atomsk --interpolate <file1> <file2> <N> [<outputfile>] [formats] [options]
This mode constructs a chain of configurations by interpolating linearly the positions of atoms between the configurations given by the <file1> and the <file2>. The number <N> gives the number of configurations generated between the initial and final states. The vectors of the simulation box are also interpolated.
The two given files must have the exact same number of particles, and shall correspond to the same system (i.e. same base vectors, same atom types, etc.) for the interpolation to make sense. The two files may be in different formats as long as these formats are supported by Atomsk.
If the initial and final systems contain shells (in the sense of an ionic core-shell model) then the positions of shells will also be interpolated. If only one of the initial or final system contains shells but not the other, then shells will be ignored and will not appear in interpolated images.
If you use this mode with one or several options, then these options will be applied to each interpolated configuration.
This mode produces <N>+2 output configurations, numbered from 0 up to <N>+1. The configuration 0 corresponds to the initial state, configuration number <N>+1 to the final one, so that the intermediate configurations are indexed from 1 to <N>.
Note that some of the configurations produced by interpolations may not correspond to stable states, or even to physically realistic states, of the system. Such a chain of configurations may be used e.g. as a starting point for a Nudged Elastic Band (NEB) calculation, or simply to produce an animation between two states.
atomsk --interpolate initial.xsf final.xsf 7 chain cfg
This will construct 7 configurations by interpolating between initial.xsf and final.xsf. The resulting configurations will be named chain_img0.cfg, chain_img1.cfg, up to chain_img8.cfg.