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Visualize atomic structures

As described in Input file section, users can specify output format of atomic configuration during an MD simulation by an option flag_out_pmd.

  • flag_out_pos 1 --- pmd format, a special format in this program that contains necessary information needed to run pmd.
  • flag_out_pos 2 --- dump format, which is a format used in LAMMPS program.

Some visualization apps such as Ovito can read dump format. And some can read other format such as POSCAR format used in VASP program. The napsys command in nappy package helps you to convert file format to some other format as,

$ napsys convert pmd_xxx to dump_xxx
or
$ napsys convert dump_xxx to POSCAR_xxx

If there are sequential pmd_#### files, one can convert those files by using bash for-statement as :

for f in pmd_[0-9]*; do /path/to/nap/nappy/napsys.py convert $f `echo $f | sed 's/pmd/dump/'`; done