[lammps-users] Number of atoms and complex shapes

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1

Hello,

I am new user of LAMMPS. My question is:

How do you calculate the number of atoms present in a given box or a circle ? For instance, is there a way to calculate the number of atoms in a 20nm Circle? How can i model a complex shape in LAMMPS?

Thanks in advance,

Peri.

2

Peri,

The following URL:

http://www.cs.sandia.gov/~sjplimp/lammps/non_features.html

states:

"LAMMPS is designed to be a fast, parallel engine for
molecular dynamics (MD) simulations. As such, LAMMPS
itself provides only a modest amount of functionality
for setting up simulations and analyzing their
output."

I'd recommend doing processes like counting atoms
within a given geometry outside of LAMMPS. You can
tell LAMMPS to dump atomic positions, see:

http://www.cs.sandia.gov/~sjplimp/lammps/doc/dump.html

Then write a pizza.py script,

http://www.cs.sandia.gov/~sjplimp/pizza.html

or your own post-processing code to count how many
atoms are within a 20 nm circle, or whatever geometry
you want.

Similarly, if you want to model a complex shape, it is
best to build the structure using your own pizza.py or
other script, code, or program. Then import it into
LAMMPS and run the MD simulation.

Paul

--- Medha Dakshina Murthy peri <[email protected]...>
wrote:

3

I'd only add that using the region command in its various
flavors you can create reasonably complex geometries,
then fill them with atoms on a lattice using the create_atoms
command. In particular, see the side in/out options for region
and also the union and intersect styles. Also, it's pretty
easy to add a new style, like "murthy-shape" to region, so
long as you can define whether a point x,y,z is inside or
outside it ...

Steve