Supported trajectory formats

In principle, ReacNetGenerator can process any kind of trajectory files containing atomic coordinates or bond information. Up to now, the following formats are supported. You can convert your trajectory to one of the following formats using tools like dpdata or ASE. If you want new formats to be supported, please submit an issue to the ReacNetGenerator repository.

LAMMPS dump files

type: dump

LAMMPS dump files are generated by dump command.[TAB+22]

dump 1 all custom 100 dump.reaxc id type x y z

The file must contain five keys id, type, x, y, and z. The location of these keys is arbitrary.

The atomic names passed to ReacNetGenerator must map to atomic types in the dump file.

XYZ files

type: xyz

The standard XYZ files are in the following format:

3
Water frame 1
H    0.7493682    0.0000000    0.4424329
O    0.0000000    0.0000000   -0.1653507
H   -0.7493682    0.0000000    0.4424329
3
Water frame 2
H    0.7493682    0.0000000    0.4424329
O    0.0000000    0.0000000   -0.1653507
H   -0.7493682    0.0000000    0.4424329

XYZ files do not contain cell information, so you have to manually pass cells to ReacNetGenerator.

LAMMPS ReaxFF bonds file

type: bond

When ReaxFF is used as the pair style, LAMMPS ReaxFF bonds files are generated by fix reaxff/bonds command.[AFPG12]

fix 1 all reaxff/bonds 100 bonds.reaxff

The atomic names passed to ReacNetGenerator must map to atomic types in the bond file.