Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/doc/html/_sources/replicate.txt
66312fac551dlammps-icms

Last Change
Raw File

replicate.txt
View Options

.. index:: replicate
replicate command
=================
Syntax
""""""
.. parsed-literal::
replicate nx ny nz
* nx,ny,nz = replication factors in each dimension
Examples
""""""""
.. parsed-literal::
replicate 2 3 2
Description
"""""""""""
Replicate the current simulation one or more times in each dimension.
For example, replication factors of 2,2,2 will create a simulation
with 8x as many atoms by doubling the simulation domain in each
dimension. A replication factor of 1 in a dimension leaves the
simulation domain unchanged. When the new simulation box is created
it is also partitioned into a regular 3d grid of rectangular bricks,
one per processor, based on the number of processors being used and
the settings of the :doc:`processors <processors>` command. The
partitioning can later be changed by the :doc:`balance <balance>` or
:doc:`fix balance <fix_balance>` commands.
All properties of the atoms are replicated, including their
velocities, which may or may not be desirable. New atom IDs are
assigned to new atoms, as are molecule IDs. Bonds and other topology
interactions are created between pairs of new atoms as well as between
old and new atoms. This is done by using the image flag for each atom
to "unwrap" it out of the periodic box before replicating it.
This means that any molecular bond you specify in the original data
file that crosses a periodic boundary should be between two atoms with
image flags that differ by 1. This will allow the bond to be
unwrapped appropriately.
Restrictions
""""""""""""
A 2d simulation cannot be replicated in the z dimension.
If a simulation is non-periodic in a dimension, care should be used
when replicating it in that dimension, as it may put atoms nearly on
top of each other.
.. note::
You cannot use the replicate command on a system which has a
molecule that spans the box and is bonded to itself across a periodic
boundary, so that the molecule is efffectively a loop. A simple
example would be a linear polymer chain that spans the simulation box
and bonds back to itself across the periodic boundary. More realistic
examples would be a CNT (meant to be an infinitely long CNT) or a
graphene sheet or a bulk periodic crystal where there are explicit
bonds specified between near neighbors. (Note that this only applies
to systems that have permanent bonds as specified in the data file. A
CNT that is just atoms modeled with the :doc:`AIREBO potential <pair_airebo>` has no such permanent bonds, so it can be
replicated.) The reason replication does not work with those systems
is that the image flag settings described above cannot be made
consistent. I.e. it is not possible to define images flags so that
when every pair of bonded atoms is unwrapped (using the image flags),
they will be close to each other. The only way the replicate command
could work in this scenario is for it to break a bond, insert more
atoms, and re-connect the loop for the larger simulation box. But it
is not clever enough to do this. So you will have to construct a
larger version of your molecule as a pre-processing step and input a
new data file to LAMMPS.
If the current simulation was read in from a restart file (before a
run is performed), there can have been no fix information stored in
the file for individual atoms. Similarly, no fixes can be defined at
the time the replicate command is used that require vectors of atom
information to be stored. This is because the replicate command does
not know how to replicate that information for new atoms it creates.
Replicating a system that has rigid bodies (defined via the :doc:`fix rigid <fix_rigid>` command), either currently defined or that
created the restart file which was read in before replicating, can
cause problems if there is a bond between a pair of rigid bodies that
straddle a periodic boundary. This is because the periodic image
information for particles in the rigid bodies are set differently than
for a non-rigid system and can result in a new bond being created that
spans the periodic box. Thus you cannot use the replicate command in
this scenario.
**Related commands:** none
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
c4science · Help