voids.py

v0.01: Implemented.

Computes the size of every channel in a pack of spheres, as defined in
the paper:

"Structure characterization of hard sphere packings in amorphous and
crystalline states"
    Vitaliy Ogarko, Nicolas Rivas, Stefan Luding
    http://arxiv.org/abs/1405.5032

For each particle, all three particle combinations of neighbors is
considered, defining neighboring triangles. For each neighboring
triangle we compute its internal apollonius circle. This circle is
highly related to the free volume of the particle as, when normalized by
the central particle's radius, a value less than one indicates a channel
through which the particle can't go through.

For more information about the analysis, please refer to the paper.

INSTALLATION

    Not needed, as it is a script.
    Python 2.7 is needed.
    python-tk package is needed. In Ubuntu:
	sudo apt-get install python-tk

USAGE

    ./voids.py 'input_file_name' 'output_file_name' --periodic

    'input_file_name':
        Particles' number, positions and radii in the file 'input'.
        First line of input should be the number of particles.
        The rest of the lines should be the data for every
        particle, in the form 'x y z r', with r the radius of the
        particle and x, y and z its coordinates.

        Example:

        6
        0.260179625853 0.583565147482 0.142286768849 0.0320041717773
        0.164713950323 0.7764730607 0.27015467405 0.0320041717773
        0.357592198576 0.75252722197 0.0642448910503 0.0320041717773
        0.250547945298 0.253359791735 0.254628654942 0.0320041717773
        0.712575326809 0.343368869233 0.948802280038 0.0320041717773
        0.518625358274 0.645391370379 0.721315845511 0.0320041717773

        A sample input file 'input' is included for reference and for
        testing purposes.

    'output_file_name'
        Filename of the output data.
        Each line contains, first, the particle index of the center
        particle of the corresponding triangle, then the position of the
        channel projected in the triangle's plane, and finally the
        radius of the channel.

    --periodic
        If the system has periodic boundary conditions. Only full
        periodic boundaries (in every direction) are supported for now.