Syntax: +
+fix ID group-ID reax/c/species Nevery Nrepeat Nfreq filename keyword value ... ++
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 species 10 10 100 species.out +fix 1 all species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55 +fix 1 all 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. +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 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. +
+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. No global or per-atom quantities are stored +by this fix for access by various output +commands. 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. +
+