units real boundary p p p atom_style full pair_style lj/class2/coul/cut 8.0 bond_style class2 angle_style class2 dihedral_style class2 improper_style class2 read_data mycell30.data velocity all create 300.0 1238 dump dump1 all dcd 500 dumpnvt.dcd dump_modify dump1 unwrap yes fix relax all box/relax iso 0.0 vmax 0.001 minimize 1.0e-14 1.0e-16 10000000 100000000 unfix relax timestep 1.0 thermo 5000 thermo_style custom step temp press etotal pe ke density pxx pyy cpu #--------------------------------------------------- #--------------------------------------------------- fix nvt1 all nvt temp 300.00 600.00 100 run 700000 unfix nvt1 fix nvt2 all nvt temp 600.0 300.0 100 run 700000 unfix nvt2 #--------------------------------------------------- #--------------------------------------------------- fix npt1 all npt temp 300.0 300.0 100 iso 0.0 0.0 1000 run 300000 write_data system_after_eq.txt unfix npt1 #--------------------------------------------------- fix nve all nve fix langevin all langevin 300 300 100 128 thermo 4000 thermo_style custom step temp press etotal pe ke run 200000 unfix langevin unfix nve undump dump1 #................................................................................................. variable t equal 300.0 variable srate equal 0.0001 # second srate can be assumed to be 0.00001 velocity all scale $t variable xyrate equal ${srate}/ly change_box all triclinic units box fix 1 all nvt/sllod temp $t $t 100 fix 2 all deform 10 xy erate ${xyrate} remap v units box compute layers all chunk/atom bin/1d y lower 0.05 units reduced fix 4 all ave/chunk 4 10 40 layers vx file profile1e-4.nemd compute usual all temp compute tilt all temp/deform thermo 4000 thermo_style custom step temp c_usual press pxy etotal pe ke density thermo_modify temp tilt run 300000 # data gathering run variable visc equal -pxy/(v_srate/ly) fix vave all ave/time 10 100 1000 v_visc ave running # start 400000 thermo_style custom step temp press pxy v_visc f_vave thermo_modify temp tilt dump 1 all dcd 1000 dump1e-4.dcd dump_modify 1 unwrap yes run 600000