Hi,
I’m trying to model a substrate like structure with Si.
I modeled the substrate with two layers by defining regions separately.
One is a fixed region and the other one is a movable region.
However, through LAMMPS log file I could see that there are some overlap between fixed and movable region.
(group ‘substrate’ = group ‘afix’ + group ‘amov’)
(# of atoms in group ‘substrate’ = 2,600)
(# of atoms in group ‘afix’ = 1,000 and # of atoms in group ‘afix’ = 1,800)
Does this indicate 200 atoms are overlapped? How does it affect the simulation?
Furthermore, if this affects the simulation how can I avoid this overlapping?
Here’s the part of the input I’ve used and the LAMMPS log file.
Best regards
Hyun-seok Kim.
(Input)
lattice diamond 5.43
region boxsim block 0 10 0 10 0 15 units lattice
region boxf block 0 10 0 10 0 1 units lattice
region boxm block 0 10 0 10 1 3 units lattice
region clus sphere 5 5 7 3 units lattice
region sub union 2 boxf boxm
create_box 1 boxsim
mass 1 28.0855
create_atoms 1 region sub
create_atoms 1 region clus
group afix region boxf
group amov region boxm
group substrate region sub
group cluster region clus
group runnve region boxsim
(LAMMPS log)
group afix region boxf
1000 atoms in group afix
group amov region boxm
1800 atoms in group amov
group substrate region sub
2600 atoms in group substrate
group cluster region clus
915 atoms in group cluster
group runnve region boxsim
3515 atoms in group runnve