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[MD] Lennard Jones

  1. Dec 24, 2013 #1

    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 [tex]F_x^{ij} = 24\varepsilon \left( 2r_{ij}^{-14}-r_{ij}^{-8}\right)\cdot \Delta x_{ij}[/tex]
    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.


    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.
    Last edited: Dec 24, 2013
  2. jcsd
  3. Dec 25, 2013 #2
    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

  4. Dec 25, 2013 #3


    Staff: Mentor

    You may have wasted 4 hours on this, but it took you 20+ years to get to this point...
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