#water wet to oil wet changing # Initalization units real atom_style full boundary p p p log pps.log dimension 3 # Atom Definition read_data oil.data extra/atom/types 5 extra/bond/types 2 extra/angle/types 2 group oil read_data calcite.data add append offset 10 10 15 0 0 group solid read_data water.data add append offset 13 11 16 0 0 group water #change_box water y final -49 49 #change_box oil y final -49 49 #change_box water x final -49 49 #change_box oil x final -49 49 set type 1 charge 0 set type 2 charge -0.18 set type 3 charge 0 set type 4 charge 0.52 set type 5 charge 0 set type 6 charge 0.06 set type 7 charge 0.45 set type 8 charge 0 set type 9 charge -0.44 set type 10 charge -0.53 set type 11 charge 1.123282 set type 12 charge 2.0 set type 13 charge -1.041094 set type 14 charge 0.4238 set type 15 charge -0.8476 pair_style hybrid lj/cut/coul/long 10 12 lj/cut 10 # Pair Coeffs # # 1 C (ndecane) # 2 C1 (heptanoic acid) # 3 C3 (toluene) # 4 C4 (duble bond heptanoic acid) # 5 H (ndecane) # 6 H1 (heptanoic acid) # 7 H2 (bond to O, heptanoic acid) # 8 H3 (toluene) # 9 O1 (duble bond-heptanoic acid) # 10 O2 (heptanoic acid) # 11 C2 (calcite) # 12 Ca1(calcite) # 13 O3 (calcite) # 14 H4 (water) # 15 O4 (water) #--------------------------------------- #rock-rock #------------------------------------------ pair_coeff 11 11 lj/cut/coul/long 0.105 3.75 pair_coeff 12 12 lj/cut/coul/long 0.1 2.895 pair_coeff 13 13 lj/cut/coul/long 0.21 2.96 #------------------------------------------------ #oil-oil #--------------------------------------------- pair_coeff 2 2 lj/cut/coul/long 0.06609 3.5 pair_coeff 4 4 lj/cut/coul/long 0.105 3.75 pair_coeff 6 6 lj/cut/coul/long 0.0150 2.420 pair_coeff 7 7 lj/cut/coul/long 0.0 0.0 pair_coeff 9 9 lj/cut/coul/long 0.2103 2.960 pair_coeff 10 10 lj/cut/coul/long 0.1702 3.0 pair_coeff 3 3 lj/cut/coul/long 0.070 3.9848 pair_coeff 8 8 lj/cut/coul/long 0.030 2.7264 pair_coeff 1 1 lj/cut/coul/long 0.066 3.5 pair_coeff 5 5 lj/cut/coul/long 0.030 2.5 #...................................... #rock-oil #-------------------------------------- pair_coeff 2 11 lj/cut/coul/long 0.0833033613 3.625 pair_coeff 4 11 lj/cut/coul/long 0.105 3.75 pair_coeff 6 11 lj/cut/coul/long 0.0396862697 3.085 pair_coeff 7 11 lj/cut/coul/long 0.0 0.0 pair_coeff 9 11 lj/cut/coul/long 0.148598452 3.355 pair_coeff 10 11 lj/cut/coul/long 0.13368246 3.375 pair_coeff 3 11 lj/cut 0.0815904406 3.94155 pair_coeff 8 11 lj/cut 0.0534134814 3.31235 pair_coeff 1 11 lj/cut 0.072976709 3.95915 pair_coeff 5 11 lj/cut 0.0568629932 3.78915 pair_coeff 2 12 lj/cut/coul/long 0.081614337 3.1975 pair_coeff 4 12 lj/cut/coul/long 0.102469508 3.32225 pair_coeff 6 12 lj/cut/coul/long 0.0387298335 2.6575 pair_coeff 7 12 lj/cut/coul/long 0.0 0.0 pair_coeff 9 12 lj/cut/coul/long 0.14501724 2.9275 pair_coeff 10 12 lj/cut/coul/long 0.130460722 2.9475 pair_coeff 3 12 lj/cut 0.0591607978 3.7284 pair_coeff 8 12 lj/cut 0.0387298335 3.0992 pair_coeff 1 12 lj/cut 0.0529150262 3.746 pair_coeff 5 12 lj/cut 0.0412310563 3.576 pair_coeff 2 13 lj/cut/coul/long 0.117808743 3.23 pair_coeff 4 13 lj/cut/coul/long 0.148492424 3.355 pair_coeff 6 13 lj/cut/coul/long 0.0561248608 2.69 pair_coeff 7 13 lj/cut/coul/long 0.0 0.0 pair_coeff 9 13 lj/cut/coul/long 0.210149946 2.96 pair_coeff 10 13 lj/cut/coul/long 0.189055547 2.98 pair_coeff 3 13 lj/cut 0.081847419 3.6947 pair_coeff 8 13 lj/cut 0.0535817133 3.0655 pair_coeff 1 13 lj/cut 0.0732065571 3.7123 pair_coeff 5 13 lj/cut 0.0570420897 3.5423 #------------------------------------------------ #water-water #------------------------------------------------ pair_coeff 14 14 lj/cut/coul/long 0.0 0.0 pair_coeff 15 15 lj/cut/coul/long 0.1553 3.166 #--------------------------------------- #other #--------------------------------------- pair_modify mix arithmetic # Bond Coeffs # # 1 C-C # 2 C-H # 3 C1-C1 # 4 C1-C4 # 5 C1-H1 # 6 C3-C3 # 7 C3-H3 # 8 C4-O1 # 9 C4-O2 # 10 H2-O2 # 11 C2-O3 # 12 H4-O4 bond_style harmonic #!Kb: kcal/mole/A**2 bond_coeff 1 536.000 1.5290 bond_coeff 2 680.000 1.09 bond_coeff 3 317.44 1.522 bond_coeff 4 317.44 1.522 bond_coeff 5 340.48 1.09 bond_coeff 6 305.000 1.3750 bond_coeff 7 340.000 1.0800 bond_coeff 8 570.80 1.229 bond_coeff 9 450.63 1.364 bond_coeff 10 553.77 0.945 bond_coeff 11 350.000 1.2200 bond_coeff 12 350.000 1.0000 # Angle Coeffs # # 1 C-C-C # 2 C-C-H # 3 C1-C1-C1 # 4 C1-C1-C4 # 5 C1-C1-H1 # 6 C1-C4-O1 # 7 C1-C4-O2 # 8 C3-C3-C3 # 9 C3-C3-H3 # 10 C4-C1-H1 # 11 C4-O2-H2 # 12 H-C-H # 13 H1-C1-H1 # 14 H3-C3-H3 # 15 O1-C4-O2 # 16 O3-C2-O3 # 17 H4-O4-H4 mass 11 12.010700 # C2 mass 12 40.077999 # Ca1 mass 13 15.999400 # O3 mass 14 1.007940 # H4 mass 15 15.999400 # O4 angle_style harmonic angle_coeff 1 0.0 0.0 angle_coeff 2 0.0 0.0 angle_coeff 3 0.0 0.0 angle_coeff 4 0.0 0.0 angle_coeff 5 0.0 0.0 angle_coeff 6 80.11 120.4 angle_coeff 7 70.1 108 angle_coeff 8 0.0 0.0 angle_coeff 9 0.0 0.0 angle_coeff 10 35.05 109.5 angle_coeff 11 35.05 113 angle_coeff 12 0.0 0.0 angle_coeff 13 0.0 0.0 angle_coeff 14 0.0 0.0 angle_coeff 15 80.11 121 angle_coeff 16 0.0 0.0 angle_coeff 17 96 109.4 kspace_style ewald 1e-4 #kspace_modify slab 3.0 group oil type 1 2 3 4 5 6 7 8 9 10 group solid type 11 12 13 group heptanoicacid type 2 4 6 7 9 10 group decane type 1 5 group toluene type 3 8 group water type 14 15 delete_atoms overlap 0.1 all all mol yes write_data after_deleting_atoms.data neighbor 0.3 bin neigh_modify delay 0 every 1 check yes #velocity all create 298.0 12345678 dist uniform fix 1 solid setforce 0.0 0.0 0.0 velocity solid set 0 0 0 fix 2 solid rigid group 1 solid fix 3 all nvt temp 298.0 298.0 10 #minimize 1.0e-4 1.0e-6 1000 10000 #min_style cg fix 5 water shake 1e-5 1000 0 b 12 a 17 #timestep 1 dump 01 all xyz 1000 dump*.xyz dump_modify 01 element C C1 C2 C3 C4 Ca1 H H1 H2 H3 H4 O1 O2 O3 O4 dump 02 all atom 1000 wetting.dump dump_modify 02 sort id compute 1 oil com compute 2 water msd compute 3 all pe/atom compute myrdf all rdf 5000 11 1 11 3 11 4 compute 01 water reduce sum c_3 compute 02 heptanoicacid reduce sum c_3 compute 03 decane reduce sum c_3 compute 04 toluene reduce sum c_3 compute 05 solid reduce sum c_3 #fix 6 oil ave/time 5 1000 10000 c_1[*] file oil_com.txt mode vector #fix 7 water ave/time 5 1000 10000 c_2[*] file water_msd.txt mode vector #fix 8 all ave/time 5 1000 10000 c_myrdf[*] file spce.rdf mode vector thermo 10 thermo_style custom step temp press c_02 c_03 c_04 c_05 write_restart restart.equil #run 100000 #reset_atom_ids write_data final*.data