Dear All,
I have an equilibrated polyurea model with periodic boundary conditions applied (thanks to valuable advice earlier), and intend to remove the periodic boundary conditions along one direction before simulating a shockwave through the model. Is there a way to use LAMMPS to “unwrap” the model in that direction when changing the boundary conditions? I realize I should equilibrate the model again before simulating the shockwave.
Regards,
Ramaswami.
Dear All,
I have an equilibrated polyurea model with periodic boundary conditions
applied (thanks to valuable advice earlier), and intend to remove the
periodic boundary conditions along one direction before simulating a
shockwave through the model. Is there a way to use LAMMPS to "unwrap" the
model in that direction when changing the boundary conditions? I realize I
should equilibrate the model again before simulating the shockwave.
what do you mean exactly by "unwrap"? can you perhaps provide a little
ASCII-art graph or a little drawing?
axel.
I mean that if I have a molecule containing a four-carbon backbone, and it appears in the cell with PBCs like this ( where the cell boundaries are denoted by || and bonds by – ):
-C–H H–C--C–C-||
with the shock propagating from left to right,
then I want to move atoms so the molecule appears like this:
H–C--C–C--C–H||
Actually, each molecule in my model has over 2000 atoms.
Regards,
Ramaswami.
I think you could do something like the following:
a) dump the atoms to a dump file with unwrapped coords
b) use the change_box command to convert to non periodic BC
c) use the read_dump command to read back in the
unwrapped coords
Steve