variable radius equal 7.5 variable d equal ${radius}*2 print "diameter of nanopore is ${d} Angstroms" variable Temp equal 300 print "Temperature is ${Temp} K" variable step equal .1 variable time equal 0.5 print "simulation time is ${time} ns" variable runtime equal ${time}*1000000/${step} print "iterations: ${runtime} steps" units real atom_style full boundary p p p special_bonds 0.0 0.0 1.0 pair_style sw bond_style none angle_style none dihedral_style none improper_style none kspace_style none read_restart restart-nve-300.5000000 newton on pair_coeff * * mW.sw Si Si neighbor 2.0 bin neigh_modify every 2 delay 10 check yes timestep ${step} # from make pore input: region within1 cylinder z 15 15 ${radius} -INF INF units box region within2 block INF INF INF INF -INF 2 units box # check that it produces a slab of about 10 A !! group inside1 region within1 group inside2 region within2 group liquid union inside1 inside2 group wall subtract all liquid set group wall type 2 set group liquid type 1 fix 1 wall spring/self 5.0 #-- reset_timestep 0 #equilibrate at the given temperature fix 2 all npt ${Temp} ${Temp} 250.0 xy NULL NULL NULL NULL 0. 0. 3000.0 #run 100000 unfix 2 reset_timestep 0 compute 2 liquid pe/atom compute 3 liquid ke/atom compute 4 liquid reduce sum c_2 compute 5 liquid reduce sum c_3 variable Eliquid equal "c_4 + c_5" thermo_style custom step temp pe etotal press vol pxx pyy pzz lx ly lz c_4 c_5 v_Eliquid thermo_modify flush yes thermo 1000 fix 3 all momentum 5000 linear 1 1 1 compute 1 all coord/atom 3.5 fix 4 all nve dump 1 all custom 10000 nve-diam$d-${Temp}.lammpstrj tag type xs ys zs ix iy iz c_1 restart 500000 restart-nve-${Temp} run ${runtime} #unfix 5 unfix 4 undump 1