JDFTx  1.5.0
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xyzToIonposOpt 
    Convert an xyz format file (cartesian Angstrom) to a JDFTx geometry specification.

       Usage: xyzToIonposOpt <file>.xyz <pad>

    NOTE: be sure to include command "coords-type cartesian" in the input file!

    This will output two files, <file>.ionpos containing Cartesian bohr coordinates
    and <file>.lattice containing the optimum orthogonal cell. The unit cell will be
    larger in each dimension by <pad> bohrs than any atom. The molecule bounding box
    will be centered at the origin, and rotated to minimize the unit cell volume.

    This generates the optimum geometry for use with "coulomb-interaction Isolated"
    and "coulomb-truncation-embed 0 0 0". (NOTE: requires octave to be available in path)