forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11903 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
ec54a12815
commit
1fb3407215
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@ -49,60 +49,66 @@ fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Write out the chemical species information computed by the ReaxFF potential
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specified by <A HREF = "pair_reax_c.html">pair_style reax/c</A>. Bond-order values
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(either averaged or instantaneous, depending on value of <I>Nrepeat</I>)
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are used to determine chemical bonds. Every <I>Nfreq</I> timesteps,
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chemical species information is written to <I>filename</I> as a two line output.
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The first line is a header containing labels. The second line consists
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of the following: timestep, total number of molecules,
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total number of distinct species, number of molecules of each species.
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The chemical formula of each species is given in the first line.
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<P>Write out the chemical species information computed by the ReaxFF
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potential specified by <A HREF = "pair_reax_c.html">pair_style reax/c</A>.
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Bond-order values (either averaged or instantaneous, depending on
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value of <I>Nrepeat</I>) are used to determine chemical bonds. Every
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<I>Nfreq</I> timesteps, chemical species information is written to
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<I>filename</I> as a two line output. The first line is a header
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containing labels. The second line consists of the following:
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timestep, total number of molecules, total number of distinct species,
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number of molecules of each species. In this context, "species" means
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a unique molecule. The chemical formula of each species is given in
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the first line.
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</P>
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<P>Optional keyword <I>cutoff</I> can be assigned to change the minimum bond-order values
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used in identifying chemical bonds between pairs of atoms. Bond-order cutoffs
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should be carefully chosen, as bond-order cutoffs that are too small may include
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too many bonds (which will result in an error), while too-large cutoffs will
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result in fragmented molecules. The default cutoff of 0.3 usually gives good
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estimate.
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<P>Optional keyword <I>cutoff</I> can be assigned to change the minimum
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bond-order values used in identifying chemical bonds between pairs of
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atoms. Bond-order cutoffs should be carefully chosen, as bond-order
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cutoffs that are too small may include too many bonds (which will
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result in an error), while cutoffs that are too large will result in
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fragmented molecules. The default cutoff of 0.3 usually gives good
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results.
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</P>
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<P>Optional keyword <I>element</I> can be used to specify the chemical symbol printed for
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each LAMMPS atom type. The number of symbols must match the number of LAMMPS atom types
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and each symbol must consist of 1 or 2 alphanumeric characters. Normally, these
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symbols should be chosen to match the chemical identity of each LAMMPS atom type,
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as specified using the <A HREF = "pair_reax_c.html">reax/c pair_coeff</A> command and
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the ReaxFF force field file.
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<P>The optional keyword <I>element</I> can be used to specify the chemical
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symbol printed for each LAMMPS atom type. The number of symbols must
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match the number of LAMMPS atom types and each symbol must consist of
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1 or 2 alphanumeric characters. Normally, these symbols should be
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chosen to match the chemical identity of each LAMMPS atom type, as
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specified using the <A HREF = "pair_reax_c.html">reax/c pair_coeff</A> command and
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the ReaxFF force field file.
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</P>
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<P>Optional keyword <I>position</I> writes center-of-mass positions of each identified
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molecules to file <I>filepos</I> every <I>posfreq</I> timesteps. The first line contains
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information on timestep, total number of molecules, total number of distinct
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species, and box dimensions. The second line is a header containing labels.
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From the third line downward, each molecule writes a line of output containing
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the following information: molecule ID, number of atoms in this molecule, chemical
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formula, total charge, and center-of-mass xyz positions of this molecule. The xyz
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positions are in fractional coordinates relative to the box dimensions.
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<P>The optional keyword <I>position</I> writes center-of-mass positions of
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each identified molecules to file <I>filepos</I> every <I>posfreq</I> timesteps.
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The first line contains information on timestep, total number of
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molecules, total number of distinct species, and box dimensions. The
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second line is a header containing labels. From the third line
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downward, each molecule writes a line of output containing the
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following information: molecule ID, number of atoms in this molecule,
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chemical formula, total charge, and center-of-mass xyz positions of
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this molecule. The xyz positions are in fractional coordinates
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relative to the box dimensions.
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</P>
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<P>Keyword <I>position</I> output file <I>filepos</I> can contain the wildcard character "*".
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If the "*" character appears in <I>filepos</I>, then one file per snapshot is written
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at <I>posfreq</I> and the "*" character is replaced with the timestep value.
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For example, AuO.pos.* becomes AuO.pos.0, AuO.pos.1000, etc.
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<P>For the keyword <I>position</I>, the <I>filepos</I> is the name of the output
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file. It can contain the wildcard character "*". If the "*"
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character appears in <I>filepos</I>, then one file per snapshot is written
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at <I>posfreq</I> and the "*" character is replaced with the timestep
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value. For example, AuO.pos.* becomes AuO.pos.0, AuO.pos.1000, etc.
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</P>
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<HR>
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<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
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timesteps the bond-order values are sampled to get the average bond
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order. The species analysis is performed using the average bond-order
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on timesteps
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that are a multiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
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bond-order samples, computed in the preceding portion of the simulation every
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<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
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<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
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contributing to the average bond-order cannot overlap, i.e. Nfreq >
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(Nrepeat-1)*Nevery is required.
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on timesteps that are a multiple of <I>Nfreq</I>. The average is over
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<I>Nrepeat</I> bond-order samples, computed in the preceding portion of the
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simulation every <I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of
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<I>Nevery</I> and <I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also,
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the timesteps contributing to the average bond-order cannot overlap,
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i.e. Nfreq > (Nrepeat-1)*Nevery is required.
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</P>
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<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order values on
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timesteps 90,92,94,96,98,100 will be used to compute the average bond-order
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for the species analysis output on timestep 100.
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<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order
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values on timesteps 90,92,94,96,98,100 will be used to compute the
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average bond-order for the species analysis output on timestep 100.
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</P>
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<HR>
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@ -110,11 +116,27 @@ timesteps 90,92,94,96,98,100 will be used to compute the average bond-order
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
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commands</A>. No parameter of this fix can
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be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
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This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
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are relevant to this fix.
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</P>
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<P>This fix computes both a global vector of length 2 and a per-atom
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vector, either of which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
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commands</A>. The values in the global
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vector are "intensive".
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</P>
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<P>The 2 values in the global vector are as follows:
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</P>
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<UL><LI>1 = total number of molecules
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<LI>2 = total number of distinct species
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</UL>
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<P>The per-atom vector stores the molecule ID for each atom as identified
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by the fix. If an atom is not in a molecule, its ID will be 0.
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For atoms in the same molecule, the molecule ID for all of them
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will be the same and will be equal to the smallest atom ID of
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any atom in the molecule.
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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@ -39,60 +39,66 @@ fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH
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[Description:]
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Write out the chemical species information computed by the ReaxFF potential
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specified by "pair_style reax/c"_pair_reax_c.html. Bond-order values
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(either averaged or instantaneous, depending on value of {Nrepeat})
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are used to determine chemical bonds. Every {Nfreq} timesteps,
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chemical species information is written to {filename} as a two line output.
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The first line is a header containing labels. The second line consists
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of the following: timestep, total number of molecules,
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total number of distinct species, number of molecules of each species.
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The chemical formula of each species is given in the first line.
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Write out the chemical species information computed by the ReaxFF
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potential specified by "pair_style reax/c"_pair_reax_c.html.
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Bond-order values (either averaged or instantaneous, depending on
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value of {Nrepeat}) are used to determine chemical bonds. Every
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{Nfreq} timesteps, chemical species information is written to
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{filename} as a two line output. The first line is a header
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containing labels. The second line consists of the following:
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timestep, total number of molecules, total number of distinct species,
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number of molecules of each species. In this context, "species" means
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a unique molecule. The chemical formula of each species is given in
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the first line.
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Optional keyword {cutoff} can be assigned to change the minimum bond-order values
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used in identifying chemical bonds between pairs of atoms. Bond-order cutoffs
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should be carefully chosen, as bond-order cutoffs that are too small may include
|
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too many bonds (which will result in an error), while too-large cutoffs will
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result in fragmented molecules. The default cutoff of 0.3 usually gives good
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estimate.
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Optional keyword {cutoff} can be assigned to change the minimum
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bond-order values used in identifying chemical bonds between pairs of
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atoms. Bond-order cutoffs should be carefully chosen, as bond-order
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cutoffs that are too small may include too many bonds (which will
|
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result in an error), while cutoffs that are too large will result in
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fragmented molecules. The default cutoff of 0.3 usually gives good
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results.
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Optional keyword {element} can be used to specify the chemical symbol printed for
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each LAMMPS atom type. The number of symbols must match the number of LAMMPS atom types
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and each symbol must consist of 1 or 2 alphanumeric characters. Normally, these
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symbols should be chosen to match the chemical identity of each LAMMPS atom type,
|
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as specified using the "reax/c pair_coeff"_pair_reax_c.html command and
|
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the ReaxFF force field file.
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The optional keyword {element} can be used to specify the chemical
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symbol printed for each LAMMPS atom type. The number of symbols must
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match the number of LAMMPS atom types and each symbol must consist of
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1 or 2 alphanumeric characters. Normally, these symbols should be
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chosen to match the chemical identity of each LAMMPS atom type, as
|
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specified using the "reax/c pair_coeff"_pair_reax_c.html command and
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the ReaxFF force field file.
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Optional keyword {position} writes center-of-mass positions of each identified
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molecules to file {filepos} every {posfreq} timesteps. The first line contains
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information on timestep, total number of molecules, total number of distinct
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species, and box dimensions. The second line is a header containing labels.
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From the third line downward, each molecule writes a line of output containing
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the following information: molecule ID, number of atoms in this molecule, chemical
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formula, total charge, and center-of-mass xyz positions of this molecule. The xyz
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positions are in fractional coordinates relative to the box dimensions.
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The optional keyword {position} writes center-of-mass positions of
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each identified molecules to file {filepos} every {posfreq} timesteps.
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The first line contains information on timestep, total number of
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molecules, total number of distinct species, and box dimensions. The
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second line is a header containing labels. From the third line
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downward, each molecule writes a line of output containing the
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following information: molecule ID, number of atoms in this molecule,
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chemical formula, total charge, and center-of-mass xyz positions of
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this molecule. The xyz positions are in fractional coordinates
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relative to the box dimensions.
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Keyword {position} output file {filepos} can contain the wildcard character "*".
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If the "*" character appears in {filepos}, then one file per snapshot is written
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at {posfreq} and the "*" character is replaced with the timestep value.
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For example, AuO.pos.* becomes AuO.pos.0, AuO.pos.1000, etc.
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For the keyword {position}, the {filepos} is the name of the output
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file. It can contain the wildcard character "*". If the "*"
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character appears in {filepos}, then one file per snapshot is written
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at {posfreq} and the "*" character is replaced with the timestep
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value. For example, AuO.pos.* becomes AuO.pos.0, AuO.pos.1000, etc.
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:line
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The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
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timesteps the bond-order values are sampled to get the average bond
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order. The species analysis is performed using the average bond-order
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on timesteps
|
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that are a multiple of {Nfreq}. The average is over {Nrepeat}
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bond-order samples, computed in the preceding portion of the simulation every
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{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and
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{Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps
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contributing to the average bond-order cannot overlap, i.e. Nfreq >
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(Nrepeat-1)*Nevery is required.
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on timesteps that are a multiple of {Nfreq}. The average is over
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{Nrepeat} bond-order samples, computed in the preceding portion of the
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simulation every {Nevery} timesteps. {Nfreq} must be a multiple of
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{Nevery} and {Nevery} must be non-zero even if {Nrepeat} is 1. Also,
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the timesteps contributing to the average bond-order cannot overlap,
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i.e. Nfreq > (Nrepeat-1)*Nevery is required.
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For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order values on
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timesteps 90,92,94,96,98,100 will be used to compute the average bond-order
|
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for the species analysis output on timestep 100.
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For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order
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values on timesteps 90,92,94,96,98,100 will be used to compute the
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average bond-order for the species analysis output on timestep 100.
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:line
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@ -100,11 +106,27 @@ timesteps 90,92,94,96,98,100 will be used to compute the average bond-order
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No information about this fix is written to "binary restart
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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
|
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vector, either of which can be accessed by various "output
|
||||
commands"_Section_howto.html#howto_15. The values in the global
|
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vector are "intensive".
|
||||
|
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The 2 values in the global vector are as follows:
|
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1 = total number of molecules
|
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2 = total number of distinct species :ul
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The per-atom vector stores the molecule ID for each atom as identified
|
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by the fix. If an atom is not in a molecule, its ID will be 0.
|
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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
|
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any atom in the molecule.
|
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|
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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
|
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minimization"_minimize.html.
|
||||
|
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[Restrictions:]
|
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@ -129,4 +151,3 @@ reax/bonds"_fix_reax_bonds.html
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The default values for bond-order cutoffs are 0.3 for all I-J pairs. The
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default element symbols are C, H, O, N. Position files are not written
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by default.
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|
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@ -189,10 +189,6 @@ performed. This can be used when the <I>reax/c</I> style is used as part
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of the <I>hybrid</I> pair style. The NULL values are placeholders for atom
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types that will be used with other potentials.
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</P>
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<P>IMPORTANT NOTE: Currently the reax/c pair style cannot be used as part
|
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of the <I>hybrid</I> pair style. Some additional work still need to be
|
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done to enable this.
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</P>
|
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<P>As an example, say your LAMMPS simulation has 4 atom types and the
|
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elements are ordered as C, H, O, N in the <I>ffield</I> file. If you want
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the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
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|
|
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@ -183,10 +183,6 @@ performed. This can be used when the {reax/c} style is used as part
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of the {hybrid} pair style. The NULL values are placeholders for atom
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types that will be used with other potentials.
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IMPORTANT NOTE: Currently the reax/c pair style cannot be used as part
|
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of the {hybrid} pair style. Some additional work still need to be
|
||||
done to enable this.
|
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|
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As an example, say your LAMMPS simulation has 4 atom types and the
|
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elements are ordered as C, H, O, N in the {ffield} file. If you want
|
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the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
|
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|
|
|
|||
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Reference in New Issue