#lammps input script file for simualting a pnc #equilibration is followed by series of nvt and npt simulations #final temperature for pullout of cnt from polymer is 100 K units real dimension 3 boundary p p p atom_style full #read data and force field files read_data box_dimensions.data include force_field.data read_data pnc_0.6.data add merge #set type ${C3} charge 0.0000 #set type ${C4} charge -0.1060 #set type ${H} charge 0.0530 thermo 100 thermo_style custom step atoms temp press pe ke evdwl ecoul epair ebond eangle edihed eimp etotal vol density compute pnc_bond all property/local btype batom1 batom2 compute pnc_bond1 all bond/local dist engpot compute pnc_temp all temp compute pnc_pe all pe/atom compute pnc_stress all stress/atom pnc_temp pair bond compute pnc_str all reduce sum c_pnc_stress[3] min_style cg minimize 1.0e-4 1.0e-6 1000 100000 reset_timestep 0 timestep 0.5 fix 1 all nvt temp 300 300 100 #dump step_1 all custom 100 dump.nvt id type x y z #dump bond_data all local 100 dump.bond index c_pnc_bond[1] c_pnc_bond[2] c_pnc_bond[3] c_pnc_bond1[1] c_pnc_bond1[2] run 200000 write_restart restart_nvt.equi unfix 1 shell mkdir npt shell cd npt reset_timestep 0 timestep 0.5 thermo_style custom step atoms temp press pe ke evdwl ecoul epair ebond eangle edihed eimp etotal vol density fix 2 all npt temp 300.0 600.0 100.0 iso 1.0 1.0 100.0 #dump npt1 all custom 100 dump.npt1 id type x y z #dump bond_data1 all local 100 dump.bond1 index c_pnc_bond[1] c_pnc_bond[2] c_pnc_bond[3] c_pnc_bond1[1] c_pnc_bond1[2] run 300000 write_restart restart.npt1 unfix 2 reset_timestep 0 timestep 0.5 thermo_style custom step atoms temp press pe ke evdwl ecoul epair ebond eangle edihed eimp etotal vol density fix 3 all npt temp 600.0 600.0 100.0 iso 1.0 1.0 100.0 #dump npt2 all custom 100 dump.npt2 id type x y z #dump bond_data2 all local 100 dump.bond2 index c_pnc_bond[1] c_pnc_bond[2] c_pnc_bond[3] c_pnc_bond1[1] c_pnc_bond1[2] run 200000 write_restart restart.npt2 unfix 3 reset_timestep 0 timestep 0.5 thermo_style custom step atoms temp press pe ke evdwl ecoul epair ebond eangle edihed eimp etotal vol density fix 4 all npt temp 600.0 100.0 100.0 iso 1.0 1.0 100.0 #dump npt3 all custom 100 dump.npt3 id type x y z #dump bond_data3 all local 100 dump.bond3 index c_pnc_bond[1] c_pnc_bond[2] c_pnc_bond[3] c_pnc_bond1[1] c_pnc_bond1[2] run 500000 write_restart restart.npt3 unfix 4 reset_timestep 0 timestep 0.5 thermo_style custom step atoms temp press pe ke evdwl ecoul epair ebond eangle edihed eimp etotal vol density fix 5 all npt temp 100.0 100.0 100.0 iso 1.0 1.0 100.0 #dump npt4 all custom 100 dump.npt4 id type x y z #dump bond_data4 all local 100 dump.bond4 index c_pnc_bond[1] c_pnc_bond[2] c_pnc_bond[3] c_pnc_bond1[1] c_pnc_bond1[2] run 600000 write_restart restart.npt4 unfix 5