CompuCell3d manual and Tutorial Version 2

IX.1.1 Lattice Type

Early versions of CompuCell3D allowed users to use only square lattice. Most recent versions however, allow the simulation to be run on hexagonal lattice as well.

To enable hexagonal lattice you need to put
Hexagonal
in the Potts section of the XML configuration file.
There are few things to be aware of. When using hexagonal lattice. Obviously your pixels are hexagons (2D) or rhombic dodecahedrons (3D) but what is more important is that surface or perimeter of the pixel (depending whether in 2D or 3D) is different than in the case of sqaure pixel. The way CompuCell3D hex lattice implementation was done was that the volume of the pixel was constrained to be 1 regardless of the lattice type.

Second, there is one to one correspondence between pixels of the square lattice and pixels of the hex lattice. Consequently we can come up with transformation equations which give positions of hex pixels as a function of square lattice pixel position: