
    cntr = Container([[1,1,1], [2,2,2]], limits=(3,3,3), periodic=False)

>>> [round(v.volume(), 3) for v in cntr]
[13.5, 13.5]

:class:`~tess.Cell` objects have many methods. Here are a few:

>>> [v.pos for v in cntr]
[(1.0, 1.0, 1.0), (2.0, 2.0, 2.0)]

>>> [v.centroid() for v in cntr]
[(1.09375, 1.09375, 1.09375), (1.90625, 1.90625, 1.90625)]

>>> [v.neighbors() for v in cntr]
[[-5, -2, -3, -1, -4, 1, -6], [0, -3, -6, -4, -5, -2, -1]]

>>> [v.face_areas() for v in cntr]
[[7.875, 1.125, 7.875, 7.875, 1.125, 11.691342951089922, 1.125],
 [11.691342951089922, 1.125, 7.875, 7.875, 1.125, 7.875, 1.125]]

>>> [v.normals() for v in cntr]
[[(0.0, 0.0, -1.0),
  (1.0, 0.0, 0.0),
  (0.0, -1.0, 0.0),
  (-1.0, 0.0, 0.0),
  (0.0, 1.0, 0.0),
  (0.5773502691896257, 0.5773502691896257, 0.5773502691896257),
  (0.0, 0.0, 1.0)],
 [(-0.5773502691896257, -0.5773502691896257, -0.5773502691896257),
  (-0.0, -1.0, -0.0),
  (0.0, 0.0, 1.0),
  (0.0, 1.0, -0.0),
  (0.0, 0.0, -1.0),
  (1.0, 0.0, -0.0),
  (-1.0, -0.0, -0.0)]]

See the Reference for more methods, or just use a Python interpreter or IPython notebook to find them on your own!

Voro++ Copyright And Acknowledgments

Copyright Notice

Voro++ Copyright (c) 2008, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.

If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Technology Transfer Department at TTD@lbl.gov.

NOTICE. This software was developed under partial funding from the U.S. Department of Energy. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly. Beginning five (5) years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.

Acknowledgments

This work (voro++) was supported by the Director, Office of Science, Computational and Technology Research, U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

FireniceCao / tess