114 lines
4.0 KiB
Plaintext
114 lines
4.0 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix reax/bonds command :h3
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fix reax/c/bonds command :h3
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fix reax/c/bonds/kk command :h3
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[Syntax:]
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fix ID group-ID reax/bonds Nevery filename :pre
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ID, group-ID are documented in "fix"_fix.html command
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reax/bonds = style name of this fix command
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Nevery = output interval in timesteps
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filename = name of output file :ul
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[Examples:]
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fix 1 all reax/bonds 100 bonds.tatb
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fix 1 all reax/c/bonds 100 bonds.reaxc :pre
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[Description:]
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Write out the bond information computed by the ReaxFF potential
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specified by "pair_style reax"_pair_reax.html or "pair_style
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reax/c"_pair_reaxc.html in the exact same format as the original
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stand-alone ReaxFF code of Adri van Duin. The bond information is
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written to {filename} on timesteps that are multiples of {Nevery},
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including timestep 0. For time-averaged chemical species analysis,
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please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
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The format of the output file should be reasonably self-explanatory.
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The meaning of the column header abbreviations is as follows:
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id = atom id
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type = atom type
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nb = number of bonds
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id_1 = atom id of first bond
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id_nb = atom id of Nth bond
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mol = molecule id
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bo_1 = bond order of first bond
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bo_nb = bond order of Nth bond
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abo = atom bond order (sum of all bonds)
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nlp = number of lone pairs
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q = atomic charge :ul
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If the filename ends with ".gz", the output file is written in gzipped
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format. A gzipped dump file will be about 3x smaller than the text
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version, but will also take longer to write.
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:line
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. None of the "fix_modify"_fix_modify.html options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various "output
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commands"_Section_howto.html#howto_15. No parameter of this fix can
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be used with the {start/stop} keywords of the "run"_run.html command.
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This fix is not invoked during "energy minimization"_minimize.html.
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:line
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Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in "Section_accelerate"_Section_accelerate.html
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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LAMMPS was built with those packages. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the "-suffix command-line
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switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
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use the "suffix"_suffix.html command in your input script.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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:line
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[Restrictions:]
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The fix reax/bonds command requires that the "pair_style
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reax"_pair_reax.html be invoked. This fix is part of the REAX
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package. It is only enabled if LAMMPS was built with that package,
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which also requires the REAX library be built and linked with LAMMPS.
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The fix reax/c/bonds command requires that the "pair_style
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reax/c"_pair_reaxc.html be invoked. This fix is part of the
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USER-REAXC package. It is only enabled if LAMMPS was built with that
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package. See the "Making LAMMPS"_Section_start.html#start_3 section
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for more info.
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To write gzipped bond files, you must compile LAMMPS with the
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-DLAMMPS_GZIP option.
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[Related commands:]
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"pair_style reax"_pair_reax.html, "pair_style
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reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
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[Default:] none
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