-reduce-cell <x|y|z|p>
This option reduces the system into a shorter cell, while maintaining the periodicity.
This option searches for pairs of equivalent atoms. If the vector joining two equivalent atoms is parallel to and shorter than an initial cell vector, then it replaces it. The box may be shortened in one, two, or in all three directions. Then, atoms that are out of the new box are removed, along with their shells and auxiliary properties if they had any.
This option preserves the crystal orientation, it just attempts to shorten the cell vectors when it is possible. The resulting final cell should be the shortest for this crystal orientation.
If this option is called with the parameter "x", "y", or "z", then the cell size is reduced only along that direction. In the absence of parameter the cell size is reduced in all dimensions.
If this option is called with the parameter "p", then Atomsk will attempt to find the primitive cell, i.e. the smallest vectors that respect the periodicity of the lattice. Note that in this case, the final box vectors may not be aligned with the initial ones.
If the system is rotated and you wish to obtain an orthorhombic unit cell, then use the option -orthogonal-cell before this one.
Note that this option is meant for use with perfect crystals. It cannot be expected to give good results in crystals containing defects, nor on non-crystalline or disordered systems. Also, Atomsk will attempt to reduce the cell size, but if it does not find suitable shorter vectors, then the cell will remain the same.
By default Atomsk does not reduce cell vectors.
atomsk system.cfg -reduce-cell xsf
This will read the file system.cfg and re-calculate the supercell base vectors. The result will be output in system.xsf.
atomsk --create fcc 4.02 Al -duplicate 10 10 10 -reduce-cell final.cfg
With this command, Atomsk will create a unit cell of fcc aluminium, which contains 4 atoms. Then it will duplicate it ten times along each direction, resulting in a supercell containing 4000 atoms. Then, the option "-reduce-cell" will try to reduce the size of this system while preserving its periodicity, and it will find that the smallest matching system is the unit cell containing just 4 atoms. Finally, Atomsk will write the final result in the file "final.cfg".
atomsk initial.cfg -rotate Z 45 -orthogonal-cell -reduce-cell final.cfg
This will rotate the system by 45° around Z, search for an equivalent orthogonal cell, and finally attempt to reduce the size of this cell. The result will be output in final.cfg.
atomsk initial.cfg -reduce-cell y final.cfg
This will read the file initial.cfg, and attempt to reduce the cell size along the Y axis. The result will be output in final.cfg.
atomsk Al_unitcell.cfg -reduce-cell p Al_primitivecell.cfg
This will read the file Al_unitcell.cfg, and try to find the primitive cell. The result will be output in Al_primitivecell.cfg.