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Mode: difference
Syntax
pikashu -diff <firstfile> <secondfile>
Description
This will read two files, convert them to extended XYZ format, and then calculate the difference in atomic positions. As for ddplot mode, both files MUST have the exact same number of particles, and shall correspond to the same system.
The results will be output in four files:
- xyz_diff.xyz: contains atomic positions from the first file, and the displacement vectors between the two files (in cartesian coordinates); this format is compatible with extended XYZ format.
- xyz_diff.xsf: same as above, but complying to XSF format; xCrysDen can read this file and display displacement vectors; beware that xCrysDen understand these vectors as FORCES (not as displacement vectors), so it may be tricky to set these vectors to the correct scale.
- xyz_diff.norm: contains the norm of the displacement vectors for each atom.
- xyz_both.xsf: contains the atomic positions of both files in the XSF format. Sometimes it can be useful to "superimpose" the two structures to see how they differ.
- xyz_stat.txt: contains statistics about the displacements: minimum/maximum displacements, average, standard deviation... Statistics are given for the whole system, as well as for each individual atom spieces.
Examples
pikashu -diff system_initial.grs system_final.xsf
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