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###   SmartAnalyzer for LAMMPS :: Tail Order Analysis (Scd) and Mean Squared Displacement (MSD)  ### 
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###   Funding gratefully provided by Unilever plc and University of Southampton.                 ###
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###   All code is "as is" and there is no implied warranty.                                      ###
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###   Donovan, Orsi and Essex (2011)		                                                 ###
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What you need to run
---------------------

1. A python interpreter (python.org) and a copy of LAMMPS 
(LAMMPS Molecular Dynamics Simulator: http://lammps.sandia.gov/) 

2. A suitable LAMMPS trajectory (dumplong.trj) created with the following columns: 
<id type mol x y z ... ...>. Only positional information is only used in both routines.


File structure
-------------
 ___________________________________________________________________________________________________
|<Input files>            |                                                                         |
|_________________________|_________________________________________________________________________|
|cfg.py                   |Initial setup and configuration files. Here you will see all the input   |
|                         |and output files that are employed, divided into two sections: MSD and   |
|                         |SCD. Specify beads, reference beads, molecule ranges and timescales.     |
|_________________________|_________________________________________________________________________|
|tailordering.py          |Performs analysis of tail parameters. Generates output files Szz, 2Sxx   |
|                         |and Scp and mScd (-Scd).                                                 |
|_________________________|_________________________________________________________________________|
|msd.py                   |Compute mean squared displacement of systems in 2D given an initial time |
|                         |start value.                                                             |
|_________________________|_________________________________________________________________________|
|dumplong.trj             |Input trajectory file of the form: <id type mol x y z ... ...>           |
|_________________________|_________________________________________________________________________|
|<Generated files>        |                                                                         |
|_________________________|_________________________________________________________________________|
|See cfg.py               |Filenames and their preferences are better shown in the cfg file. Files  |
|                         |will appear in the working directory of the folder.                      |
|_________________________|_________________________________________________________________________|



Running the analysis
---------------------

A. Copy the trajectory file into the working directory: <dumplong.trj>.
B. Run with the command:
	python msd.py
	
	or

	python tailordering.py