[lammps-users] Segmentation Fault


I am getting a Segmentation fault when trying to run an NVT on an epoxy graphite system. I have had a few fellow students look at my input data and nobody knows why I am getting this. Also, there is very little explanation on this error. Would you please take a look at my input file and see if you can tell why I am getting this fault?

# NVT file for epoxy graphite system VDW set at 1% for minimization

units real

dimension 3
boundary p p f

atom_style molecular

neighbor 5.0 bin
neigh_modify every 10 delay 20 one 4000 page 250000

echo screen

#AMBER potentials

bond_style harmonic
angle_style harmonic
dihedral_style opls
pair_style lj/cut/opt 10.0
pair_modify mix arithmetic

read_data finalsystem.nvt01.xyz

group graphite id > 15936
group epoxy id <= 15936

#initial velocities

compute 1 all temp
compute 2 all pe
compute 3 all ke/atom

velocity epoxy create 300.0 300.0


fix 1 graphite setforce 0.0 0.0 0.0
fix 2 epoxy nvt 300.0 300.0 10.0


timestep 0.2
thermo 100
thermo_style custom step temp press pe ke etotal evdwl ebond eangle edihed emol

dump ratio all xyz 50000 dump.fs.nvt01.xyz

run 500000

finalsystemVDW01.nvt (772 Bytes)


it is near impossible to debug this without a full input
(including the data file).

most likely the error is in the initial coordinates and
you have an overflow of some sorts.

if you get a segmentation fault, you can always force
a core dump and then generate a stack trace to find
out in which subroutine the executable craters.



I am trying to apply the FENE force field for my current simulations. I have looked into literature to help define the parameters needed for this force field. Where can I find the sigma and epsilon values for the FENE force field? Are these the same as the LJ sigma and epsilon values? Also, is there a predefined cut-off distance R_0, or do people just experiment with arbitrary values? How exactly does lammps use these parameters when running a simulation?

Any help on the subject of the FENE force field would be extremely helpful!


Cameron Hadden
Michigan Technological University

finalsystemVDW01.nvt (772 Bytes)

The formula for FENE is on the bond_style fene doc page,
so that's what LAMMPS computes. Look for papers by G Grest
on how to use it for polymer models. See bench/in.chain for typical bead/spring
polymer chain FENE params.


Hi, Cameron. For the Kremer-Grest bead-spring model of polymers, the typical FENE parameters are

sigma = sigma_{LJ}
epsilon = epsilon_{LJ}
k = 30epsilon/(sigma^2)
R_0 = 1.5sigma

i. e. 1.0 1.0 30 1.5 if you use units where sigma_{LJ} = epsilon_{LJ} = 1.0. If you’re not using the K-G bead spring model, best thing to do is play with plotting the potential for different k and R_0 to get a feel for the implications of varying them for your model.