[lammps-users] creating polymer beads!

Hi all,

I am trying to set up a poiseulli polymer flow in a channel. I modified the ‘chain.f’ from tools directory to
meet my requirements. However, there are certain issues, which I think you guys can help with.

i) There are two types of atoms in the system. The flow atoms are of bond type and the wall atoms are
atomic style. So I use more general bond style to create the data file. But when I run it, an error occurs saying
FENE bond too long. I am attaching input script and data file.

ii) Is it possible to create two types atoms in the data file. I mean a number of atoms as bond type
and a number of atoms as atomic type.

iii) How to define group/region command in a data file?

Any of help would be greatly aprreciated. If any body has attempted a similar kind of please let me know.

Thanks in advance
Srikanth

equil.chain (673 Bytes)

newdata.chain (98.1 KB)

Srikanth,

i) There are two types of atoms in the system. The flow atoms are of bond
type and the wall atoms are
atomic style. So I use more general bond style to create the data file. But
when I run it, an error occurs saying
FENE bond too long. I am attaching input script and data file.

What you've done in using the bond style for both atomic and bond
style atoms is fine. The error "FENE bond too long" indicates that
bonded atoms are being pulled too far apart. You'll need to get your
system to equilibrate more gently or for longer time or shorter
timesteps so that the bonded atoms don't pull apart. You might even
experiment with a run then minimize then run then minimize type
scheme.

ii) Is it possible to create two types atoms in the data file. I mean a
number of atoms as bond type
and a number of atoms as atomic type.

You can create as many atom "types" as you like in a single data file.
I think you mean can you create multiple atom "styles". The answer to
that is yes as well. See:
http://lammps.sandia.gov/doc/angle_style.html . But you don't need
multiple styles for your problem. The way you have it set up for this
particular problem is fine as is.

iii) How to define group/region command in a data file?

You should issue group/region commands in the input script rather than
the data file. See:

http://lammps.sandia.gov/doc/group.html

http://lammps.sandia.gov/doc/region.html

Paul

Hi Paul,

I have tried all three methods suggested by you to equilibrate. But still get the same error.
Can you please see where I am going wrong?
I tried to use region and group commands in the input script but an error "Use of region with undefined lattice". Is this because I use a continuum description, if so how to define region/group commands in continuum description?

Thanks
Srikanth

Srikanth,

Using the following input script, I was able to get you system to
relax to a much more reasonable state:

units lj
atom_style bond
read_data newdata.chain.data
special_bonds 0 1 1
pair_style soft 1.12246
pair_coeff * * 1.0 20.0 1.12246
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
fix 1 all nve
fix 2 all temp/rescale 1 1.0 1.0 10.0 1.0
thermo 1
thermo_style custom step ebond etotal
timestep 1e-5
run 1000
timestep 1e-4
run 2000
timestep 1e-3
run 2000
timestep 0.005
run 2000
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff * * 1.0 1.0 1.12
minimize 1.0e-4 100 1000
run 2000
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
run 10000

Paul