From 1fb3407215036cc4ecafcd6bc42e6f4e75c80784 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 2 May 2014 21:38:24 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11903 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_reaxc_species.html | 118 +++++++++++++++++++++--------------- doc/fix_reaxc_species.txt | 119 ++++++++++++++++++++++--------------- doc/pair_reax_c.html | 4 -- doc/pair_reax_c.txt | 4 -- 4 files changed, 140 insertions(+), 105 deletions(-) diff --git a/doc/fix_reaxc_species.html b/doc/fix_reaxc_species.html index 5289f6ed49..a507564a2d 100644 --- a/doc/fix_reaxc_species.html +++ b/doc/fix_reaxc_species.html @@ -49,60 +49,66 @@ fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH

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. +

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 too-large cutoffs will -result in fragmented molecules. The default cutoff of 0.3 usually gives good -estimate. +

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.

-

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 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. +

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.

-

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. +

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. +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. +

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.

@@ -110,11 +116,27 @@ timesteps 90,92,94,96,98,100 will be used to compute the average bond-order

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. +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: +

+ +

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:

diff --git a/doc/fix_reaxc_species.txt b/doc/fix_reaxc_species.txt index 87ab883026..ef8aa5a702 100644 --- a/doc/fix_reaxc_species.txt +++ b/doc/fix_reaxc_species.txt @@ -39,60 +39,66 @@ fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH [Description:] -Write out the chemical species information computed by the ReaxFF potential -specified by "pair_style reax/c"_pair_reax_c.html. 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. +Write out the chemical species information computed by the ReaxFF +potential specified by "pair_style reax/c"_pair_reax_c.html. +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 too-large cutoffs will -result in fragmented molecules. The default cutoff of 0.3 usually gives good -estimate. +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. -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"_pair_reax_c.html command and -the ReaxFF force field file. +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"_pair_reax_c.html 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. +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. -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. +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. :line 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. +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. +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. :line @@ -100,11 +106,27 @@ timesteps 90,92,94,96,98,100 will be used to compute the average bond-order No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +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"_Section_howto.html#howto_15. 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 :ul + +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.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] @@ -129,4 +151,3 @@ reax/bonds"_fix_reax_bonds.html 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. - diff --git a/doc/pair_reax_c.html b/doc/pair_reax_c.html index a9d78ac2a5..49e0e59e1a 100644 --- a/doc/pair_reax_c.html +++ b/doc/pair_reax_c.html @@ -189,10 +189,6 @@ performed. This can be used when the reax/c style is used as part of the hybrid pair style. The NULL values are placeholders for atom types that will be used with other potentials.

-

IMPORTANT NOTE: Currently the reax/c pair style cannot be used as part -of the hybrid pair style. Some additional work still need to be -done to enable this. -

As an example, say your LAMMPS simulation has 4 atom types and the elements are ordered as C, H, O, N in the ffield file. If you want the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be diff --git a/doc/pair_reax_c.txt b/doc/pair_reax_c.txt index 5a3d8ed3a5..4aba65dc53 100644 --- a/doc/pair_reax_c.txt +++ b/doc/pair_reax_c.txt @@ -183,10 +183,6 @@ performed. This can be used when the {reax/c} style is used as part of the {hybrid} pair style. The NULL values are placeholders for atom types that will be used with other potentials. -IMPORTANT NOTE: Currently the reax/c pair style cannot be used as part -of the {hybrid} pair style. Some additional work still need to be -done to enable this. - As an example, say your LAMMPS simulation has 4 atom types and the elements are ordered as C, H, O, N in the {ffield} file. If you want the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be