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. type: LAMMPS dump files are generated by The file must contain five keys The atomic names passed to ReacNetGenerator must map to atomic types in the dump file. type: The standard XYZ files are in the following format: XYZ files do not contain cell information, so you have to manually pass cells to ReacNetGenerator. type: When ReaxFF is used as the pair style, LAMMPS ReaxFF bonds files are generated by The atomic names passed to ReacNetGenerator must map to atomic types in the bond file.LAMMPS dump files#
dump
dump
command.[TAB+22]dump 1 all custom 100 dump.reaxc id type x y z
id
, type
, x
, y
, and z
. The location of these keys is arbitrary.XYZ files#
xyz
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
LAMMPS ReaxFF bonds file#
bond
fix reaxff/bonds
command.[AFPG12]fix 1 all reaxff/bonds 100 bonds.reaxff