#making groups variable r equal 1 variable a equal 0.0 shell mkdir dir$r/dump shell mkdir dir$r/restart shell mkdir dir$r/logfile shell mkdir dir$r/output variable conc equal 1 #doesn't mean anything ###################################### units real atom_style full dimension 3 newton on processors * * 2 boundary p p f read_data input_data/embfnew.dat #read_restart dir$r/input_data/ ################################################ ############force field######################## ############################################ pair_style lj/cut/coul/long 12 bond_style harmonic angle_style harmonic dihedral_style opls kspace_style pppm/electrode 1.0e-6 kspace_modify slab 3 fix zwalls all wall/reflect zlo EDGE zhi EDGE units box pair_coeff 1 1 0.095 3.5814 # B1 pair_coeff 2 2 0.085 3.55 # C1 pair_coeff 3 3 0.085 3.55 # C2 pair_coeff 4 4 0.085 3.55 # C3 pair_coeff 5 5 0.109 3.55 # C4 pair_coeff 6 6 0.109 3.55 # C5 pair_coeff 7 7 0.109 3.55 # C6 pair_coeff 8 8 0.06 3.1181 # F1 pair_coeff 9 9 0.06 3.1181 # F2 pair_coeff 10 10 0.06 3.1181 # F3 pair_coeff 11 11 0.06 3.1181 # F4 pair_coeff 12 12 0.0474 3.211 # A1 pair_coeff 13 13 0.03 2.42 # H1 pair_coeff 14 14 0.03 2.5 # H10 pair_coeff 15 15 0.03 2.42 # H11 pair_coeff 16 16 0.03 2.42 # H2 pair_coeff 17 17 0.03 2.5 # H3 pair_coeff 18 18 0.03 2.5 # H4 pair_coeff 19 19 0.03 2.5 # H5 pair_coeff 20 20 0.03 2.5 # H6 pair_coeff 21 21 0.03 2.5 # H7 pair_coeff 22 22 0.03 2.5 # H8 pair_coeff 23 23 0.03 2.5 # H9 pair_coeff 24 24 0.17 3.25 # N1 pair_coeff 25 25 0.17 3.25 # N2 pair_coeff 26 26 0.0474 3.211 # A2 pair_modify shift yes mix arithmetic bond_coeff 1 386.36 1.39 bond_coeff 2 340 1.08 bond_coeff 3 340 1.08 bond_coeff 4 340 1.09 bond_coeff 5 340 1.09 bond_coeff 6 340 1.09 bond_coeff 7 268 1.529 bond_coeff 8 337 1.466 bond_coeff 9 477 1.315 bond_coeff 10 427 1.378 bond_coeff 11 521 1.341 angle_coeff 1 35 130.9 # C1-C2-H2 angle_coeff 2 70 107.1 # C1-C2-N2 angle_coeff 3 70 108 # C1-N1-C3 angle_coeff 4 70 125.6 # C1-N1-C5 angle_coeff 5 35 130.9 # C2-C1-H1 angle_coeff 6 70 107.1 # C2-C1-N1 angle_coeff 7 70 108 # C2-N2-C3 angle_coeff 8 70 126.8 # C2-N2-C6 angle_coeff 9 70 126.4 # C3-N1-C5 angle_coeff 10 70 126.4 # C3-N2-C6 angle_coeff 11 37.5 109.7 # C4-C6-H3 angle_coeff 12 37.5 109.7 # C4-C6-H4 angle_coeff 13 58.35 112.7 # C4-C6-N2 angle_coeff 14 37.5 110.7 # C6-C4-H10 angle_coeff 15 37.5 110.7 # C6-C4-H8 angle_coeff 16 37.5 110.7 # C6-C4-H9 angle_coeff 17 80 109.47 # F1-B1-F2 angle_coeff 18 80 109.47 # F1-B1-F3 angle_coeff 19 80 109.47 # F1-B1-F4 angle_coeff 20 80 109.47 # F2-B1-F3 angle_coeff 21 80 109.47 # F2-B1-F4 angle_coeff 22 80 109.47 # F3-B1-F4 angle_coeff 23 35 122 # H1-C1-N1 angle_coeff 24 33 107.9 # H10-C4-H8 angle_coeff 25 33 107.9 # H10-C4-H9 angle_coeff 26 35 125.1 # H11-C3-N1 angle_coeff 27 35 125.1 # H11-C3-N2 angle_coeff 28 35 122 # H2-C2-N2 angle_coeff 29 33 108.9 # H3-C6-H4 angle_coeff 30 37.5 107.5 # H3-C6-N2 angle_coeff 31 37.5 107.5 # H4-C6-N2 angle_coeff 32 33 109.8 # H5-C5-H6 angle_coeff 33 33 109.8 # H5-C5-H7 angle_coeff 34 37.5 109.2 # H5-C5-N1 angle_coeff 35 33 109.8 # H6-C5-H7 angle_coeff 36 37.5 109.2 # H6-C5-N1 angle_coeff 37 37.5 109.2 # H7-C5-N1 angle_coeff 38 33 107.9 # H8-C4-H9 angle_coeff 39 70 109.8 # N1-C3-N2 dihedral_coeff 1 -3.23 0 0 0 # C1-C2-N2-C3 dihedral_coeff 2 -3.23 0 0 0 # C1-C2-N2-C6 dihedral_coeff 3 -3.23 0 0 0 # C2-C1-N1-C3 dihedral_coeff 4 -3.23 0 0 0 # C2-C1-N1-C5 dihedral_coeff 5 -3.23 0 0 0 # C4-C6-N2-C2 dihedral_coeff 6 -3.23 0 0 0 # C4-C6-N2-C3 dihedral_coeff 7 0 0 1.331 0 # H1-C1-C2-H2 dihedral_coeff 8 0 0 0.35 0 # H1-C1-C2-N2 dihedral_coeff 9 0 0 0 0 # H1-C1-N1-C3 dihedral_coeff 10 0 0 0 0 # H1-C1-N1-C5 dihedral_coeff 11 0 0 1.331 0 # H10-C4-C6-H3 dihedral_coeff 12 0 0 1.331 0 # H10-C4-C6-H4 dihedral_coeff 13 0 0 0.35 0 # H10-C4-C6-N2 dihedral_coeff 14 0 0 0 0 # H11-C3-N1-C1 dihedral_coeff 15 0 0 0 0 # H11-C3-N1-C5 dihedral_coeff 16 0 0 0 0 # H11-C3-N2-C2 dihedral_coeff 17 0 0 0 0 # H11-C3-N2-C6 dihedral_coeff 18 0 0 0 0 # H2-C2-N2-C3 dihedral_coeff 19 0 0 0 0 # H2-C2-N2-C6 dihedral_coeff 20 0 0 0 0 # H3-C6-N2-C2 dihedral_coeff 21 0 0 0 0 # H3-C6-N2-C3 dihedral_coeff 22 0 0 0 0 # H4-C6-N2-C2 dihedral_coeff 23 0 0 0 0 # H4-C6-N2-C3 dihedral_coeff 24 0 0 0 0 # H5-C5-N1-C1 dihedral_coeff 25 0 0 0 0 # H5-C5-N1-C3 dihedral_coeff 26 0 0 0 0 # H6-C5-N1-C1 dihedral_coeff 27 0 0 0 0 # H6-C5-N1-C3 dihedral_coeff 28 0 0 0 0 # H7-C5-N1-C1 dihedral_coeff 29 0 0 0 0 # H7-C5-N1-C3 dihedral_coeff 30 0 0 1.331 0 # H8-C4-C6-H3 dihedral_coeff 31 0 0 1.331 0 # H8-C4-C6-H4 dihedral_coeff 32 0 0 0.35 0 # H8-C4-C6-N2 dihedral_coeff 33 0 0 1.331 0 # H9-C4-C6-H3 dihedral_coeff 34 0 0 1.331 0 # H9-C4-C6-H4 dihedral_coeff 35 0 0 0.35 0 # H9-C4-C6-N2 dihedral_coeff 36 0 0 0.35 0 # N1-C1-C2-H2 dihedral_coeff 37 0 0 0 0 # N1-C1-C2-N2 dihedral_coeff 38 0 4.65 0 0 # N1-C3-N2-C2 dihedral_coeff 39 0 4.65 0 0 # N1-C3-N2-C6 dihedral_coeff 40 0 4.65 0 0 # N2-C3-N1-C1 dihedral_coeff 41 0 4.65 0 0 # N2-C3-N1-C5 #dihedral_modify mix arithmetic mass 1 10.811 # B1 mass 2 12.0107 # C1 mass 3 12.0107 # C2 mass 4 12.0107 # C3 mass 5 12.0107 # C4 mass 6 12.0107 # C5 mass 7 12.0107 # C6 mass 8 18.998404 # F1 mass 9 18.998404 # F2 mass 10 18.998404 # F3 mass 11 18.998404 # F4 mass 12 12.0107 # A1 mass 13 1.00794 # H1 mass 14 1.00794 # H10 mass 15 1.00794 # H11 mass 16 1.00794 # H2 mass 17 1.00794 # H3 mass 18 1.00794 # H4 mass 19 1.00794 # H5 mass 20 1.00794 # H6 mass 21 1.00794 # H7 mass 22 1.00794 # H8 mass 23 1.00794 # H9 mass 24 14.0067 # N1 mass 25 14.0067 # N2 mass 26 12.0107 # A2 #systems group emim type 2 3 4 5 6 7 13 14 15 16 17 18 19 20 21 22 23 24 25 group bf4 type 1 8 9 10 11 group elec1 type 12 group elec2 type 26 group sol type 1 2 3 4 5 6 7 8 9 10 11 13 14 15 16 17 18 19 20 21 22 23 24 25 group syst type 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 26 group ele type 12 26 group electrolyte_atoms type 1 2 3 4 5 6 7 8 9 10 11 13 14 15 16 17 18 19 20 21 22 23 24 25 #charges set type 1 charge 0.8276 # B1 set type 2 charge -0.234152 # C1 set type 3 charge -0.1743 # C2 set type 4 charge -0.193391 # C3 set type 5 charge -0.2382 # C4 set type 6 charge -0.4592 # C5 set type 7 charge -0.059 # C6 set type 8 charge -0.4569 # F1 set type 9 charge -0.4569 # F2 set type 10 charge -0.4569 # F3 set type 11 charge -0.4569 # F4 set type 12 charge 0 # A1 set type 13 charge 0.216 # H1 set type 14 charge 0.08989 # H10 set type 15 charge 0.24425 # H11 set type 16 charge 0.216 # H2 set type 17 charge 0.079913 # H3 set type 18 charge 0.080778 # H4 set type 19 charge 0.1965 # H5 set type 20 charge 0.1997 # H6 set type 21 charge 0.1934 # H7 set type 22 charge 0.114394 # H8 set type 23 charge 0.096046 # H9 set type 24 charge 0.3385 # N1 set type 25 charge 0.1165 # N2 set type 26 charge 0 # A2 #modification run_style verlet neighbor 2.0 bin neigh_modify exclude group ele ele check no neigh_modify delay 0 every 1 check yes log dir$r/logfile/log_${conc} timestep 0.05 thermo 1000 compute t_sol sol temp fix 5 ele setforce 0.0 0.0 0.0 fix 6 sol shake 0.0001 20 0 b 7 8 a 1 2 minimize 1.0e-4 1.0e-6 100 1000 velocity sol create 0.1 86289 dump 1 syst custom 10000 dir$r/dump/dump-${conc}.lammpstrj id mol type x y z q dump_modify 1 sort id dump 2 syst custom 50000 dir$r/dump/dumpall-${conc}.lammpstrj id mol type x y z q dump_modify 2 sort id restart 100000 dir$r/output/x.r_${conc} dump 3 syst custom 1000 dir$r/dump/dump1.lammpstrj id type x y z q dump_modify 3 sort id fix 3 sol nvt temp 298.0 298.0 $(100.0*dt) fix_modify 3 temp t_sol run 4000000 unfix 3 write_restart dir$r/finalpart1.rest write_data dir$r/finalpart1.dat undump 3