Dear LAMMPS users ,
In my simulation I need to have a Lennard-Jones tube instead of nano tube . Can I define it by lammps commands ?
Best,
Saeed.
Dear LAMMPS users ,
In my simulation I need to have a Lennard-Jones tube instead of nano tube
. Can I define it by lammps commands ?
for that to even try to answer, we would first have to know what a
"lennard-jones tube" is and in which way it would be different from a
"nanotube".
since lennard-jones is a potential and nano an indicator of size, it is
difficult to see where the difference is. plenty of nanotubes get simulated
with a lennard-jones potential. on the other hand, lennard-jones potentials
can be applied to all kinds of length scales (nano, micro, milli and so on).
axel.
I don’t know if this is what you are looking for.
If you have moltemplate, then you could build the tube this way:
WallParticle {
atomID molID atomType charge x y z
write(“Data Atoms”) {
$atom:w $mol:. @atom:w 0.0 0.0 0.0 0.0
}
write_once(“Data Masses”) {
@atom:w 10.0
}
write_once(“In Settings”) {
i j epsilon sigma cutoff
pair_coeff @atom:w @atom:w 0.05 3.0 7.5 #<–repulsive (approximately)
group groupW type @atom:w #(Atoms of this type belong to the “W” group)
}
}
tube = new WallParticle.move(0,9.6,0)
[20].rot(18,3.0,0,0)
[20].move(3.0,0,0)
…Then, save this text in a file (eg “system.lt”), install moltemplate, and enter this into the terminal:
moltemplate -vmd system.lt
This will create system.in.init, system.in.settings and system.data containing LAMMPS commands and the DATA file containing the tube geometry.
You can edit this file to change the pair_coeff command to change the size and properties of the particles in the simulation. And you can change the number of particles in the tube, and its radius and length by modifying the “tube = …” command above. Currently the particles have a diameter and inter-particle-spacing of 3.0 (distance units).
I added some additional particles to create a liquid in the tube (also made from Lennard Jones particles, colored light-blue in the picture). You can replace them with something else by modifying the end of the “system.lt” file in that example.
The complete example, including the liquid, and including a LAMMPS run script, is in the “examples/coarse_grained_examples” subdirectory with moltemplate:
https://github.com/jewettaij/moltemplate/tree/master/examples/coarse_grained_examples/abstract_lennard_jones_tube
However I might change the name of the example, so this link could break in the future.
Cheers
Andrew