# Bead-spring polymer simulation log log.nvt.2000 boundary p f f atom_style bond read_data data.chain neighbor 0.3 bin neigh_modify every 1 delay 1 bond_style fene bond_coeff 1 30.0 1.5 1.0 1.0 special_bonds 0.0 1.0 1.0 # interaction between polymer molecules in different regions pair_style hybrid lj/cut 2.5 soft 1.12246 pair_coeff 1 1 soft 0.0 60.0 1.12246 pair_coeff 1 2* lj/cut 1.0 1.0 1.0 pair_coeff 2* 2* lj/cut 1.0 1.0 0.0 # setting wall atoms as boundary group boundary molecule 0 group flow subtract all boundary group l1 type 2 group l2 type 3 group l3 type 4 group l4 type 5 group u1 type 6 group u2 type 7 group u3 type 8 group u4 type 9 group lowerwall union l1 l2 l3 l4 group upperwall union u1 u2 u3 u4 group crosssection union flow lowerwall upperwall compute mobile flow temp velocity flow create 1.0 387093 loop geom fix 1 all nve fix 2 flow langevin 1.0 1.0 1.0 987234 thermo_modify temp mobile fix 3 boundary setforce 0.0 0.0 0.0 thermo 1000 timestep 1.0e-2 #dump 1 crosssection custom 1000 type.xyz type #dump 2 crosssection custom 1000 index.xyz tag ##dump 3 crosssection custom 1000 flowx.xyz x #dump 4 crosssection custom 1000 flowy.xyz y #dump 5 crosssection custom 1000 flowz.xyz z ##dump 1 all xyz 1000 flow.xyz #dump 15 flow custom 1 y1.xyz y #dump 16 flow custom 1 z1.xyz z run 50000 # main run with LJ potentials # interaction between polymer molecules in different regions pair_style lj/cut 1.12246 pair_modify shift yes pair_coeff 1 1 1.0 1.0 1.12246 pair_coeff 1 2* 1.0 1.0 1.12 pair_coeff 2* 2* 1.0 1.0 0.0 reset_timestep 0 #dump 6 all custom 2001 atom_id.xyz tag #dump 7 all custom 2001 mol_id.xyz mol #dump 8 all custom 2001 x.xyz x #dump 9 all custom 2001 y.xyz y #dump 10 all custom 2001 z.xyz z #dump 11 all custom 2001 ix.xyz ix #dump 12 all custom 2001 iy.xyz iy #dump 13 all custom 2001 iz.xyz iz #dump 14 all custom 2001 atom_type.xyz type run 2000