atomsk --ddplot <file1> <file2> [<outputfile>] [options]
In this mode Atomsk reads two input files and builds a file in the ddplot format (.dd). The <file1> should correspond to the ideal system (with no dislocation) and the <file2> to the system containing a dislocation. Both files MUST have the exact same number of particles. They may be of two different formats as long as they are supported formats.
In this mode, any <format> statement is ignored, as output is forced (and restricted) to the ddplot format (.dd).
If you use this mode with one or several options, then these options will be applied on the two files before the ddplot file is constructed.
Beware that there is a limitation in the number of atoms that the program ddplot can display, and Atomsk will display a warning if your system exceeds this number. You can use the ddplot mode with the option -cut in order to display only the part you are interested in.
atomsk --ddplot initial.gin dislocation.xyz visual.dd
This will read the files initial.gin and dislocation.xyz, and create the ddplot file visual.dd.
atomsk --ddplot initial.gin dislocation.xyz -cut above 60 z -cut below 40 z visual.dd
This examples uses the cut option. Here the program will use the files initial.gin and dislocations.xyz, and remove all atoms that have a Z coordinate greater than 60 Å or smaller than 40 Å. The final result will be output in the file visual.dd.