[lammps-users] setting polymer flow problem!

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1

Hi,

I want to set a polymer flow problem. How to initialize the polymer chains in the simulation box?
Want to use FENE potential between the fluid-fluid molecules and LJ between the fluid-wall molecules.
I am pretty sure some one might have done some thing similar to this, looking to hear from you guys.

Srikanth

2

If you are asking how do you create a set of FENE chains,
see the tools/chain.f program or the chain tool in Pizza.py
which does the same thing. Then you will need to run MD
for a while with a pair_style soft to un-overlap the chains.

See bond_style fene for the FENE potential you ask about.
You can put a pair_style LJ with this to model the
rest of what you ask.

Steve

3

The file ‘chain.f’ creates set of polymer chains. But what we are interested in slightly different thing.
We want to place set of polymers in a long rectangular channel. I was trying to create a rectangular geometry first and then place the polymer chains to fill the channel volume.

Cheers
Srikanth

4

Building polymer chains from scratch is tricky, especially in parallel.
So LAMMPS doesn't do it. You'd need to write your own pre-processor
that does what you want and read the coords into LAMMPS via
the read_data command. Like what chain.f does as a pre-processor.

Steve

5

Hi all,

I am running polymer benchmark problem. Wanted to see how the atom positions change with time.
So I use the dump command to do this but the “dump.polymer” file is empty. This is what I am doing

dump 1 all bond 100 dump.polymer

Any comments/suggestions would be greatly appreciated.

Thanks
Srikanth

6

I just added this line to bench/in.chain and ran it

dump 1 all bond 100 dump.polymer

I get a file with 2 snapshots of all the bonds. If
you want atom coords you should use a dump
style of atom, not bond.

Steve

7

The dump file produced doesn’t contain any data. I tried bond and atom both styles
in the dump command but doesn’t produce anything in the output file.
Moreover, when tried to produce a different ‘data.chain’ file using ‘chain.f’, I get an errors saying

ERROR on proc 33: Bond atoms 6688 6689 missing on proc 33 at step 1
ERROR on proc 119: Bond atoms 7124 7125 missing on proc 119 at step 1
ERROR on proc 97: Bond atoms 77 78 missing on proc 97 at step 1
ERROR on proc 63: Bond atoms 207 208 missing on proc 63 at step 1
ERROR on proc 57: Bond atoms 417 418 missing on proc 57 at step 1
ERROR on proc 118: Bond atoms 3893 3894 missing on proc 118 at step 1
ERROR on proc 113: Bond atoms 7038 7039 missing on proc 113 at step 1
ERROR on proc 5: Bond atoms 1230 1231 missing on proc 5 at step 1

I looked at the error section on lammps website, and followed the instructions.
Varied the cut-off to as suggested but get the same kinda error.

8

Please post a small version of your input script and data file
that exhibits the problem.

Steve