Coding Considerations for Standalone Molecular Dynamics Simulations of Atomistic Structures

The laws of Newtonian mechanics allow ab-initio
molecular dynamics to model and simulate particle trajectories in
material science by defining a differentiable potential function. This
paper discusses some considerations for the coding of ab-initio
programs for simulation on a standalone computer and illustrates
the approach by C language codes in the context of embedded
metallic atoms in the face-centred cubic structure. The algorithms use
velocity-time integration to determine particle parameter evolution
for up to several thousands of particles in a thermodynamical
ensemble. Such functions are reusable and can be placed in a
redistributable header library file. While there are both commercial
and free packages available, their heuristic nature prevents dissection.
In addition, developing own codes has the obvious advantage of
teaching techniques applicable to new problems.

Authors:

• R. O. Ocaya
• J. J. Terblans

Keywords:

• C-language
• molecular dynamics
• simulation
• embedded atom method.

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