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GPU-Accelerated Computing with Python 3 and CUDA
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The system we want to model is a collection of particles. Particles are initialized with starting positions and velocities, based on experimental data and physical conditions such as desired temperature and pressure.
In an MD simulation, particles are constrained to a finite region of space called a simulation box. To mimic an infinite system, which is a good approximation for gases, liquids, and bulk materials, the boundaries of this box are usually defined to be periodic. This means when an atom moves outside one boundary, it reappears on the opposite side, mimicking a continuous space. This concept is known as periodic boundary conditions (PBCs) and helps to avoid edge effects, which would happen if boundaries were rigid.
Here, we consider a system composed of a single type of atom positioned within a 2D box. This setup restricts the particles to movement along the
and
axes, while motion along the
axis is prohibited. This configuration is ideal for our demonstration...