Hello:
I am trying to perform a study using bead spring method. The problem is I cannot solve the overlap problem. I used chain tool to generate a small test data file. Below is the definition file.
Hai,
With such a dense system, it is a bit tricky to get the soft potential to adequately push off the bad LJ contacts. I’d recommend using the minimizer instead of the soft potential. If you just take the lammps/bench/in.chain input script and add a minimize command before the run command (see below), it works fine (but does give a few long FENE bond warnings at the start). Similarly, skipping the soft potential step and adding a minimize command before the run command for your script works fine.
Paul
FENE beadspring benchmark
units lj
atom_style bond
special_bonds 0.0 1.0 1.0
read_data data.chain
neighbor 0.4 bin
neigh_modify every 1 delay 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
thermo 100
timestep 0.012
minimize 1.0e-4 100 1000
run 100
Paul:
Minimize did work if my system is composed of thousands of beads. But if I increase my sytem to tens of thousands of beads, I still got “bad fene bond error”. I wonder if you have suggestions for that.
Thanks,
Hai
Hai,
You might try different minimizer settings. See:
http://lammps.sandia.gov/doc/minimize.html
and
http://lammps.sandia.gov/doc/min_style.html
Another thing that might help is to alternate minimize commands with short run commands using a small timestep, like this:
timestep 0.001
minimize 1.0e-4 100 1000
run 2
minimize 1.0e-4 100 1000
run 2
minimize 1.0e-4 100 1000
run 2
.
.
.
Hopefully this helps.
Paul