# [MD] Lennard Jones

by JorisL
Tags: divergence, jones, lennard, lennard-jones, molecular dynamics
 P: 35 Hi For a simulation regarding Lennard Jones fluids I'm getting divergences. I have particles in a fixed volume. I calculate distances between these particles to find the force. However in the first iteration I already get divergences (NaN values in matlab). I use $$F_x^{ij} = 24\varepsilon \left( 2r_{ij}^{-14}-r_{ij}^{-8}\right)\cdot \Delta x_{ij}$$ Where the i,j have to do with the particles I'm viewing. For each direction I get such a force. But some of the particles get so close that this force and hence the acceleration effectively become infinity. My simulation obviously breaks down at this point. I tried changing the timestep, this doesn't do anything. It worked at some point but I don't recall changing anything after that. Except adding the thermostat code which I can turn off. The divergence remains. You can find my (messy) code in this pastebin http://pastebin.com/62v1yTCY I've been looking at it for hours already yet I can't find any solution. JorisL Edit; I had divergences before. Those were caused by an error in applying the periodic boundary conditions. I forgot using the nearest image convention at that time.
 P: 35 I found the mistake. In my initialization of the cubic lattice, I had a break off variable g. I initialized this one as g = 1. Which caused the last point to to coincide with my first point and so I got immediate divergences. At least 4 hours to waste :S J
 P: 2,491 You may have wasted 4 hours on this, but it took you 20+ years to get to this point...

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