fix reax/c/species command — LAMMPS 15 May 2015 version documentation

# fix reax/c/species command

## Syntax

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

- ID, group-ID are documented in fix command
- reax/c/species = style name of this command
- Nevery = sample bond-order every this many timesteps
- Nrepeat = # of bond-order samples used for calculating averages
- Nfreq = calculate average bond-order every this many timesteps
- filename = name of output file
- zero or more keyword/value pairs may be appended
- keyword = cutoff or element or position

    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

## 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

## Description

Write out the chemical species information computed by the ReaxFF potential specified by pair_style reax/c. 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. In this context, “species” means a unique molecule. 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 cutoffs that are too large will result in fragmented molecules. The default cutoff of 0.3 usually gives good results.

The 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 command and the ReaxFF force field file.

The 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.

For the keyword position, the filepos is the name of the output file. It 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.

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.

## 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.

This fix computes both a global vector of length 2 and a per-atom vector, either of which can be accessed by various output commands. The values in the global vector are “intensive”.

The 2 values in the global vector are as follows:

- 1 = total number of molecules
- 2 = total number of distinct species

The per-atom vector stores the molecule ID for each atom as identified by the fix. If an atom is not in a molecule, its ID will be 0. For atoms in the same molecule, the molecule ID for all of them will be the same and will be equal to the smallest atom ID of any atom in the molecule.

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.

## Restrictions

The fix species currently only works with pair_style reax/c and it 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.

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

## Related commands

pair_style reax/c, fix reax/bonds

## 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.