Polymeric Structure Simulation with LAMMPS
This is a LAMMPS input to show what happens to a polymer chain at a certain temperature after some time. Chain’s movement is caused by a molecular forces between atoms in the chain and by temperature of them. During the simulation, firstly, the chain was left for do deform freely under the molecular forces and a random atomic fluctuation due to the temperature. After that the chain was minimized to find it’s minimal energy condition.
# Polymer simulation with LAMMPS. # Dr. Mark A. Tschopp, 2010. # Variables variable fname index PE_cl100.txt variable simname index PE_cl100 # Initialization units real boundary f f f atom_style molecular log log.${simname}.txt read_data ${fname} # Dreiding potential information neighbor 0.4 bin neigh_modify every 10 one 10000 bond_style harmonic bond_coeff 1 350 1.53 angle_style harmonic angle_coeff 1 60 109.5 dihedral_style multi/harmonic dihedral_coeff 1 1.73 -4.49 0.776 6.99 0.0 pair_style lj/cut 10.5 pair_coeff 1 1 0.112 4.01 10.5 compute csym all centro/atom fcc compute peratom all pe/ato # Equilibration (Langevin dynamics at 5000 K) velocity all create 5000.0 1231 fix 1 all nve/limit 0.05 fix 2 all langevin 5000.0 5000.0 10.0 904297 thermo_style custom step temp thermo 10000 timestep 1 run 1000000 unfix 1 unfix 2 write_restart restart.${simname}.dreiding1 # Define Settings compute eng all pe/atom compute eatoms all reduce sum c_eng # Minimization dump 1 all cfg 6 dump.comp_*.cfg mass type xs ys zs c_csym c_peratom fx fy fz reset_timestep 0 fix 1 all nvt temp 500.0 500.0 100.0 thermo 20 thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms min_style cg minimize 1e-25 1e-25 500000 1000000 print "All done"
1. In this LAMMPS input file, “Variable” section defines some variables in polymeric structure simulation.
2. “Initialization” section defines the style of units, the boundary condition, and LAMMPS data file reading.
3. We need to define the interatomic potentials for particles interactions. Simulation is run with the DREIDING interatomic potential in this simulation.
4. It’s now time for simulation to actually run, which begins with the energy equilibration. The simulated polymeric structure has to be equilibrated before the minimization process.
5. “Minimization section” is last section of the simulation. This is where geometry optimization is actually carried out. Different parameters such as potential energy, pressures, stress has been defined and then later printed in the log files.
Here is an example datafile for a polymeric structure with LAMMPS package. Download this file and add this to the directory with the LAMMPS input script above: PE_cl100.txt
Reference
https://icme.hpc.msstate.edu