lammps/doc/fix_reaxc_species.txt

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)

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fix reax/c/species command :h3

[Syntax:]

fix ID group-ID reax/c/species Nevery Nrepeat Nfreq filename keyword value ... :pre

ID, group-ID are documented in "fix"_fix.html command :ulb,l
reax/c/species = style name of this command :l

Nevery = sample bond-order every this many timesteps :l
Nrepeat = # of bond-order samples used for calculating averages :l
Nfreq = calculate average bond-order every this many timesteps :l
filename = name of output file :l

zero or more keyword/value pairs may be appended :l
keyword = {cutoff} or {element} or {position} :l
  {cutoff} value = I J Cutoff
    I, J = atom types
    Cutoff = Bond-order cutoff value for this pair of atom types
  {element} value = Element1, Element2, ... 
  {position} value = posfreq filepos
    posfreq = write position files every this many timestep
    filepos = name of position output file :pre
:ule

[Examples:]

fix 1 all reax/c/species 10 10 100 species.out
fix 1 all reax/c/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH.pos :pre

[Description:]

Write out the chemical species information computed by the ReaxFF potential
specified by "pair_style reax/c"_pair_reax_c.html.  Bond-order values 
(either averaged or instantaneous, depending on value of {Nrepeat}) 
are used to determine chemical bonds. Every {Nfreq} timesteps,
chemical species  information is written to {filename} as a two line output.
The first line is a header containing labels. The second line consists 
of the following: timestep, total number of molecules, 
total number of distinct species, number of molecules of each species.
The chemical formula of each species is given in the first line.

Optional keyword {cutoff} can be assigned to change the minimum bond-order values 
used in identifying chemical bonds between pairs of atoms.  Bond-order cutoffs 
should be carefully chosen, as bond-order cutoffs that are too small may include 
too many bonds (which will result in an error), while too-large cutoffs will 
result in fragmented molecules.  The default cutoff of 0.3 usually gives good 
estimate. 

Optional keyword {element} can be used to specify the chemical symbol printed for
each LAMMPS atom type. The number of symbols must match the number of LAMMPS atom types
and each symbol must consist of 1 or 2 alphanumeric characters. Normally, these
symbols should be chosen to match the chemical identity of each LAMMPS atom type,
as specified using the "reax/c pair_coeff"_pair_reax_c.html command and 
the ReaxFF force field file. 

Optional keyword {position} writes center-of-mass positions of each identified 
molecules to file {filepos} every {posfreq} timesteps.  The first line contains
information on timestep, total number of molecules, total number of distinct 
species, and box dimensions.  The second line is a header containing labels.
From the third line downward, each molecule writes a line of output containing 
the following information: molecule ID, number of atoms in this molecule, chemical 
formula, total charge, and center-of-mass xyz positions of this molecule.  The xyz
positions are in fractional coordinates relative to the box dimensions.  

Keyword {position} output file {filepos} can contain the wildcard character "*".  
If the "*" character appears in {filepos}, then one file per snapshot is written 
at {posfreq} and the "*" character is replaced with the timestep value.  
For example, AuO.pos.* becomes AuO.pos.0, AuO.pos.1000, etc.

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The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
timesteps the bond-order values are sampled to get the average bond
order.  The species analysis is performed using the average bond-order
on timesteps
that are a multiple of {Nfreq}.  The average is over {Nrepeat}
bond-order samples, computed in the preceding portion of the simulation every
{Nevery} timesteps.  {Nfreq} must be a multiple of {Nevery} and
{Nevery} must be non-zero even if {Nrepeat} is 1.  Also, the timesteps
contributing to the average bond-order cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.

For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order values on
timesteps 90,92,94,96,98,100 will be used to compute the average bond-order
 for the species analysis output on timestep 100.  

:line

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

No information about this fix is written to "binary restart
files"_restart.html.  None of the "fix_modify"_fix_modify.html options
are relevant to this fix.  No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15.  No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.

[Restrictions:]

The fix species currently only works with 
"pair_style reax/c"_pair_reax_c.html and it requires that the "pair_style
reax/c"_pair_reax_c.html 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_start.html#start_3 section
for more info.

It should be possible to extend it to other reactive pair_styles (such as 
"rebo"_pair_airebo.html, "airebo"_pair_airebo.html, 
"comb"_pair_comb.html, and "bop"_pair_bop.html), but this has not yet been done.

[Related commands:]

"pair_style reax/c"_pair_reax_c.html, "fix
reax/bonds"_fix_reax_bonds.html

[Default:] 

The default values for bond-order cutoffs are 0.3 for all I-J pairs.  The
default element symbols are C, H, O, N.  Position files are not written 
by default.