This directory has input scripts which demonstrate how to use the
replicate command both for systems with and without periodic bond
loops.  A periodic bond loop is where a chain of bonds spans a
periodic dimension of the box and includes one or more bonds which
cross the periodic boundary to close the loop.

To run these scripts, LAMMPS should be built with the MOLECULE and
CLASS2 packages.  The latter is only needed for the CNT example.

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These scripts are tiny examples which illustrate both kinds of
systems.  Each produces a series of images which can be visualized.
If the 3 lines for a dump movie command are uncommented, a MPG movie
is produced, assuming LAMMPS is build with FFMPEG support.

in.replicate.bond.x    # linear chains in x direction, bond loop in x
in.replcate.bond.x.y   # 2d grid of bonded atoms, bond loops in x and y
in.replicate.bond.xy   # linear chains in diagonal direction, bond loop in x and y
in.replicate.bond.noloop  # linear chains in x direction, no bond loop

If you do not use the bond/periodic keyword with the replicate command
in the first 3 of these scripts (which have periodic bond loops), and
visualize the dynamics of hee simulation, you will see how the
replication creates a bogus system.

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This script is for a complex system of 3 orthogonal CNTs which has
periodic bond loops in all 3 dimensions xyz.

in.replicate.cnt
