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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14255 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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79 lines
3.0 KiB
HTML
<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H3>compute cluster/atom command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID cluster/atom cutoff
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>cluster/atom = style name of this compute command
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<LI>cutoff = distance within which to label atoms as part of same cluster (distance units)
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute 1 all cluster/atom 1.0
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Define a computation that assigns each atom a cluster ID.
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</P>
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<P>A cluster is defined as a set of atoms, each of which is within the
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cutoff distance from one or more other atoms in the cluster. If an
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atom has no neighbors within the cutoff distance, then it is a 1-atom
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cluster. The ID of every atom in the cluster will be the smallest
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atom ID of any atom in the cluster.
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</P>
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<P>Only atoms in the compute group are clustered and assigned cluster
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IDs. Atoms not in the compute group are assigned a cluster ID = 0.
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</P>
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<P>The neighbor list needed to compute this quantity is constructed each
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time the calculation is performed (i.e. each time a snapshot of atoms
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is dumped). Thus it can be inefficient to compute/dump this quantity
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too frequently or to have multiple compute/dump commands, each of a
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<I>clsuter/atom</I> style.
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</P>
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<P>IMPORTANT NOTE: If you have a bonded system, then the settings of
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<A HREF = "special_bonds.html">special_bonds</A> command can remove pairwise
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interactions between atoms in the same bond, angle, or dihedral. This
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is the default setting for the <A HREF = "special_bonds.html">special_bonds</A>
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command, and means those pairwise interactions do not appear in the
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neighbor list. Because this fix uses the neighbor list, it also means
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those pairs will not be included when computing the clusters. This
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does not apply when using long-range coulomb (<I>coul/long</I>, <I>coul/msm</I>,
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<I>coul/wolf</I> or similar. One way to get around this would be to set
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special_bond scaling factors to very tiny numbers that are not exactly
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zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
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use the <A HREF = "rerun.html">rerun</A> command to compute the clusters for
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snapshots in the dump file. The rerun script can use a
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<A HREF = "special_bonds.html">special_bonds</A> command that includes all pairs in
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the neighbor list.
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</P>
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<P><B>Output info:</B>
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</P>
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<P>This compute calculates a per-atom vector, which can be accessed by
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any command that uses per-atom values from a compute as input. See
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<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
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LAMMPS output options.
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</P>
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<P>The per-atom vector values will be an ID > 0, as explained above.
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</P>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute_coord_atom.html">compute coord/atom</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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