From e85fdb8d637f28084ce4a4db97865e8a54f902f6 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 23 May 2013 18:02:16 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9900 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_reaxc_species.html | 143 +++++++++++++++++++++++++++++++++++++ 1 file changed, 143 insertions(+) create mode 100644 doc/fix_reaxc_species.html diff --git a/doc/fix_reaxc_species.html b/doc/fix_reaxc_species.html new file mode 100644 index 0000000000..e1af71daa4 --- /dev/null +++ b/doc/fix_reaxc_species.html @@ -0,0 +1,143 @@ + +
LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

fix reax/c/species command +

+

Syntax: +

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

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. +

+