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exercise_11 - Molecular Dynamics Simulations 2011 Exercise...

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Unformatted text preview: Molecular Dynamics Simulations 2011 Exercise 11: Suggested solutions Eero Holmstr¨ om November 30, 2011 1. To create and rotate the clusters, we modify the program created for Exercise 1 into the program makeclusters . The program creates two Cu clusters of user-defined diameter and distance from one another and rotates them by evenly distributed random Euler angles φ, Θ , and ψ (See Fig. 1). The rotation is performed using the rotation matrix R , so that r ′ = Rr where R = cos ψ cos φ- cos Θ sin φ sin ψ cos ψ sin φ + cos Θ cos φ sin ψ sin ψ sin Θ- sin ψ cos φ- cos Θ sin φ cos ψ- sin ψ sin φ + cos Θ cos φ cos ψ cos ψ sin Θ sin Θ sin φ- sin Θ cos φ cos Θ . Since again we’ll be doing a series of runs, it’s best to write a script to do this for us ( runner_script ). So, what’s going on in the simulations? Well, it looks like the two clusters coalesce to form a larger cluster of elongated form. This is because the system wants to saturate as many bonds as possible, or equivalently to minimize the...
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