fix reax/bonds command

fix reax/c/bonds command

fix reax/c/bonds/kk command

Syntax

fix ID group-ID reax/bonds Nevery filename
  • ID, group-ID are documented in fix command
  • reax/bonds = style name of this fix command
  • Nevery = output interval in timesteps
  • filename = name of output file

Examples

fix 1 all reax/bonds 100 bonds.tatb
fix 1 all reax/c/bonds 100 bonds.reaxc

Description

Write out the bond information computed by the ReaxFF potential specified by pair_style reax or pair_style reax/c in the exact same format as the original stand-alone ReaxFF code of Adri van Duin. The bond information is written to filename on timesteps that are multiples of Nevery, including timestep 0. For time-averaged chemical species analysis, please see the fix reaxc/c/species command.

The format of the output file should be reasonably self-explanatory. The meaning of the column header abbreviations is as follows:

  • id = atom id
  • type = atom type
  • nb = number of bonds
  • id_1 = atom id of first bond
  • id_nb = atom id of Nth bond
  • mol = molecule id
  • bo_1 = bond order of first bond
  • bo_nb = bond order of Nth bond
  • abo = atom bond order (sum of all bonds)
  • nlp = number of lone pairs
  • q = atomic charge

If the filename ends with ”.gz”, the output file is written in gzipped format. A gzipped dump file will be about 3x smaller than the text version, but will also take longer to write.


Restart, fix_modify, output, run start/stop, minimize info:

No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.


Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in Section_accelerate of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the Making LAMMPS section for more info.

You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.


Restrictions

The fix reax/bonds command requires that the pair_style reax be invoked. This fix is part of the REAX package. It is only enabled if LAMMPS was built with that package, which also requires the REAX library be built and linked with LAMMPS. The fix reax/c/bonds command requires that the pair_style reax/c be invoked. This fix is part of the USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.

To write gzipped bond files, you must compile LAMMPS with the -DLAMMPS_GZIP option.