| | 1 | == How to make the periodic image real? == |
| | 2 | |
| | 3 | 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? |
| | 4 | |
| | 5 | 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: |
| | 6 | {{{ |
| | 7 | ./molecuilder --change-box "88,0,88,0,0,88" -i cluster.xyz --repeat-box "1,2,2 |
| | 8 | }}} |
| | 9 | |
| | 10 | That is: |
| | 11 | * first, we use ''--change-box'' to set the correct box dimensions, essential for this operator and not contained in the ''xyz'' format, |
| | 12 | * Next, we parse the file ''-i''. |
| | 13 | * 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. |
