replicate nx ny nz keyword
nx,ny,nz = replication factors in each dimension
- optional keyword = bbox bbox = only check atoms in replicas that overlap with a processor’s sub-domain
replicate 2 3 2
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 processors command. The partitioning can later be changed by the balance or 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.
The optional keyword bbox uses a bounding box to only check atoms in replicas that overlap with a processor’s sub-domain when assigning atoms to processors, and thus can result in substantial speedups for calculations using a large number of processors. It does require temporarily using more memory.
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.
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 effectively 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 AIREBO potential 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 must not be any 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. To work around this restriction, restart files may be converted into data files and fixes may be undefined via the unfix command before and redefined after the replicate command.
Related commands: none