Hi,
I am using LAMMPS to simulate a simple system in which a few bead-spring polymer chains are surrounded by a solvent of Lennard-Jones particles. When I run the simulation, I keep incurring a warning read “WARNING: FENE bond too long” on the command prompt screen during the minimization process.
Memory usage per processor = 12.7333 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 1.9578366e+014 0.93383588 1.9578366e+014 5.4819424e+014
WARNING: FENE bond too long: 59 4819 4820 1.89832 (…/bond_fene.cpp:91)
WARNING: FENE bond too long: 60 4819 4820 1.92026 (…/bond_fene.cpp:91)
…
…
WARNING: FENE bond too long: 135 4841 4842 1.96394 (…/bond_fene.cpp:91)
882 0 -5.9281953 0.78562692 -5.1425684 -0.83201377
Loop time of 133.022 on 1 procs for 882 steps with 30000 atoms
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
The input script I construct is:
FENE beadspring chain solution
units lj
boundary p p p
atom_style bond
#special_bonds fene dihedral no
read_data mydata3.chain
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 2.5
special_bonds fene dihedral no
bond_style fene
bond_coeff * 7.0 2.0 1.0 1.0
minimize 1.0e-5 1.0e-8 3000 30000
neighbor 0.4 bin
neigh_modify every 1 delay 1
velocity all create 1.0 1
fix 1 all nve
#fix 2 all temp/rescale 1 1.0 1.0 0.01 1.0
thermo 100
#thermo_style custom step ebond etotal
#timestep 1e-6
#run 3000
#minimize 1.0e-6 1.0e-8 5000 40000
#timestep 1e-8
#run 20000
#minimize 0.0 1.0e-8 1000 10000
timestep 1e-9
run 8000
The output file (log.lammps) I got after running the simulation is:
LAMMPS (5 Sep 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (…/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
FENE beadspring chain solution
units lj
boundary p p p
atom_style bond
#special_bonds fene dihedral no
read_data mydata3.chain
orthogonal box = (-17.4976 -17.4976 -17.4976) to (17.4976 17.4976 17.4976)
1 by 1 by 1 MPI processor grid
reading atoms …
30000 atoms
scanning bonds …
1 = max bonds/atom
reading bonds …
4900 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 2.5
special_bonds fene dihedral no
2 = max # of 1-2 neighbors
2 = max # of special neighbors
bond_style fene
bond_coeff * 7.0 2.0 1.0 1.0
minimize 1.0e-5 1.0e-8 3000 30000
WARNING: Resetting reneighboring criteria during minimization (…/min.cpp:168)
Memory usage per processor = 12.7333 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 1.9578366e+014 0.93383588 1.9578366e+014 5.4819424e+014
882 0 -5.9281953 0.78562692 -5.1425684 -0.83201377
Loop time of 133.022 on 1 procs for 882 steps with 30000 atoms
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
1.9578365527e+014 -5.14252702438 -5.14256835118
Force two-norm initial, final = 1.82867e+021 29.1916
Force max component initial, final = 6.91786e+020 7.66752
Final line search alpha, max atom move = 0.00105646 0.00810044
Iterations, force evaluations = 882 1654
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total