LAMMPS Input Deck for Atomistic Deformation of Amorphous Polyethylene

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Here is an example LAMMPS input script. The 'fname' variable is the name of the LAMMPS data file which contains the atom positions along with all of the bond, angle, and dihedral angle lists. An example LAMMPS datafile for PE is attached below after the input script.

##################################################### # # # DEFORM DREIDING LAMMPS INPUT SCRIPT # # # # Filename: in.deform_dreiding.txt # # Author: Mark Tschopp, 2010 # # # # The methodology outlined here follows that from # # Hossain, Tschopp, et al. 2010, Polymer. Please # # cite accordingly. The following script requires # # a LAMMPS data file containing the coordinates and # # appropriate bond/angle/dihedral lists for each # # united atom. # # # # Execute the script through: # # lmp_exe < in.deform_dreiding.txt # # # ##################################################### # VARIABLES variable fname index PE_nc10_cl1000.dat variable simname index PE_nc10_cl1000 # Initialization units real boundary p p p atom_style molecular log log.${simname}.txt read_data ${fname} # Dreiding potential information neighbor 0.4 bin neigh_modify every 10 one 10000 bond_style harmonic bond_coeff 1 350 1.53 angle_style harmonic angle_coeff 1 60 109.5 dihedral_style multi/harmonic dihedral_coeff 1 1.73 -4.49 0.776 6.99 0.0 pair_style lj/cut 10.5 pair_coeff 1 1 0.112 4.01 10.5 ##################################################### # Equilibration Stage 1 (Langevin dynamics at 500 K) velocity all create 500.0 1231 fix 1 all nve/limit 0.05 fix 2 all langevin 500.0 500.0 10.0 904297 thermo_style custom step temp press thermo 100 timestep 1 run 10000 unfix 1 unfix 2 write_restart restart.${simname}.dreiding1 ##################################################### # Equilibration Stage 2 (NPT dynamics at 500 K) fix 1 all npt temp 500.0 500.0 50 iso 0 0 1000 drag 2 fix 2 all momentum 1 linear 1 1 1 thermo_style custom step temp press thermo 100 timestep 0.5 reset_timestep 0 run 50000 unfix 1 unfix 2 write_restart restart.${simname}.dreiding2 ##################################################### # Equilibration Stage 3 (NPT dynamics from 500 K --> 100 K) fix 1 all npt temp 500 100 50 iso 0 0 1000 drag 2 fix 2 all momentum 1 linear 1 1 1 thermo_style custom step temp press thermo 10 timestep 0.5 reset_timestep 0 run 50000 unfix 1 unfix 2 write_restart restart.${simname}.dreiding3 ##################################################### # Equilibration Stage 4 (NPT dynamics at 100 K) fix 1 all npt temp 100 100 50 iso 0 0 1000 drag 2 fix 2 all momentum 1 linear 1 1 1 thermo_style custom step temp press epair ebond eangle edihed pxx pyy pzz lx ly lz thermo 10 timestep 0.5 reset_timestep 0 run 50000 unfix 1 unfix 2 write_restart restart.${simname}.dreiding4 ##################################################### # Uniaxial Tensile Deformation run 0 variable tmp equal "lx" variable L0 equal ${tmp} variable strain equal "(lx - v_L0)/v_L0" variable p1 equal "v_strain" variable p2 equal "-pxx/10000*1.01325" variable p3 equal "-pyy/10000*1.01325" variable p4 equal "-pzz/10000*1.01325" variable p5 equal "lx" variable p6 equal "ly" variable p7 equal "lz" variable p8 equal "temp" variable t2 equal "epair" variable t3 equal "ebond" variable t4 equal "eangle" variable t5 equal "edihed" fix 1 all npt temp 100 100 50 y 0 0 1000 z 0 0 1000 drag 2 fix 2 all deform 1 x erate 1e-5 units box remap x fix def1 all print 100 "${p1} ${p2} ${p3} ${p4} ${p5} ${p6} ${p7} ${p8}" file ${simname}.def1.txt screen no fix def2 all print 100 "${p1} ${t2} ${t3} ${t4} ${t5}" file ${simname}.def2.txt screen no thermo_style custom step temp pxx pyy pzz lx ly lz epair ebond eangle edihed thermo 100 timestep 1 reset_timestep 0 run 171800 unfix 1 unfix 2 unfix def1 unfix def2 print "All done"