2013-05-24 02:02:16 +08:00
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>fix reax/c/species command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID reax/c/species Nevery Nrepeat Nfreq filename keyword value ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>reax/c/species = style name of this command
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<LI>Nevery = sample bond-order every this many timesteps
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<LI>Nrepeat = # of bond-order samples used for calculating averages
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<LI>Nfreq = calculate average bond-order every this many timesteps
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<LI>filename = name of output file
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>cutoff</I> or <I>element</I> or <I>position</I>
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<PRE> <I>cutoff</I> 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
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<I>element</I> value = Element1, Element2, ...
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<I>position</I> value = posfreq filepos
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posfreq = write position files every this many timestep
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filepos = name of position output file
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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2013-11-07 22:51:08 +08:00
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<PRE>fix 1 all reax/c/species 10 10 100 species.out
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fix 1 all reax/c/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
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fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
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2013-05-24 02:02:16 +08:00
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</PRE>
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<P><B>Description:</B>
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</P>
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2014-05-03 05:38:24 +08:00
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<P>Write out the chemical species information computed by the ReaxFF
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potential specified by <A HREF = "pair_reax_c.html">pair_style reax/c</A>.
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Bond-order values (either averaged or instantaneous, depending on
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value of <I>Nrepeat</I>) are used to determine chemical bonds. Every
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<I>Nfreq</I> timesteps, chemical species information is written to
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<I>filename</I> as a two line output. The first line is a header
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containing labels. The second line consists of the following:
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timestep, total number of molecules, total number of distinct species,
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number of molecules of each species. In this context, "species" means
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a unique molecule. The chemical formula of each species is given in
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the first line.
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</P>
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<P>Optional keyword <I>cutoff</I> can be assigned to change the minimum
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bond-order values used in identifying chemical bonds between pairs of
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atoms. Bond-order cutoffs should be carefully chosen, as bond-order
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cutoffs that are too small may include too many bonds (which will
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result in an error), while cutoffs that are too large will result in
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fragmented molecules. The default cutoff of 0.3 usually gives good
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results.
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</P>
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<P>The optional keyword <I>element</I> can be used to specify the chemical
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symbol printed for each LAMMPS atom type. The number of symbols must
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match the number of LAMMPS atom types and each symbol must consist of
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1 or 2 alphanumeric characters. Normally, these symbols should be
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chosen to match the chemical identity of each LAMMPS atom type, as
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specified using the <A HREF = "pair_reax_c.html">reax/c pair_coeff</A> command and
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the ReaxFF force field file.
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</P>
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<P>The optional keyword <I>position</I> writes center-of-mass positions of
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each identified molecules to file <I>filepos</I> every <I>posfreq</I> timesteps.
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The first line contains information on timestep, total number of
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molecules, total number of distinct species, and box dimensions. The
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second line is a header containing labels. From the third line
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downward, each molecule writes a line of output containing the
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following information: molecule ID, number of atoms in this molecule,
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chemical formula, total charge, and center-of-mass xyz positions of
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this molecule. The xyz positions are in fractional coordinates
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relative to the box dimensions.
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</P>
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<P>For the keyword <I>position</I>, the <I>filepos</I> is the name of the output
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file. It can contain the wildcard character "*". If the "*"
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character appears in <I>filepos</I>, then one file per snapshot is written
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at <I>posfreq</I> and the "*" character is replaced with the timestep
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value. For example, AuO.pos.* becomes AuO.pos.0, AuO.pos.1000, etc.
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2013-05-24 02:02:16 +08:00
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</P>
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<HR>
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<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> 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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2014-05-03 05:38:24 +08:00
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on timesteps that are a multiple of <I>Nfreq</I>. The average is over
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<I>Nrepeat</I> bond-order samples, computed in the preceding portion of the
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simulation every <I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of
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<I>Nevery</I> and <I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also,
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the timesteps contributing to the average bond-order cannot overlap,
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i.e. Nfreq > (Nrepeat-1)*Nevery is required.
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</P>
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<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order
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values on timesteps 90,92,94,96,98,100 will be used to compute the
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average bond-order for the species analysis output on timestep 100.
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2013-05-24 02:02:16 +08:00
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</P>
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<HR>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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2014-05-03 05:38:24 +08:00
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are relevant to this fix.
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</P>
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<P>This fix computes both a global vector of length 2 and a per-atom
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vector, either of which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
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commands</A>. The values in the global
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vector are "intensive".
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</P>
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<P>The 2 values in the global vector are as follows:
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</P>
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<UL><LI>1 = total number of molecules
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<LI>2 = total number of distinct species
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</UL>
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<P>The per-atom vector stores the molecule ID for each atom as identified
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by the fix. If an atom is not in a molecule, its ID will be 0.
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For atoms in the same molecule, the molecule ID for all of them
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will be the same and will be equal to the smallest atom ID of
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any atom in the molecule.
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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2013-05-24 02:02:16 +08:00
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>The fix species currently only works with
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<A HREF = "pair_reax_c.html">pair_style reax/c</A> and it requires that the <A HREF = "pair_reax_c.html">pair_style
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reax/c</A> 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 <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
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for more info.
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</P>
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<P>It should be possible to extend it to other reactive pair_styles (such as
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<A HREF = "pair_airebo.html">rebo</A>, <A HREF = "pair_airebo.html">airebo</A>,
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<A HREF = "pair_comb.html">comb</A>, and <A HREF = "pair_bop.html">bop</A>), but this has not yet been done.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "pair_reax_c.html">pair_style reax/c</A>, <A HREF = "fix_reax_bonds.html">fix
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reax/bonds</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>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. Position files are not written
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by default.
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</P>
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</HTML>
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