2006-09-22 00:22:34 +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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<H3>replicate command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>replicate nx ny nz
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</PRE>
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<UL><LI>nx,ny,nz = replication factors in each dimension
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>replicate 2 3 2
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Replicate the current simulation one or more times in each dimension.
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For example, replication factors of 2,2,2 will create a simulation
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with 8x as many atoms by doubling the simulation domain in each
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dimension. A replication factor of 1 in a dimension leaves the
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2014-05-13 22:04:47 +08:00
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simulation domain unchanged. When the new simulation box is created
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it is also partitioned into a regular 3d grid of rectangular bricks,
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one per processor, based on the number of processors being used and
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the settings of the <A HREF = "processors.html">processors</A> command. The
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partitioning can later be changed by the <A HREF = "balance.html">balance</A> or
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<A HREF = "fix_balance.html">fix balance</A> commands.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>All properties of the atoms are replicated, including their
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2009-01-06 06:26:31 +08:00
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velocities, which may or may not be desirable. New atom IDs are
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assigned to new atoms, as are molecule IDs. Bonds and other topology
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interactions are created between pairs of new atoms as well as between
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old and new atoms. This is done by using the image flag for each atom
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2013-08-01 22:38:21 +08:00
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to "unwrap" it out of the periodic box before replicating it.
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</P>
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<P>This means that any molecular bond you specify in the original data
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file that crosses a periodic boundary should be between two atoms with
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image flags that differ by 1. This will allow the bond to be
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unwrapped appropriately.
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2006-09-22 00:22:34 +08:00
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>A 2d simulation cannot be replicated in the z dimension.
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</P>
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<P>If a simulation is non-periodic in a dimension, care should be used
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when replicating it in that dimension, as it may put atoms nearly on
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top of each other.
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</P>
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2013-08-01 22:38:21 +08:00
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<P>IMPORTANT NOTE: You cannot use the replicate command on a system which
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has a molecule that spans the box and is bonded to itself across a
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periodic boundary, so that the molecule is efffectively a loop. A
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simple example would be a linear polymer chain that spans the
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simulation box and bonds back to itself across the periodic boundary.
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More realistic examples would be a CNT (meant to be an infinitely long
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CNT) or a graphene sheet or a bulk periodic crystal where there are
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explicit bonds specified between near neighbors. (Note that this only
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applies to systems that have permanent bonds as specified in the data
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file. A CNT that is just atoms modeled with the <A HREF = "pair_airebo.html">AIREBO
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potential</A> has no such permanent bonds, so it can be
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replicated.) The reason replication does not work with those systems
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is that the image flag settings described above cannot be made
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consistent. I.e. it is not possible to define images flags so that
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when every pair of bonded atoms is unwrapped (using the image flags),
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they will be close to each other. The only way the replicate command
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2012-09-21 22:52:59 +08:00
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could work in this scenario is for it to break a bond, insert more
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2013-08-01 22:38:21 +08:00
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atoms, and re-connect the loop for the larger simulation box. But it
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is not clever enough to do this. So you will have to construct a
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larger version of your molecule as a pre-processing step and input a
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new data file to LAMMPS.
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2012-09-21 22:52:59 +08:00
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</P>
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2006-09-22 00:22:34 +08:00
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<P>If the current simulation was read in from a restart file (before a
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run is performed), there can have been no fix information stored in
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the file for individual atoms. Similarly, no fixes can be defined at
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the time the replicate command is used that require vectors of atom
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information to be stored. This is because the replicate command does
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not know how to replicate that information for new atoms it creates.
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</P>
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2008-10-08 23:02:35 +08:00
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<P>Replicating a system that has rigid bodies (defined via the <A HREF = "fix_rigid.html">fix
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rigid</A> command), either currently defined or that
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created the restart file which was read in before replicating, can
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cause problems if there is a bond between a pair of rigid bodies that
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straddle a periodic boundary. This is because the periodic image
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information for particles in the rigid bodies are set differently than
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for a non-rigid system and can result in a new bond being created that
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spans the periodic box. Thus you cannot use the replicate command in
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this scenario.
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</P>
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2006-09-22 00:22:34 +08:00
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<P><B>Related commands:</B> none
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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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