Population number in a cubic cell with face-centered cubic arrangement: , with . Therefore typical particle numbers in simulations are etc.

When simulating two-dimensional systems, the setting up of periodic base cells and of initial configurations is an issue that takes some considering. Since 2D systems are important both in the teaching and in the application of simulation, some suggestions are compiled here.

A dense packing of discs is hexagonal. The most convenient periodic cell in two dimensions would be quadratic. Unfortunately, these are contradictory requirements.

There are two possible periodic cells compatible with a hexagonal structure: (a) rectangular; (b) rhombic.

**Rectangular unit cell:**The unit cell then has and contains discs.

**Periodic boundary conditions**are handled as usually, but with different base cell lengths along the axes: , ( may or may not be equal to .)

**Nearest image convention:**as usual, but again with different thresholds along the axes: and , respectively.

**Rhombic unit cell:**The crystallographic unit is now a rhombus with and ; it contains particle.

**Periodic boundary conditions**are best handled in a non-orthogonal coordinate system. Let denote the cartesian coordinates, and the coordinates in the rhombic system. Then with

(2.1) - Compute

(2.2) (2.3)

- Apply PBC as always, but in rhombic coordinates:

(2.4) (2.5)

- Now transform back to Cartesius:

(2.6) (2.7)

**Nearest image convention:**

Is applied in cartesian coordinates, possibly with a potential cutoff at :

(2.8) (2.9)

- Compute

(2.10) |

Given , the

The

(with ) or, in reduced units,

we first take the average of over a number of MD steps to determine the actual temperature of the simulated system. Then we scale each velocity component according to

Since is a fluctuating quantity it can be adjusted only approximately.

F. J. Vesely / University of Vienna