Hi,
I have copied a single solvent molecule using by “replicate” command. The dump file, however, contains only atoms (not bonds, angles, …) data which can be used for “Atoms” section in Data file; please help me how to replicate bonds, angles and dihedrals in addition to atoms. I’ve found this part in Users Manual of lammps but i don’t know what it means by image flagging atoms
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.
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 molecular bonds you specify in
the original data file that span the periodic box should be between two atoms with image flags that differ by 1.
This will allow them to be unwrapped appropriately.
Thank you,