# input script for SWNT simulation in LAMMPS #-------10--------20--------30--------40--------50--------60--------70--------80 # Variables variable input index gps-silane-model-2240atoms.txt # INITIALIZATION units real boundary s s s atom_style full processors 3 3 2 # ATOM DEFINITION read_data ${input} # FORCE FIELD pair_style reax/c NULL pair_coeff * * ffield.reax C H O Si # SETTINGS neighbor 1.0 bin neigh_modify delay 1 # ------------------------------ RELAXATION ----------------------------------- # ------------------------------------------------------------------------------ variable peng equal pe variable keng equal ke variable temp equal temp variable Pr equal press variable istep equal step group HinWater type 1 group OinWater type 2 group OinSilica type 3 group SiinSilica type 4 group water type 1 type 2 group silica type 3 type 4 region section block INF 25.0 INF INF INF INF units box region leftsisur block INF INF INF INF -1.5 20.0 units box region rightsisur block INF INF INF INF 20.0 40.5 units box group section region section group leftsisur region leftsisur group rightsisur region rightsisur # ------- calculate mean square distance --------------------------------------- compute 5 HinWater msd compute 6 OinWater msd compute 7 OinSilica msd compute 8 SiinSilica msd variable msd_HinWater equal c_5[4] variable msd_OinWater equal c_6[4] variable msd_OinSilica equal c_7[4] variable msd_SiinSilica equal c_8[4] fix 5 HinWater print 100 "${istep},${msd_HinWater}" file msd_HinWater.txt screen no fix 6 OinWater print 1000 "${istep},${msd_OinWater}" file msd_OinWater.txt screen no fix 7 OinSilica print 1000 "${istep},${msd_OinSilica}" file msd_OinSilica.txt screen no fix 8 SiinSilica print 1000 "${istep},${msd_SiinSilica}" file msd_SiinSilica.txt screen no # ------- calculate RDF -------------------------------------------------------- compute 10 all rdf 50 4 1 compute 11 all rdf 50 4 2 compute 12 all rdf 50 4 3 compute 13 all rdf 50 4 4 fix 10 all ave/time 10 10 50000 c_10 file water-silane-rdf41.rdf mode vector fix 11 all ave/time 10 10 50000 c_11 file water-silane-rdf42.rdf mode vector fix 12 all ave/time 10 10 50000 c_12 file water-silane-rdf43.rdf mode vector fix 13 all ave/time 10 10 50000 c_13 file water-silane-rdf44.rdf mode vector # ------- calculate mass density ----------------------------------------------- fix 24 HinWater ave/spatial 10 10 50000 z lower 0.5 density/mass file density-HinWater.profile units box fix 25 OinWater ave/spatial 10 10 50000 z lower 0.5 density/mass file density-OinWater.profile units box fix 26 OinSilica ave/spatial 10 10 50000 z lower 0.5 density/mass file density-OinSilica.profile units box fix 27 SiinSilica ave/spatial 10 10 50000 z lower 0.5 density/mass file density-SiinSilica.profile units box # ------------------------------------------------------------------------------ thermo_style custom step cpu temp pe vol pzz # ------- calculate RDF -------------------------------------------------------- # ------- calculate RDF -------------------------------------------------------- # output for VMD dump 2 all xyz 5000 dump.silica-water-coord-xyz-format dump_modify 2 element C H O Si dump 3 water custom 5000 dump.water-coordinate id type x y z dump 4 silica custom 5000 dump.silica-coordinate id type x y z dump 5 section custom 10000 dump.silica-water-section id type x y z # dump 6 leftsisur custom 10000 dump.silica-left-surface id type x y z # dump 7 rightsisur custom 10000 dump.silica-right-surface id type x y z fix 30 all print 100 "${istep}, ${peng}, ${keng}, ${temp},${Pr}" file silica-water-silane-etp-data.txt screen no thermo 500 # ------------------------------------------------------------------------------ timestep 0.5 # fix 41 all reax/c/species 1 1 10 species-water.out cutoff 1 2 0.35 cutoff 4 3 0.35 cutoff 3 1 0.35 cutoff 4 2 0.35 fix 410 all reax/c/species 1 1 100 species-water.out element C H O Si # fix 420 silica reax/c/species 1 1 100 species-silica.out cutoff 4 3 0.35 # fix 430 all reax/c/species 1 1 100 species-silanol-01.out cutoff 3 1 0.35 # fix 440 all reax/c/species 1 1 100 species-silanol-02.out cutoff 4 2 0.35 fix 450 all reax/c/bonds 5000 bonds.txt velocity all create 300.0 12345 mom yes rot no fix 46 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c fix 50 all wall/reflect xlo -0.5 xhi 50.5 ylo -0.5 yhi 50.5 zlo 22.5 zhi 43.0 units box fix 60 all nvt temp 300.0 300.0 100.0 run 200000 print "Run is complete!"