Running the Main program:
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To run the program you need to have the following files on your MATLAB works space.

1) heatcurrent.m
2) KEnergy.m
3) LJEnergy.m
4) LJForce.m
5) Main.m
6) partsep.m
7) position_xyz.m
8) totenergy.m
9) velocity_xyz.m
10) a4.txt
11) initialdata_4.txt
12) phi4.txt
13) PlotAll.m

When you have these files in your workspace, you can go into the Main.m file and change certain 
variables to your liking:
Line 45 - tstep_total = 100000. (This is the number of iterations you want the program to run)
Line 46 - tramp = 10. (This tells the program to take data every 10 steps)
Line 47 - tstart = 0. (This tells the program to start taking data after the specified time)
Line 51 - block_NVT = 30000. (This is the length of NVT block before NVE calculation, which is used to set the temperature and volume)
Line 59 - Tint = 20.0; (This is the temperature for the system)
Line 31,32,33- rstar, estar and mstar (rstar and estar is the paramters in the L-J potential for the atom, and mstar is the mass of an atom)
To run the program then, just type Main in the Command window in MATLAB.

*A note: On an AMD 1700 XP+ Processor, with tstep_total = 10000, it takes 5 mins to run and at 
approximately 100000, it will take a 2-3 hours to run. So please be patient.


Obtaining the plots:
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When you run the main program above, the program will spit out 4 output files.
1) position.xyz
2) velocity.xyz
3) energy.txt
4) heatcurrent.txt
To obtain the plots of the temperature, KE, PE, total energy and heat current, first make sure that the file
PlotAll.m is also in your workspace. Then at the MATLAB command window, type PlotAll and in the Figure window
that pops up should show you all 5 plots.

Obtaining the integral of heatcurrent correlation function:
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After obtaining heatcurrent.txt
1)type CalcACK to do the autocorrelation and produce two files:ACDataOut.txt and IntOut.txt
2)after step 1), type PlotACK to plot the autocorrelation function and its integral .