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###################  DebyeByPy readme!  ###########################

Last update: 4/3/2015

Use policy: 
This code is open source and available for use by anyone. When publishing please
use the following citation:
Trigg, E.B. DebyeByPy (2015), GitHub repository, https://github.com/etrigg/DebyeByPy

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Welcome to DebyeByPy, the Python code that calculates X-ray scattering of an 
assembly of atoms using the pairwise Debye function. We designed this code to be
simple to use. It was written for Python 2.7 and depends on the numpy library. 
To run it, you need to have Python 2.7 and Numpy installed on your computer 
(these are available for free online).

This code reads in an XYZ file. An XYZ file is a tab-delimited file that
specifies the position of each atom in your assembly of atoms. For more
information visit http://en.wikipedia.org/wiki/XYZ_file_format. An important
note is that the XYZ file should NOT have any comments in it. 

The Debye function uses Cromer Mann atomic scattering factors which are defined 
in the accompanying file, cromer_mann.tab. The atomic scattering factor 
depends on the oxidation state of the atom. Specify which oxidation state you'd
like to use for each atom in the debyeByPyWrapper.py file. 

To use DebyeByPy, you'll need to open up the wrapper script, debyeByPyWrapper.py.
Open it in any text editor (Notepad is fine). Here, you can define all the 
settings, which are explained in the comments of the file. When the settings are
to your liking, save the file and run it! Make sure that the following files are
all in the same directory:
- debyeByPy.py
- debyeByPyWrapper.py
- cromer_mann.tab
- your input XYZ file

This code was written by Edward B. Trigg with help from Vicky V. T. Doan-Nguyen. 
Please address any questions to:
[email protected]