I was bugged by the behaviour of the region command in my reply to this post.
I believe there is a bug in LAMMPS (verified with versions 7 Feb 2024 - Update 1, 21Nov23, and 2Jun22) in the definition of regions and groups. This is a small example to reproduce the issue:
cube.in
# Check the region intersect command.
units metal
dimension 3
boundary p p p
atom_style atomic
# Define the simulation box
region sample block 0 20 0 20 0 20 units box
create_box 2 sample
lattice fcc 3.615
create_atoms 1 region sample
# Define atomic type and mass
mass 1 63.546
mass 2 63.546
pair_style eam/alloy
pair_coeff * * Cu_zhou.eam.alloy Cu Cu
# Thermodynamic output.
thermo 500
thermo_style custom step etotal epair pe ke temp press vol
thermo_modify flush yes
dump 1 all custom 20 Cu_bulk.dump id type x y z
# Relax the structure.
velocity all create 300 68748
fix NPT all npt temp 300. 300. 0.1 iso 0. 0. 1.
run 5000
unfix NPT
# Change the atom type on the outside of the cube.
region inner block 5 15 5 15 5 15 units box
group inner region inner
region side intersect 2 sample inner
group side region side
set group side type 2
# Integrate only the atoms inside the cube.
fix NVT inner nvt temp 300. 300. 0.1
run 5000
The inconsistencies begin with the definition of the inner and side regions. From the log:
create_atoms 1 region sample
Created 864 atoms
region inner block 5 15 5 15 5 15 units box
group inner region inner
103 atoms in group inner
region side intersect 2 sample inner
group side region side
103 atoms in group side
set group side type 2
Setting atom values ...
103 settings made for type
The inner group is correctly populated and should be of type 1. If I understand correctly the command region intersect, the side group should have 864-103=761 atoms of type 2, but LAMMPS reports only 103. However, the DUMP file has the following composition:
761 atoms of type 1 # side
103 atoms of type 2 # inner
with the atom types swapped and the group side having more atoms than reported in the log. The integration in fix nvt seems correct, except for the swapped atom types. Here is a rendering of the exploded sample:
The
inner group is coloured in blue and has type 2 in the DUMP file.
Is this a bug?
