How to make the periodic image real?

At times one wants to give all those periodic images a true shape, i.e. one wants to duplicate the cell contents. How can this be achieved?

Assume we have a file cluster.xyz containing a cluster of calcium-silicate-hydrate (CSH)-gel. The box is a cuboid with 88 Angstroem length. Then, we duplicate this cluster in the y and z direction as follows:

./molecuilder --change-box "88,0,88,0,0,88" -i cluster.xyz --repeat-box "1,2,2

That is:

• first, we use --change-box to set the correct box dimensions, essential for this operator and not contained in the xyz format,
• Next, we parse the file -i.
• And finally, we call --repeat-box which duplicates the cell contents in x and y direction, creating a 1x2x2 grid out of the initial box containing the cluster.