forked from lijiext/lammps
133 lines
5.4 KiB
HTML
133 lines
5.4 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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<HR>
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<H3>neigh_modify command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>neigh_modify keyword values ...
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</PRE>
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<UL><LI>one or more keyword/value pairs may be listed
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<PRE>keyword = <I>delay</I> or <I>every</I> or <I>check</I> or <I>exclude</I> or <I>page</I> or <I>one</I>
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<I>delay</I> value = N
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N = delay building until this many steps since last build
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<I>every</I> value = M
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M = build neighbor list every this many steps
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<I>check</I> value = <I>yes</I> or <I>no</I>
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<I>yes</I> = only build if some atom has moved half the skin distance or more
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<I>no</I> = always build on 1st step that <I>every</I> and <I>delay</I> are satisfied
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<I>exclude</I> values:
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type M N
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M,N = exclude if one atom in pair is type M, other is type N
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group group1-ID group2-ID
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group1-ID,group2-ID = exclude if one atom is in 1st group, other in 2nd
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molecule group-ID
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groupname = exclude if both atoms are in the same molecule and in the same group
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none
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delete all exclude settings
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<I>page</I> value = N
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N = number of pairs stored in a single neighbor page
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<I>one</I> value = N
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N = max number of neighbors of one atom
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>neigh_modify every 2 delay 10 check yes page 100000
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neigh_modify exclude type 2 3
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neigh_modify exclude group frozen frozen check no
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neigh_modify exclude group residue1 chain3
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neigh_modify exclude molecule rigid
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This command sets parameters that affect the pairwise neighbor list.
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</P>
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<P>The <I>every</I>, <I>delay</I>, and <I>check</I> options affect how often the list is
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built as a simulation runs. The <I>delay</I> setting means never build a
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new list until at least N steps after the previous build. The <I>every</I>
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setting means build the list every M steps (after the delay has
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passed). If the <I>check</I> setting is <I>no</I>, the list is built on the 1st
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step that satisfies the <I>delay</I> and <I>every</I> settings. If the <I>check</I>
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setting is <I>yes</I>, then the list is only built on a particular step if
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some atom has moved more than half the skin distance (specified in the
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<A HREF = "neighbor.html">neighbor</A> command) since the last build.
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</P>
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<P>When the rRESPA integrator is used (see the <A HREF = "run_style.html">run_style</A>
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command), the <I>every</I> and <I>delay</I> parameters refer to the longest
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(outermost) timestep.
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</P>
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<P>The <I>exclude</I> option turns off pairwise interactions between certain
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pairs of atoms, by not including them in the neighbor list. These are
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sample scenarios where this is useful:
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</P>
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<UL><LI>In crack simulations, pairwise interactions can be shut off between 2
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slabs of atoms to effectively create a crack.
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<LI>When a large collection of atoms is treated as frozen, interactions
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between those atoms can be turned off to save needless
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computation. E.g. Using the <A HREF = "fix_setforce.html">fix setforce</A> command
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to freeze a wall or portion of a bio-molecule.
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<LI>When one or more rigid bodies are specified, interactions within each
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body can be turned off to save needless computation. See the <A HREF = "fix_rigid.html">fix
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rigid</A> command for more details.
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</UL>
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<P>The <I>exclude type</I> option turns off the pairwise interaction if one
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atom is of type M and the other of type N. M can equal N. The
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<I>exclude group</I> option turns off the interaction if one atom is in the
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first group and the other is the second. Group1-ID can equal
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group2-ID. The <I>exclude molecule</I> option turns off the interaction if
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both atoms are in the specified group and in the same molecule, as
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determined by their molecule ID.
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</P>
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<P>Each of the exclude options can be specified multiple times. The
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<I>exclude type</I> option is the most efficient option to use; it requries
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only a single check, no matter how many times it has been specified.
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The other exclude options are more expensive if specified multiple
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times; they require one check for each time they have been specified.
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</P>
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<P>Note that the exclude options only affect pairwise interactions; see
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the <A HREF = "delete_bonds.html">delete_bonds</A> command for information on
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turning off bond interactions.
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</P>
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<P>The <I>page</I> and <I>one</I> options affect how memory is allocated for the
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neighbor lists. For most simulations the default settings for these
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options are fine, but if a very large problem is being run or a very
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long cutoff is being used, these parameters can be tuned. The indices
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of neighboring atoms are stored in "pages", which are allocated one
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after another as they fill up. The size of each page is set by the
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<I>page</I> value. A new page is allocated when the next atom's neighbors
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could potentially overflow the list. This threshhold is set by the
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<I>one</I> value which tells LAMMPS the maximum number of neighbor's one
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atom can have.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>If the "delay" setting is non-zero, then it must be a multiple of the
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"every" setting.
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</P>
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<P>The exclude molecule option can only be used with atom styles that
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define molecule IDs.
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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 = "neighbor.html">neighbor</A>, <A HREF = "delete_bonds.html">delete_bonds</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are delay = 10, every = 1, check = yes, exclude =
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none, page = 10000, and one = 2000.
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</P>
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</HTML>
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