2007-03-27 05:33:10 +08:00
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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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2014-05-13 22:04:47 +08:00
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<H3>comm_modify command
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2007-03-27 05:33:10 +08:00
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</H3>
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<P><B>Syntax:</B>
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</P>
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2014-05-13 22:04:47 +08:00
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<PRE>comm_modify keyword value ...
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2007-03-27 05:33:10 +08:00
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</PRE>
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<UL><LI>zero or more keyword/value pairs may be appended
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2008-02-15 07:13:41 +08:00
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<LI>keyword = <I>mode</I> or <I>cutoff</I> or <I>group</I> or <I>vel</I>
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2008-02-15 07:13:41 +08:00
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2014-05-13 22:04:47 +08:00
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<PRE> <I>mode</I> value = <I>single</I> or <I>multi</I> = communicate atoms within a single or multiple distances
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<I>cutoff</I> value = Rcut (distance units) = communicate atoms from this far away
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2009-11-10 02:30:55 +08:00
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<I>group</I> value = group-ID = only communicate atoms in the group
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<I>vel</I> value = <I>yes</I> or <I>no</I> = do or do not communicate velocity info with ghost atoms
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2008-02-15 07:13:41 +08:00
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</PRE>
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2007-03-27 05:33:10 +08:00
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</UL>
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<P><B>Examples:</B>
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</P>
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2014-06-02 22:25:02 +08:00
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<PRE>comm_modify mode multi
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comm_modify mode multi group solvent
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comm_modify vel yes
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comm_modify cutoff 5.0 vel yes
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2007-03-27 05:33:10 +08:00
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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 inter-processor
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communication of atom information that occurs each timestep as
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coordinates and other properties are exchanged between neighboring
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processors and stored as properties of ghost atoms.
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</P>
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<P>IMPORTANT NOTE: These options apply to the currently defined comm
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style. When you specify a <A HREF = "comm_style.html">comm_style</A> command, all
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communication settings are restored to their default values, including
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those previously reset by a comm_modify command. Thus if your input
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script specifies a comm_style command, you should use the comm_modify
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command after it.
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</P>
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<P>The <I>mode</I> keyword determines whether a single or multiple cutoff
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distances are used to determine which atoms to communicate.
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2007-03-27 05:33:10 +08:00
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</P>
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2014-05-13 22:04:47 +08:00
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<P>The default mode is <I>single</I> which means each processor acquires
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2007-03-27 05:33:10 +08:00
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information for ghost atoms that are within a single distance from its
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sub-domain. The distance is the maximum of the neighbor cutoff for
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all atom type pairs.
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</P>
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<P>For many systems this is an efficient algorithm, but for systems with
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widely varying cutoffs for different type pairs, the <I>multi</I> mode can
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2007-03-27 05:33:10 +08:00
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be faster. In this case, each atom type is assigned its own distance
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cutoff for communication purposes, and fewer atoms will be
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communicated. See the <A HREF = "neighbor.html">neighbor multi</A> command for a
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neighbor list construction option that may also be beneficial for
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simulations of this kind.
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</P>
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2014-05-13 22:04:47 +08:00
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<P>The <I>cutoff</I> keyword allows you to set a ghost cutoff distance, which
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2008-08-21 22:03:21 +08:00
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is the distance from the borders of a processor's sub-domain at which
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2008-08-21 21:53:06 +08:00
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ghost atoms are acquired from other processors. By default the ghost
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2008-08-21 22:03:21 +08:00
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cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin. See
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the <A HREF = "neighbor.html">neighbor</A> command for more information about the
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skin distance. If the specified Rcut is greater than the neighbor
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cutoff, then extra ghost atoms will be acquired. If it is smaller,
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the ghost cutoff is set to the neighbor cutoff.
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2008-08-21 21:53:06 +08:00
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</P>
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2012-10-12 00:31:08 +08:00
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<P>These are simulation scenarios in which it may be useful or even
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necessary to set a ghost cutoff > neighbor cutoff:
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2008-08-21 21:53:06 +08:00
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</P>
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<UL><LI>a single polymer chain with bond interactions, but no pairwise interactions
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<LI>bonded interactions (e.g. dihedrals) extend further than the pairwise cutoff
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<LI>ghost atoms beyond the pairwise cutoff are needed for some computation
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</UL>
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2012-10-13 07:50:19 +08:00
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<P>In the first scenario, a pairwise potential is not defined. Thus the
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pairwise neighbor cutoff will be 0.0. But ghost atoms are still
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2008-08-21 21:53:06 +08:00
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needed for computing bond, angle, etc interactions between atoms on
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2012-10-13 07:50:19 +08:00
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different processors, or when the interaction straddles a periodic
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2012-10-12 00:31:08 +08:00
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boundary.
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</P>
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<P>The appropriate ghost cutoff depends on the <A HREF = "newton.html">newton bond</A>
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setting. For newton bond <I>off</I>, the distance needs to be the furthest
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distance between any two atoms in the bond, angle, etc. E.g. the
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distance between 1-4 atoms in a dihedral. For newton bond <I>on</I>, the
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distance between the central atom in the bond, angle, etc and any
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other atom is sufficient. E.g. the distance between 2-4 atoms in a
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dihedral.
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2008-08-21 21:53:06 +08:00
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</P>
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<P>In the second scenario, a pairwise potential is defined, but its
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neighbor cutoff is not sufficiently long enough to enable bond, angle,
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etc terms to be computed. As in the previous scenario, an appropriate
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ghost cutoff should be set.
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</P>
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<P>In the last scenario, a <A HREF = "fix.html">fix</A> or <A HREF = "compute.html">compute</A> or
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<A HREF = "pair_style.html">pairwise potential</A> needs to calculate with ghost
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atoms beyond the normal pairwise cutoff for some computation it
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performs (e.g. locate neighbors of ghost atoms in a multibody pair
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potential). Setting the ghost cutoff appropriately can insure it will
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find the needed atoms.
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</P>
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2012-10-13 07:50:19 +08:00
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<P>IMPORTANT NOTE: In these scenarios, if you do not set the ghost cutoff
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long enough, and if there is only one processor in a periodic
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dimension (e.g. you are running in serial), then LAMMPS may "find" the
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atom it is looking for (e.g. the partner atom in a bond), that is on
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the far side of the simulation box, across a periodic boundary. This
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will typically lead to bad dynamics (i.e. the bond length is now the
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simulation box length). To detect if this is happening, see the
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<A HREF = "neigh_modify.html">neigh_modify cluster</A> command.
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</P>
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2014-05-13 22:04:47 +08:00
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<P>The <I>group</I> keyword will limit communication to atoms in the specified
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2009-11-10 02:30:55 +08:00
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group. This can be useful for models where no ghost atoms are needed
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for some kinds of particles. All atoms (not just those in the
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specified group) will still migrate to new processors as they move.
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The group specified with this option must also be specified via the
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<A HREF = "atom_modify.html">atom_modify first</A> command.
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</P>
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2014-05-13 22:04:47 +08:00
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<P>The <I>vel</I> keyword enables velocity information to be communicated with
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2009-11-10 02:30:55 +08:00
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ghost particles. Depending on the <A HREF = "atom_style.html">atom_style</A>,
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velocity info includes the translational velocity, angular velocity,
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and angular momentum of a particle. If the <I>vel</I> option is set to
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<I>yes</I>, then ghost atoms store these quantities; if <I>no</I> then they do
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not. The <I>yes</I> setting is needed by some pair styles which require
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the velocity state of both the I and J particles to compute a pairwise
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I,J interaction.
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</P>
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2011-03-08 07:01:59 +08:00
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<P>Note that if the <A HREF = "fix_deform.html">fix deform</A> command is being used
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with its "remap v" option enabled, then the velocities for ghost atoms
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(in the fix deform group) mirrored across a periodic boundary will
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also include components due to any velocity shift that occurs across
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that boundary (e.g. due to dilation or shear).
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</P>
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2007-03-27 05:33:10 +08:00
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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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2014-05-13 22:04:47 +08:00
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<P><A HREF = "comm_style.html">comm_style</A>, <A HREF = "neighbor.html">neighbor</A>
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2007-03-27 05:33:10 +08:00
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</P>
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<P><B>Default:</B>
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</P>
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2014-05-13 22:04:47 +08:00
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<P>The option defauls are mode = single, group = all, cutoff = 0.0, vel =
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no. The cutoff default of 0.0 means that ghost cutoff = neighbor
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cutoff = pairwise force cutoff + neighbor skin.
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2007-03-27 05:33:10 +08:00
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</P>
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</HTML>
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