forked from lijiext/lammps
87 lines
3.7 KiB
Plaintext
87 lines
3.7 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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replicate command :h3
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[Syntax:]
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replicate nx ny nz :pre
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nx,ny,nz = replication factors in each dimension :ul
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[Examples:]
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replicate 2 3 2 :pre
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[Description:]
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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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simulation domain unchanged.
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All properties of the atoms are replicated, including their
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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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to "unwrap" it out of the periodic box before replicating it. This
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means that molecular bonds you specify in the original data file that
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span the periodic box should be between two atoms with image flags
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that differ by 1. This will allow them to be unwrapped appropriately.
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[Restrictions:]
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A 2d simulation cannot be replicated in the z dimension.
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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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IMPORTANT NOTE: You cannot use the replicate command to replicate a
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molecule that is bonded to itself across a periodic boundary, so the
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molecule is efffectively a loop. A simple example would be a linear
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polymer chain that spans the simulation box and bonds back to itself
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across the periodic boundary. More realistic examples would be a CNT
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(meant to be an infinitely long CNT) or graphene sheet. (Note that
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this only applies to such molecules that have permanent bonds as
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specified in the data file. A CNT that is just atoms modeled with the
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"AIREBO potential"_pair_airebo.html has no such permanent bonds, so it
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is not a problem to replicate it.) The reason replicate does not work
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with those systems is that the image flag settings described above
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cannot be made consistent. I.e. it is not possible to have every pair
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of bonded atoms have the same image flags, when they are unwrapped so
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as to be close to each other. The only way the replicate command
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could work in this scenario is for it to break a bond, insert more
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atoms, and re-connect the loop for the larger simulation box. It is
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not clever enough to do this. So you will have to construct a larger
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version of your molecule as a pre-processing step and input a new data
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file to LAMMPS.
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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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Replicating a system that has rigid bodies (defined via the "fix
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rigid"_fix_rigid.html 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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[Related commands:] none
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[Default:] none
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