Constructing tubes
##################

This chapter demonstrates the tube generator in Zeobuilder. It is a generic tool
that converts a two-dimensional (flat) molecular system into a tube-shaped
periodic or aperiodic system. It can be used to generate carbon nano-tubes, but
we will also demonstrate how it can be used for other kinds of (hypothetical)
tubes. It might be instructive to refresh your background on
`nanotubes <http://en.wikipedia.org/wiki/Carbon_nanotube>`_.


The carbon nanotube
===================

The tube tool is relatively simple to use, so we immediately kick of with an
example:

1. Load the model :download:`graphite_sheet.zml <examples/graphite_sheet.zml>`. This is a
   two-dimensional periodic model of an infinite and flat graphite sheet.

2. Select the global reference frame.

3. Activate the menu function ``Object -> Builder -> Create tube``. A Popup
   dialog appears that looks like the top left window in the figure below.
   Several parameters have to be entered:

   * The parameters **n** and **m** define the chiral vector of the tube.

   * When the **flat** option is checked, the extended graphite sheet is not
     folded into a tube.

   * The tube tool can create periodic tubes, but it is hard to control the
     length of periodic tubes for certain combinations of n and m. Aperiodic
     tubes on the other hand, can be easily generated with a prescribed length.

  Click ``OK``.

4. Now we can safely add bonds to the model: ``press Ctrl-B``.

An example of a carbon nanotube is presented in the figure below. Experiment
with different parameters for the tube tool.

.. figure:: images/carbon_tube_overview.png
    :align: center


    Carbon applications of the tube tool. TOP-LEFT: The orignal model, a minimal
    two-dimensional unit cell of a graphite layer. TOP-RIGHT: The dialog window
    with the tube parameters. BOTTOM-LEFT: The result when the `flat` option is
    checked. BOTTOM-RIGHT: The result when the `flat` option is not checked.


The silica nanotube
===================


In this section we show the results of the tube tool when applied to an
hexagonal silica layer: `silica_sheet.zml <examples/silica_sheet.zml>`_. The
tube parameters are the same as in the previous example.}}

.. figure:: images/silica_tube_overview.png
    :align: center

    Silica applications of the tube tool. TOP-LEFT: The orignal model, a minimal
    two-dimensional unit cell of a silica layer. TOP-RIGHT: The dialog window
    with the tube parameters. BOTTOM-LEFT: The result when the `flat` option is
    checked. BOTTOM-RIGHT: The result when the `flat` option is not checked.