BASH shell scripts for converting dump files from structural relaxations in LAMMPS to CSSR file format for use in molecular simulation software packages. Avoids using multiple different software packages by carrying out the conversion process in one simple (albeit slow) step.
lamms2cssr-triclinic.sh can convert dump files in which the box bounds are written for a triclinic simulation box. For more information on the relationship between the box bounds used in simulation and the triclinic lattice vectors (change of basis), see Section 6.12. "Triclinic (non-orthogonal) simulation boxes" under "How-to discussions" in the LAMMPS manual.
lammps2cssr-ortho.sh can convert dump files for simulations in which the box bounds are orthogonal.
Place trajectory snapshot in same directory as lammps2cssr-{triclinic, orthogonal}.sh. At the top of lammps2cssr-{triclinic, orthogonal}.sh, specify 1) the types of coordinates (fractional/Cartesian) to write to the CSSR and 2) the file extension for the dump files to convert. Then run the script. Make sure the script corresponds to the type of box bounds in the dump files.
TODO: merge the triclinic and ortho scripts
TODO: rewrite in Python, this is too slow (can take up to 30 seconds for large structures)
Rocío Mercado
Repository -- https://github.com/rociomer/lammps2cssr
LAMMPS Manual -- http://lammps.sandia.gov/doc/Section_howto.html