# fix reaxff/species command Accelerator Variants: *reaxff/species/kk* ## Syntax fix ID group-ID reaxff/species Nevery Nrepeat Nfreq filename keyword value ... - ID, group-ID are documented in [fix](fix) command - reaxff/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* or *delete* *cutoff* value = I J Cutoff I, J = atom types (see asterisk form below) 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 *delete* value = filedel keyword value filedel = name of delete species output file keyword = *specieslist* or *masslimit* *specieslist* value = Nspecies Species1 Species2 ... Nspecies = number of species in list *masslimit* value = massmin massmax massmin = minimum molecular weight of species to delete massmax = maximum molecular weight of species to delete *delete_rate_limit* value = Nlimit Nsteps Nlimit = maximum number of deletions allowed to occur within interval Nsteps = the interval (number of timesteps) over which to count deletions ## Examples ``` LAMMPS fix 1 all reaxff/species 10 10 100 species.out fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2*3 0.55 fix 1 all reaxff/species 1 100 100 species.out element Au O H position 1000 AuOH.pos fix 1 all reaxff/species 1 100 100 species.out delete species.del masslimit 0 50 ``` ## Description Write out the chemical species information computed by the ReaxFF potential specified by [pair_style reaxff](pair_reaxff). 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. :::: warning ::: title Warning ::: In order to compute averaged data, it is required that there are no neighbor list rebuilds for at least Nrepeat\*Nevery steps preceding each *Nfreq* step. For that reason, fix *reaxff/species* may change your neighbor list settings. Reneighboring will occur no more frequently than every Nrepeat\*Nevery timesteps, and will occur less frequently if *Nfreq* is not a multiple of Nrepeat\*Nevery. There will be a warning message showing the new settings. Having a *Nfreq* setting that is larger than what is required for correct computation of the ReaxFF force field interactions, in combination with certain *Nrepeat* and *Nevery* settings, can thus lead to incorrect results. For typical ReaxFF calculations, reneighboring only every 100 steps is already quite a low frequency. :::: If the filename ends with \".gz\", the output file is written in gzipped format. A gzipped dump file will be about 3x smaller than the text version, but will also take longer to write. ::: versionadded 15Jun2023 Support for wildcards added ::: 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. A wildcard asterisk can be used in place of or in conjunction with the I,J arguments to set the bond-order cutoff for multiple pairs of atom types. This takes the form \"\*\" or \"\*n\" or \"n\*\" or \"m\*n\". If $N$ is the number of atom types, then an asterisk with no numeric values means all types from 1 to $N$. A leading asterisk means all types from 1 to n (inclusive). A trailing asterisk means all types from n to $N$ (inclusive). A middle asterisk means all types from m to n (inclusive). 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 [reaxff pair_coeff](pair_reaxff) 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. ::: versionadded 3Aug2022 ::: The optional keyword *delete* enables the periodic removal of molecules from the system. Criteria for deletion can be either a list of specific chemical formulae or a range of molecular weights. Molecules are deleted every *Nfreq* timesteps, and bond connectivity is determined using the *Nevery* and *Nrepeat* keywords. The *filedel* argument is the name of the output file that records the species that are removed from the system. The *specieslist* keyword permits specific chemical species to be deleted. The *Nspecies* argument specifies how many species are eligible for deletion and is followed by a list of chemical formulae, whose strings are compared to species identified by this fix. For example, \"specieslist 2 CO CO2\" deletes molecules that are identified as \"CO\" and \"CO2\" in the species output file. When using the *specieslist* keyword, the *filedel* file has the following format: the first line lists the chemical formulae eligible for deletion, and each additional line contains the timestep on which a molecule deletion occurs and the number of each species deleted on that timestep. The *masslimit* keyword permits deletion of molecules with molecular weights between *massmin* and *massmax*. When using the *masslimit* keyword, each line of the *filedel* file contains the timestep on which deletions occurs, followed by how many of each species are deleted (with quantities preceding chemical formulae). The *specieslist* and *masslimit* keywords cannot both be used in the same *reaxff/species* fix. The *delete_rate_limit* keyword can enforce an upper limit on the overall rate of molecule deletion. The number of deletion occurrences is limited to Nlimit within an interval of Nsteps timesteps. Nlimit can be specified with an equal-style [variable](variable). When using the *delete_rate_limit* keyword, no deletions are permitted to occur within the first Nsteps timesteps of the first run (after reading a either a data or restart file). ------------------------------------------------------------------------ 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. Nrepeat\*Nevery can not exceed Nfreq. 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](restart). None of the [fix_modify](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](Howto_output). 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](run) command. This fix is not invoked during [energy minimization](minimize). ------------------------------------------------------------------------ Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the [Accelerator packages](Speed_packages) page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, INTEL, KOKKOS, OPENMP, and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the [Build package](Build_package) page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the [-suffix command-line switch](Run_options) when you invoke LAMMPS, or you can use the [suffix](suffix) command in your input script. See the [Accelerator packages](Speed_packages) page for more instructions on how to use the accelerated styles effectively. ------------------------------------------------------------------------ ## Restrictions The \"fix reaxff/species\" requires that [pair_style reaxff](pair_reaxff) is used. This fix is part of the REAXFF package. It is only enabled if LAMMPS was built with that package. See the [Build package](Build_package) page for more info. To write gzipped species files, you must compile LAMMPS with the -DLAMMPS_GZIP option. ## Related commands [pair_style reaxff](pair_reaxff), [fix reaxff/bonds](fix_reaxff_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.