tubeXYZ Project

How to use tubeXYZ

We were trying to keep this program as simple as possible for the user but still provide all the necessary features. In this guide I will walk you through the user prompt screens and give an example of how to construct your first tube.

My first tube

Lets fire up tubeXYZ and start constructing your first nanotube!

You are given an option to either construct only one tube or to construct a bunch of tubes in the same file, this will construct a .XYZ file containing the tubes one after the other in the X direction with a space of 2*radii between each tube. The reason is that you may want to apply some kind of calculation of several nanotubes. We choose the first option for this guide.

In this software you can construct multiple nanotubes in the same XYZ file
The tubes will be constructing one by one from the input you provide
Please choose the mode of operation
1. Construct one nanotube (default)
2. Construct multiple nanotubes in the same file
> 1

Next we have a choice of which type of nanotube to construct


Choose the nanotube type
1. Carbon nanotube (default)
2. Silicon nanotube
3. Boron nanotube
> 1

Now we define the chiral vector usinga pair of integer numbers separated by a comma

Choose the nanotube chiral vector n,m default (5,5)
> 9,3

The length of the bonds between the atoms are specified here, the program has a default measured bond length for each tube type so if you are not sure just choose the default, we will also choose the default in this guide.
Choose the bond length (angstrom):
1. Use default bond length : 1.42 (default)
2. Set the bond length
> 1
The length of the tube in tubeXYZ is measured in atomic layers that we calculate for the current tube helix, in a general sense it’s the number of “rings” in a zigzag type nanotube. Here we choose the second option to set length
Choose the nanotube length in atom layers units
this will determine how many helix turns the program will generate
1. Use default length of 30 (default)
2. Set the length
> 2
We choose the length to be 50
Enter the tube length

> 50

We are asked to name the data file, two files will be created the file name you specify ( you must add the .xyz extension yourself) and a file with an extension .info that contains a table with some additional output data about the tube, we name the file tubedemo.xyz
We are now ready to write the tubes to a data file
An XYZ file will be constructed to be compatible with Aviz
An additional file with the same name but with an extension of xyz.info
Will be constructed and will contain the tubes data for future reference
Please set the filename for the output data (default = tubes.xyz)
> tubedemo.xyz

*Please notice that a default value is always present and use the default value by hitting the return (enter) key.

The results

here you can see the output of tubeXYZ

Visualizing the XYZ file

For information on how to use AViz read the guide, we have used AViz just to load the XYZ file and I've captured the following images