How to create a polymer melt?
How to create a data file of a polymer system for Lammps.
Creating data files for polymer systems appears to be a daunting task. The process of creating a data file includes three stages. One of possible ways of tackling this problem would be:
- Create initial configuration using Monte-Carlo random walk
- Run a Lammps simulation for equilibrating melt
- Analyze chain confirmation, if not satisfactory go to stage 2.
Creating initial configuration is relatively easy. The Lammps package comes with an tool called chain.f. Very fast Fortran program for creating initial configurations.
To create a melt we need to create a file def.chain, which is located in the tools/ directory.
Polymer chain definition 0.8442 rhostar 592984 random # seed (8 digits or less) 1 # of sets of chains (blank line + 6 values for each set) 0 molecule tag rule: 0 = by mol, 1 = from 1 end, 2 = from 2 ends 320 number of chains 100 monomers/chain 1 type of monomers (for output into LAMMPS file) 1 type of bonds (for output into LAMMPS file) 0.97 distance between monomers (in reduced units) 1.02 no distance less than this from site i-1 to i+1 (reduced unit)
gfortran chain.f -o chain.out
We may create a polymer melt using this command:
./chain.out < def.chain > init.data
Now the init.data looks like:
LAMMPS FENE chain data file 140 atoms 134 bonds 0 angles 0 dihedrals 0 impropers ...