I want to thermostat just the outer boundary of a simulation box. I was creating a region that went almost to the edge of the boundary, then chose the side out option to get the outer boundary layers. Then I applied microcanonical ensemble to the interior region. I suspect that where I chose the boundary, there must be atoms that sit along both sides because the atoms are included in both regions. Is there a way to ensure that the atoms are not included in both systems? This seems like it could certainly be an issue for an amorphous system.
region exterior block 3 82 3 95 3 98 side out
group exterior region exterior
region interior block 3 82 3 95 3 98
group interior region interior
17806 atoms in group exterior
54705 atoms in group interior
But I only have 72,000 atoms.
The screen print from the group command will
tell you how many atoms are in the group.
You can viz them or dump them for time 0
to insure they are the ones you want. Groups
are static, so after atoms start moving, the
ones in the group will not necessarily remain
in the region.
I understand what you are saying but I am not sure that that is my problem. I am looking to see how many atoms are in each group the second the simulation starts. They do not add up to my total number of atoms. I am guessing this is because my region crosses through some atoms and so they get counted twice. This must be the case since there a few hundred more atoms in the groups total than in the total simulation.
You’ll have to debug your input and figure
out exactly which atoms are in each group (e.g. dump them
to different files), and why they don’t add up. Maybe some
are counted twice or zero times if they are exactly on the