forked from lijiext/lammps
115 lines
4.6 KiB
Plaintext
115 lines
4.6 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 species command :h3
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[Syntax:]
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fix ID group-ID species Nevery Nrepeat Nfreq filename keyword value ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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species = style name of this command :l
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Nevery = sample bond-order every this many timesteps :l
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Nrepeat = # of bond-order samples used for calculating averages :l
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Nfreq = calculate average bond-order every this many timesteps :l
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filename = name of output file :l
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zero or more keyword/value pairs may be appended :l
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keyword = {cutoff} or {element} :l
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{cutoff} value = I J Cutoff
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I, J = atom types
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Cutoff = Bond-order cutoff value for this pair of atom types:pre
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{element} value = Element1, Element2, ... :pre
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:ule
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[Examples:]
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fix 1 all species 10 10 100 species.out
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fix 1 all species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
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fix 1 all species 10 10 100 species.out element Au O H :pre
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[Description:]
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Write out the chemical species information computed by the ReaxFF potential
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specified by "pair_style reax/c"_pair_reax_c.html. Bond-order values
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(either averaged or instantaneous, depending on value of {Nrepeat})
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are used to determine chemical bonds. Every {Nfreq} timesteps,
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chemical species information is written to {filename} as a two lines.
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The first line is a header containing labels. The second line consists
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of the following: timestep, total number of molecules,
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total number of distinct species, number of molecules of each species.
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The chemical formula of each species is given in the first line.
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Optional keyword {cutoff} can be assigned to change the minimum bond-order values
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used in identifying chemical bonds between pairs of atoms. Bond-order cutoffs
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should be carefully chosen, as bond-order cutoffs that are too small may include
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too many bonds (which will result in an error), while too-large cutoffs will
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result in fragmented molecules. The default cutoff of 0.3 usually gives good
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estimate.
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Optional keyword {element} can be used to specify the chemical symbol printed for
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each LAMMPS atom type. The number of symbols must match the number of LAMMPS atom types
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and each symbol must consist of 1 or 2 alphanumeric characters. Normally, these
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symbols should be chosen to match the chemical identity of each LAMMPS atom type,
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as specified using the "reax/c pair_coeff"_pair_reax_c.html command and
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the ReaxFF force field file.
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:line
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The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
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timesteps the bond-order values are sampled to get the average bond
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order. The species analysis is performed using the average bond-order
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on timesteps
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that are a multiple of {Nfreq}. The average is over {Nrepeat}
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bond-order samples, computed in the preceding portion of the simulation every
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{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and
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{Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps
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contributing to the average bond-order cannot overlap, i.e. Nfreq >
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(Nrepeat-1)*Nevery is required.
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For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order values on
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timesteps 90,92,94,96,98,100 will be used to compute the average bond-order
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for the species analysis output on timestep 100.
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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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[Restrictions:]
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The fix species currently only works with
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"pair_style reax/c"_pair_reax_c.html and it requires that the "pair_style
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reax/c"_pair_reax_c.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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It should be possible to extend it to other reactive pair_styles (such as
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"rebo"_pair_airebo.html, "airebo"_pair_airebo.html,
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"comb"_pair_comb.html, and "bop"_pair_bop.html), but this has not yet been done.
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[Related commands:]
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"pair_style reax/c"_pair_reax_c.html, "fix
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reax/bonds"_fix_reax_bonds.html
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[Default:]
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The default values for bond-order cutoffs are 0.3 for all I-J pairs. The
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default element symbols are C, H, O, N.
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