#LAMMPS Input file # aqueous uranyl nitrate in zeo 2.43 # Intialization units real dimension 3 boundary p p p atom_style full atom_modify map array sort 500 2.0 # Atom Definition #read_restart restart.500000.equil read_data data.zeounw replicate 1 1 1 bond_style harmonic bond_coeff 1 300.290000000000 1.600000000000000 #Si-O bond_coeff 2 222.200000000000 1.70000000000000 #Al-O bond_coeff 3 30.0200000000000 3.12000000000000 #Si-O-Si bond_coeff 4 30.0200000000000 3.18000000000000 #Al-O-Si bond_coeff 5 1000.95000000000 1.80000000000000 #U-OU bond_coeff 6 600.57000000000 1.26000000000000 #N-ON bond_coeff 7 700.000000000000 1.08000000000000 #O-H angle_style harmonic angle_coeff 1 7.01000000000000 149.500000000000 #Si-O-Si angle_coeff 2 5.00000000000000 149.500000000000 #Al-O-Si angle_coeff 3 75.0700000000000 109.500000000000 #O-Si-O angle_coeff 4 65.0500000000000 109.500000000000 #O-Al-O angle_coeff 5 300.280000000000 180.000000000000 #Ou-U-Ou angle_coeff 6 300.280000000000 120.000000000000 #On-N-On angle_coeff 7 700.000000000000 109.470000000000 #H-O-H #pair_style lj/long/coul/long long long 12.0 pair_style lj/cut/coul/long 12.0 #kspace_style pppm 1.0e-4 kspace_style ewald/disp 1.0e-4 pair_coeff 1 1 0.6004 3.9200 pair_coeff 1 2 0.6250 3.9200 pair_coeff 1 3 0.3032 3.5350 pair_coeff 1 4 0.3032 3.5350 pair_coeff 1 5 0.3101 3.1750 pair_coeff 1 6 0.1280 3.6350 pair_coeff 1 7 0.5130 3.3850 pair_coeff 1 8 0.3101 3.5200 pair_coeff 1 9 0.3002 3.4300 pair_coeff 1 10 0.3023 3.5350 pair_coeff 1 11 0.0000 1.9600 pair_coeff 2 2 0.6507 3.9200 pair_coeff 2 3 0.3156 3.5350 pair_coeff 2 4 0.3156 3.5350 pair_coeff 2 5 0.3229 3.1750 pair_coeff 2 6 0.1333 3.6350 pair_coeff 2 7 0.5341 3.3850 pair_coeff 2 8 0.3228 3.5200 pair_coeff 2 9 0.3126 3.4300 pair_coeff 2 10 0.3147 3.5350 pair_coeff 2 11 0.0000 1.9600 pair_coeff 3 3 0.1531 3.1500 pair_coeff 3 4 0.1531 3.1500 pair_coeff 3 5 0.1566 2.7900 pair_coeff 3 6 0.0647 3.2500 pair_coeff 3 7 0.2591 3.0000 pair_coeff 3 8 0.1566 3.1350 pair_coeff 3 9 0.1516 3.0450 pair_coeff 3 10 0.1526 3.1500 pair_coeff 3 11 0.0000 1.5750 pair_coeff 4 4 0.1531 3.1500 pair_coeff 4 5 0.1566 2.7900 pair_coeff 4 6 0.0647 3.2500 pair_coeff 4 7 0.2591 3.0000 pair_coeff 4 8 0.1566 3.1350 pair_coeff 4 9 0.1516 3.0450 pair_coeff 4 10 0.1526 3.1500 pair_coeff 4 11 0.0000 1.5750 pair_coeff 5 5 0.1602 2.4300 pair_coeff 5 6 0.0661 2.8900 pair_coeff 5 7 0.2650 2.6400 pair_coeff 5 8 0.1602 2.7750 pair_coeff 5 9 0.1551 2.6850 pair_coeff 5 10 0.1561 2.7900 pair_coeff 5 11 0.0000 1.2150 pair_coeff 6 6 0.0273 3.3500 pair_coeff 6 7 0.1094 3.1000 pair_coeff 6 8 0.0661 3.2350 pair_coeff 6 9 0.0640 3.1450 pair_coeff 6 10 0.0645 3.2500 pair_coeff 6 11 0.0000 1.6750 pair_coeff 7 7 0.4384 2.8500 pair_coeff 7 8 0.2650 2.9850 pair_coeff 7 9 0.2566 2.8950 pair_coeff 7 10 0.2583 3.0000 pair_coeff 7 11 0.0000 1.4250 pair_coeff 8 8 0.1601 3.1200 pair_coeff 8 9 0.1551 3.0300 pair_coeff 8 10 0.1561 3.1350 pair_coeff 8 11 0.0000 1.5600 pair_coeff 9 9 0.1501 2.9400 pair_coeff 9 10 0.1512 3.0450 pair_coeff 9 11 0.0000 1.4700 pair_coeff 10 10 0.1522 3.1500 pair_coeff 10 11 0.0000 1.5750 pair_coeff 11 11 0.0000 0.0000 group zeolite type 1:5 group freeze id 4609:5056 group uranyl type 6:7 group nitrate type 8:9 group water type 10:11 # Settings #velocity uranyl create 300.0 4928459 rot yes dist gaussian #velocity nitrate create 300.0 4928458 rot yes dist gaussian #velocity water create 300.0 4928457 rot yes dist gaussian #velocity guest scale 200.0 velocity freeze set 0.0 0.0 0.0 units box fix 1 all nve fix 2 all temp/rescale 10 300.0 301.0 0.1 1.0 fix 3 water shake 0.0001 10 0 b 7 a 7 fix 4 freeze setforce 0.0 0.0 0.0 unfix 3 minimize 1.0e-6 1.0e-6 1000 1000 fix 5 water shake 0.0001 10 0 b 7 a 7 neighbor 2.0 bin neigh_modify every 1 delay 0 check yes timestep 1.0 # Output #Equilibration 100 ps #restart 200000 restart.*.equil thermo_style custom step temp etotal pe ke ecoul elong evdwl ebond eangle thermo 200 # Run the simulation run 100000 #Step 1 1 ns vacf and msd dump unfix 2 restart 500000 restart.*.equil #dump trjfile all custom 1000 dump.lammpstrj id mol type x y z #dump dumpXYZ guest xyz 1000 waterpos1ps.xyz #dump dump1XYZ uranyl xyz 10 uranylpos10fs.xyz #dump dump2XYZ nitrate xyz 10 nitratepos10fs.xyz #dump dump3XYZ water xyz 10 waterpos10fs.xyz #dump dump4XYZ freeze xyz 10 freeze10fs.xyz #dump dumpV1XYZ uranyl custom 10 uranylvel10fs.dat id vx vy vz #dump dumpV2XYZ nitrate custom 10 nitratevel10fs.dat id vx vy vz #dump dumpV3XYZ water custom 10 watervel10fs.dat id vx vy vz #dump dumpFXYZ guest custom 1000 ethenefrc1ps.dat id fx fy fz thermo 200 # Run the simulation run 200000 #undump trjfile # #thermo 20000 # ## Run the simulation #run 1000000 #