Input Script:
2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style bond
bond_style harmonic
read_data /fs/home/sm868/lammps_melting/data.melt-nvt-1
mass 1 1.0
velocity all create 1.0 87287 dist gaussian
pair_style lj/cut 1.1225
pair_coeff 1 1 1.0 1.0 1.1225
pair_modify shift yes
neighbor 0.1 bin
neigh_modify delay 0 every 5 check yes
fix 1 all nvt 1.0 1.0 0.01
fix 2 all enforce2d
fix 3 all shake 0.0001 100 10 b 1 t 1
compute 1 all coord/atom 1.1225
compute 2 all rdf 100
timestep 0.001
thermo 0
dump 1 all xyz 0 dump.melt-nvt-1
log log.melt-nvt-1
run 1
I had to attach the data file as copy pasting terminates the file.
I am using a 2d system but I am not sure what boundary conditions to use. I have a system in the x-y plane to start with and I would like to keep it confined to the xy plane. I used enforced 2d. But ldid not change the default boundary condition. If I do … use something like p fs p the program gives an error. Shake does not converge.
Pooja
This output shows the problem:
Neighs: 8953 ave 8953 max 8953 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4.32371e+08 ave 4.32371e+08 max 4.32371e+08 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 432371056
Ave neighs/atom = 120103
You are requesting a full neighbor list with some other
command, probably compute coord/atom, and that
is the one with all the neighbors. If you delete
that command (you don’t appear to be using it), then
you should get a smaller value. But I don’t see
why the full neighbor list is so large either. Could
be a bug in the way it is being counted for size for output.
Can you post you full input script and data file?
Steve
2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style bond
bond_style harmonic
read_data /fs/home/sm868/lammps_melting/data.melt-nvt-1
mass 1 1.0
velocity all create 1.0 87287 dist gaussian
pair_style lj/cut 1.1225
pair_coeff 1 1 1.0 1.0 1.1225
pair_modify shift yes
neighbor 0.1 bin
neigh_modify delay 0 every 5 check yes
fix 1 all nvt 1.0 1.0 0.01
fix 2 all enforce2d
fix 3 all shake 0.0001 100 10 b 1 t 1
compute 1 all coord/atom 1.1225
compute 2 all rdf 100
timestep 0.001
thermo 0
dump 1 all xyz 0 dump.melt-nvt-1
log log.melt-nvt-1
run 1
z
data.melt-nvt-1 (178 KB)