Structure conversion and manipulation

The following examples showcase some of sconv’s structure manipulation capabilities.

  • Interconversion between the various supported file formats is straightforward with sconv. If the format of the input and/or output file is not uniquely defined by the file name, the formats must be specified using the flags -i and -o. Here a few examples:

$ # convert VASP POSCAR to XSF format
$ aenet sconv POSCAR structure.xsf
$ # conversion to LAMMPS dump
$ aenet sconv structure.xsf structure.dump
$ # protein database format
$ aenet sconv structure.dump structure.pdb

  • sconv can also manipulate atomic structures. If no output file name is specified, the output will be printed to the terminal (i.e., to standard out). Here just a few examples:

$ # shift unit cell such that atom 10 is on the origin
$ aenet sconv structure.xsf -o vasp --shift origin 10
$ # scale the atomic structure uniformly by a factor of 1.1
$ aenet sconv structure.xsf -o vasp --scale 1.1
$ # rotate the structure by 45 degrees around the z axis
$ aenet sconv structure.xyz -o vasp --rotate-angle 3 45
$ # return a spherical region around atom 5 with radius 10 Angstrom
$ aenet sconv structure.xsf -o xsf --cut 5 10.0

  • Multiple instructions can be piped (if supported by the shell). In that case, the input file is replaced by a hyphen (-), and the input format needs to be defined:

$ aenet sconv structure.xsf -o vasp --shift origin 10 \
  | aenet sconv - -i vasp -o vasp --scale 1.1 \
  | aenet sconv - -i vasp -o vasp --rotate-angle 3 45