I would need some advices from you. I am trying to reduce the size of my
simulation box in order to reduce the CPU time.
I have a large cubic box with millions of atoms. Now, I am interested only
in some of the atoms of the box (with some particular kinetic energy). For
the sake of simplicity, let's say these atoms are initially located along a
line that would coincide with the 111 diagonal. Clearly, many of the atoms
in the simulation box are not of interest, but are consuming CPU time. They
are just far from these atoms and are thermalised. Therefore, I would like
to delete them in order to reduce their number.
I was thinking of defining a cylinder (for instance) with a given radius
around the line of atoms of interest, using group command. Then I would
remove the atoms outside of the cylinder with delete_atoms command.
And these are my questions:
Is is possible to define such a cylinder inside an existing box (cubic
here) ? A cylinder that would contain a given region.
If so, once the cylinder would be created and the atoms around are deleted,
would it be possible to set the surface of the cylinder as periodic ?
Many thank in advance for any advice !