Hi,
For a simulation run I want to relax a LJ copper substrate @ T=0 && p=0 with lateral fixed boundaries and fixed/open boundaries in y-direction. Therefore I intend to use the minimization method. The thermodynamic variables p and T are looking reasonable. But when I visualize the surface particles with the centro symmetric parameter P>10 (threshold can also be lower), the surface is only detected at the upper boundaries and not at the lower boundaries (x,y,z=0).
This is my setup:
boundary mm ms mm
units metal
atom_style atomic
lattice fcc 3.615
region simulationbox_region block 0 55 0 55 0 55
create_box 1 simulationbox_region
create_atoms 1
mass * 63.55
pair_style lj/cut/opt 7.23
pair_coeff * * 0.4229 2.338
fix nve_fix all nve
timestep 0.002
thermo 1
min_style cg
dump dump_pos all custom 1 pos/dump.*.gz x y z centro
minimize 1.0e-40 10000 10000
run 50000
Has anybody an idea, why the centro symmetric parameter doesn’t detect the surface at the lower boundaries? Is this a problem with LAMMPS or maybe a problem with my physical setup?
Best regards:
Gerolf
Hi Gerolf. I ran your problem here, and am seeing P>10 for the atom at
the origin and others nearby. So I'm not seeing the issue you
describe. I did make a couple of minor/necessary changes to your input
script though. Here's what I ran (on 8 procs):
boundary mm ms mm
units metal
atom_style atomic
lattice fcc 3.615
region simulationbox_region block 0 55 0 55 0 55
create_box 1 simulationbox_region
create_atoms 1
mass * 63.55
pair_style lj/cut 7.23
pair_coeff * * 0.4229 2.338
fix nve_fix all nve
timestep 0.002
thermo 1
min_style cg
dump dump_pos all custom 1 pos/dump.* x y z centro
minimize 1.0e-40 10000 10000
run 50000
On timestep zero, here's what the first part of the dump looks like:
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
671550
ITEM: BOX BOUNDS
-0.0001 198.825
ITEM: ATOMS
0 0 0 117.614
1.8075 1.8075 0 26.1365
1.8075 0 1.8075 26.1365
0 1.8075 1.8075 26.1365
3.615 0 0 32.6706
5.4225 1.8075 0 19.6023
5.4225 0 1.8075 19.6023
3.615 1.8075 1.8075 0
7.23 0 0 32.6706
9.0375 1.8075 0 19.6023
9.0375 0 1.8075 19.6023
7.23 1.8075 1.8075 3.15544e-30
Note that the atom at 0, 0, 0 has P = 117.614, which is a lot bigger
than 10. I let it run for about 20 timesteps before killing it. At
timestep 20, here's what I'm seeing:
ITEM: TIMESTEP
20
ITEM: NUMBER OF ATOMS
671550
ITEM: BOX BOUNDS
-0.0001 198.825
ITEM: ATOMS
-0.0154624 -0.0154624 -0.0154624 119.677
1.8277 1.8277 -0.041923 25.4101
1.8277 -0.041923 1.8277 25.4101
-0.041923 1.8277 1.8277 25.4101
3.62016 -0.0315278 -0.0315278 34.0988
5.42335 1.82721 -0.0392691 18.9969
5.42335 -0.0392691 1.82721 18.9969
3.62415 1.82676 1.82676 0.0363907
7.23015 -0.029459 -0.029459 33.636
9.03748 1.82745 -0.0389133 19.0782
9.03748 -0.0389133 1.82745 19.0782
7.23014 1.82799 1.82799 0.0365764
10.8448 -0.0294477 -0.0294477 33.6859
Still nice big centro values near the origin. You might try using
lj/cut instead of lj/cut/opt as I've done here, but I doubt this will
change things. Other than that, just make sure your using the latest
version of LAMMPS.
Paul