# # polymer melt variable chi equal 0.1 variable run equal 1 variable kappa equal 25 variable rho0 equal 2.276 variable tname string chi${chi} variable name string ${tname}_${run} variable datafile string melt.data units lj atom_style molecular boundary p p p log log.${name} read_data ${datafile} pair_style zero 3.0 nocoeff pair_coeff * * bond_style harmonic ## group NPs, blocks, homopolymers group A type 1 group B type 1 bond_coeff * 1.5 0 ## Communication - binding sites do not particiapte in non-bonded interactions so exclude from the list to save time comm_modify cutoff 5 neighbor 3 bin neigh_modify every 01 delay 0 check yes velocity all zero linear ## output frequency variables variable nsteps equal 1e4 variable gridFreq equal ${nsteps}/10 variable Ngridevery equal ${gridFreq}/100 variable Ngridrepeat equal 10 variable partFreq equal ${nsteps}/20 variable partFreq equal 1 variable thermoFreq equal ${nsteps}/100 variable densityFreq equal ${nsteps}/20 variable msdFreq equal ${nsteps}/20 ## Interactions mass 1 1.0 mass 2 1.0 ## fixes ## create bonds wiht a certain probability # fix 1 all bond/create Nevery itype jtype Rmin bondtype iparam max_bonds new_atomtype keyword values ... fix 1 all bond/create 10 1 2 1.0 1 prob 0.5 12345 iparam 2 1 jparam 2 2 ## integrators fix 2 all langevin 1.0 1.0 1.0 12345 gjf yes zero yes fix 3 all nve ## equilibrate if first run at lower timestep if "(${run} == 1)" then & "timestep 0.0001" & "run 1000" # Traj output dump trj all custom ${partFreq} ${name}.dump id type mol x y z dump_modify trj sort id # Thermo output thermo ${thermoFreq} thermo_style custom step ebond epair ecoul pe temp press pxx pyy pzz pxy pxz pyz thermo_modify norm no ## Run timestep 0.02 run ${nsteps} write_data ${name}.data write_restart ${name}.restart