[lammps-users] Problem running a 3 step bead-spring model, 2 polymer system

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#1

Hi,

I am trying to run (Lammps version July 22, 2009) a 2 chain system on
Jaguar, bead-spring polymer model. Running in 3 steps, 1st soft
potential, 2nd lj potential with first chain attractive and 2nd chain
repulsive, 3rd all attractive chains. Soft part is working well, but
in second stage the error is, "FENE bond too long". Following is the
input file, can somebody please see what's wrong!! I can send the
data.chain file which was created using chain.f.

Thanks,
Monojoy

SP_2step.inp (INPUT FILE)

# Bead-spring polymer simulation
# use soft potential to un-overlap, follow with FENE potential

units lj
atom_style bond

neighbor 0.3 bin
neigh_modify every 1 delay 10

# soft potential start-up in one stage

read_data dataSP2.chain
special_bonds 0.0 1.0 1.0

bond_style fene
bond_coeff 1 30.0 1.5 2.0 1.0
bond_coeff 2 30.0 1.5 4.0 1.0

pair_style soft 2.5
pair_coeff 1 1 1.0 30.0
pair_coeff 2 2 1.0 30.0
pair_coeff 1 2 1.0 30.0

velocity all create 1.0 2349852 rot yes dist gaussian

fix 1 all nve 0.1
fix 2 all langevin 1.0 1.0 10.0 904297

timestep 0.006

thermo 100
run 100000

# Run with LJ potentials to form the PDMS droplet

bond_style fene
bond_coeff 1 30.0 1.5 2.0 1.0
bond_coeff 2 30.0 1.5 4.0 1.0

pair_style lj/cut 2.5
pair_modify shift yes mix arithmetic
pair_coeff 1 1 2.0 1.0 1.12246
pair_coeff 2 2 4.0 1.0 2.5

thermo 100
dump 1 all xyz 10000 dump01.xyz
timestep 0.012

reset_timestep 0
run 10000

# MAIN RUN with LJ

bond_style fene
bond_coeff 1 30.0 1.5 2.0 1.0
bond_coeff 2 30.0 1.5 4.0 1.0

pair_style lj/cut 2.5
pair_modify shift yes mix arithmetic
pair_coeff 1 1 2.0 1.0 2.5
pair_coeff 2 2 4.0 1.0 2.5

thermo 100
dump 2 all xyz 10000 dump02.xyz
timestep 0.012

reset_timestep 0
run 10000

#2

First, please try it with the current version of
LAMMPS (not one more than a year old). Note
that the syntax for pair_style soft has changed.
Now use it with fix adapt.

Second, try the bench/in.chain test case. It
is FENE chains and should work fine.

The error you are getting is typically b/c the
system is not well-equilibrated and is stretching
one or more bonds too far.

Steve

#3

Hi Steve,

Now we have the 9 Sept 2010 version of Lammps. Still having the same
problem of FENE bond too long. Single chain system runs perfectly
fine. 2 chains system runs fine too, if all the chains have similar
kind of interactions. Input and data files attached with.

Thanks,
Monojoy

dataSP2.chain (388 KB)

SP_2step.inp (1.45 KB)