#################initialization################## units real atom_style full boundary p p p pair_style lj/cut/coul/long 9 bond_style harmonic angle_style harmonic dihedral_style opls kspace_style pppm 1.0e-4 ######## atom definition ######### read_restart fixed.restart ######## settings ######### neighbor 1.0 bin neigh_modify delay 0 every 1 check yes page 100000 one 2000 timestep 2 ####### groups & fixes #################### group g type 8 group Et type <> 3 7 group w type 1 2 group sol type <> 1 7 group w-g type 1 2 8 group Et-g type <> 3 8 group g1 id <> 13270 13949 group g2 id <> 13950 14629 neigh_modify exclude molecule g delete_bonds g bond 6 variable k equal 1000 fix g1 g1 spring/self ${k} z fix g11 g1 spring/self ${k} xy fix g2 g2 spring/self ${k} z fix g22 g2 spring/self ${k} xy fix rig g rigid/nvt molecule temp 298.15 298.15 100 fix shake w shake 0.0001 20 0 b 1 a 1 ################## variable ####################### variable D equal (f_rig[2][3]-f_rig[1][3]) variable x1 equal bound(g,xmin)-0.1 variable x2 equal bound(g,xmax)+0.1 variable y1 equal bound(g,ymin)-0.1 variable y2 equal bound(g,ymax)+0.1 variable z1 equal bound(g1,zmin)-0.1 variable z2 equal bound(g2,zmax)+0.1 ######### region #################### region confined block ${x1} ${x2} ${y1} ${y2} ${z1} ${z2} side in units box region bulk block EDGE EDGE EDGE EDGE EDGE ${z1} side in units box variable wc equal count(w,confined)/3 variable ec equal count(Et,confined)/9 variable sc equal v_wb+v_eb variable wb equal count(w,bulk)/3 variable eb equal count(Et,bulk)/9 variable sb equal v_wb+v_eb ################# thermo ###################### fix 3 sol nvt temp 298.15 298.15 100 thermo 50 thermo_style custom step cpu temp press pe v_D v_wc v_ec v_sc v_wb v_eb v_sb ################## dump & run & restart ################## restart 10000 run1.restart run2.restart run 300000 ################### average density & number ##################### fix avemass_Et Et ave/spatial 100 100 10000 z lower 0.5 density/mass file mass_densityEt ave running units box overwrite fix avenum_Et Et ave/spatial 100 100 10000 z lower 0.5 density/number file number_densityEt ave running units box overwrite fix avemass_w w ave/spatial 100 100 10000 z lower 0.5 density/mass file mass_densityw ave running units box overwrite fix avenum_w w ave/spatial 100 100 10000 z lower 0.5 density/number file number_densityw ave running units box overwrite fix avemass_sol sol ave/spatial 100 100 10000 z lower 0.5 density/mass file mass_densitysol ave running units box overwrite fix avenum_sol sol ave/spatial 100 100 10000 z lower 0.5 density/number file number_densitysol ave running units box overwrite fix avemass_Et1 Et ave/spatial 100 100 10000 z lower 1.0 density/mass file mass_densityEt1 ave running units box overwrite fix avenum_Et1 Et ave/spatial 100 100 10000 z lower 1.0 density/number file number_densityEt1 ave running units box overwrite fix avemass_w1 w ave/spatial 100 100 10000 z lower 1.0 density/mass file mass_densityw1 ave running units box overwrite fix avenum_w1 w ave/spatial 100 100 10000 z lower 1.0 density/number file number_densityw1 ave running units box overwrite fix avemass_sol1 sol ave/spatial 100 100 10000 z lower 1.0 density/mass file mass_densitysol1 ave running units box overwrite fix avenum_sol1 sol ave/spatial 100 100 10000 z lower 1.0 density/number file number_densitysol1 ave running units box overwrite ################### rdf ############################ compute myrdf all rdf 100 1 1 1 2 1 8 1 6 1 7 2 1 2 2 2 8 2 6 2 7 6 1 6 2 6 8 6 6 6 7 7 1 7 2 7 8 7 6 7 7 8 1 8 2 8 8 8 6 8 8 ##########################1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 fix frdf all ave/time 100 100 1000 c_myrdf file averdf.txt ave running mode vector overwrite dump 3 all custom 400 25ethgra-run.lammpstrj id mol type q x y z dump_modify 3 sort id dump 4 all custom 400 conf-25eth-run.lammpstrj id mol type q x y z dump_modify 4 sort id region confined dump 5 all custom 400 bulk-25eth-run.lammpstrj id mol type q x y z dump_modify 5 sort id region bulk dump 6 w custom 400 w25ethgra-run.lammpstrj id mol type q x y z dump_modify 6 sort id dump 7 w custom 400 wconf-25eth-run.lammpstrj id mol type q x y z dump_modify 7 sort id region confined dump 8 w custom 400 wbulk-25eth-run.lammpstrj id mol type q x y z dump_modify 8 sort id region bulk dump 9 Et custom 400 e25ethgra-run.lammpstrj id mol type q x y z dump_modify 9 sort id dump 10 Et custom 400 econf-25eth-run.lammpstrj id mol type q x y z dump_modify 10 sort id region confined dump 11 Et custom 400 ebulk-25eth-run.lammpstrj id mol type q x y z dump_modify 11 sort id region bulk dump 12 w-g custom 400 gw25ethgra-run.lammpstrj id mol type q x y z dump_modify 12 sort id dump 13 w-g custom 400 gwconf-25eth-run.lammpstrj id mol type q x y z dump_modify 13 sort id region confined dump 14 w-g custom 400 gwbulk-25eth-run.lammpstrj id mol type q x y z dump_modify 14 sort id region bulk dump 15 Et-g custom 400 gEethgra-run.lammpstrj id mol type q x y z dump_modify 15 sort id dump 16 Et-g custom 400 gEconf-25eth-run.lammpstrj id mol type q x y z dump_modify 16 sort id region confined dump 17 Et-g custom 400 gEbulk-25eth-run.lammpstrj id mol type q x y z dump_modify 17 sort id region bulk dump 18 sol custom 400 sol25ethgra-run.lammpstrj id mol type q x y z dump_modify 18 sort id dump 19 sol custom 400 solconf-25eth-run.lammpstrj id mol type q x y z dump_modify 19 sort id region confined dump 20 sol custom 400 solbulk-25eth-run.lammpstrj id mol type q x y z dump_modify 20 sort id region bulk restart 10000 run3.restart run4.restart run 200000