# water adsorption in MOF Simulation from data file ######################## #### Initialization #### ######################## dimension 3 boundary p p p units real atom_style full neighbor 2.0 bin neigh_modify every 1 delay 10 check yes ######################### #### Atom Definition #### ######################### read_data MOF.lmpdat set type 4 charge +3.28 #################### ##### Settings ##### #################### pair_style hybrid/overlay lj/cut/coul/long 12.0 lj/cut/tip4p/long 5 6 6 9 0.1546 12.0 kspace_style pppm/tip4p 1.0e-6 pair_coeff 1 1 lj/cut/coul/long 0.3050 3.725 #C pair_coeff 2 2 lj/cut/coul/long 0.0100 2.852 #H pair_coeff 3 3 lj/cut/coul/long 0.4150 3.306 #O pair_coeff 4 4 lj/cut/coul/long 0.0690 2.784 #Zr pair_coeff 5 5 lj/cut/tip4p/long 0.1852 3.1589 #O-water pair_coeff 6 6 lj/cut/tip4p/long 0.0 0.0 #H-water pair_coeff 1 2 lj/cut/coul/long 0.0552 3.289 #C:H pair_coeff 1 3 lj/cut/coul/long 0.3558 3.516 #C:O pair_coeff 1 4 lj/cut/coul/long 0.0145 3.255 #C:Zr pair_coeff 1 5 lj/cut/tip4p/long 0.0494 3.442 #C:O-water pair_coeff 1 6 lj/cut/coul/long 0.0 1.862 #C:H-water pair_coeff 2 3 lj/cut/coul/long 0.0644 3.079 #H:O pair_coeff 2 4 lj/cut/coul/long 0.0263 2.818 #H:Zr pair_coeff 2 5 lj/cut/tip4p/long 0.0089 3.005 #H:O-water pair_coeff 2 6 lj/cut/coul/long 0.0 1.426 #H:H-water pair_coeff 3 4 lj/cut/coul/long 0.1692 3.045 #O:Zr pair_coeff 3 5 lj/cut/tip4p/long 0.0576 3.232 #O:O-water pair_coeff 3 6 lj/cut/coul/long 0.0 1.653 #O:H-water pair_coeff 4 5 lj/cut/tip4p/long 0.0235 2.971 #Zr:O-water pair_coeff 4 6 lj/cut/tip4p/long 0.0 1.392 #Zr:H-water #pair_coeff 5 6 lj/cut/tip4p/long 0.0 0.0 #H-water and O-water bond_style hybrid zero harmonic bond_coeff 1 harmonic 350 1.53 #C:C bond_coeff 2 harmonic 350 1.09 #C:H bond_coeff 3 harmonic 350 1.42 #O:C bond_coeff 4 harmonic 350 0.98 #O:H bond_coeff 5 harmonic 254.767 2.2235 #Zr:O bond_coeff 6 zero 0.9574 angle_style hybrid zero harmonic angle_coeff 1 harmonic 50 109.471 #C:C:C angle_coeff 2 harmonic 50 109.471 #C:C:H angle_coeff 3 harmonic 50 109.417 #O:C:C angle_coeff 4 harmonic 50 109.471 #O:C:O angle_coeff 5 harmonic 50 109.47 #O:Zr:O angle_coeff 6 harmonic 50 104.51 #Zr:O:C angle_coeff 7 harmonic 50 104.51 #Zr:O:H angle_coeff 8 harmonic 50 104.51 #Zr:O:Zr angle_coeff 9 zero 104.52 #H:O:H for water dihedral_style harmonic dihedral_coeff 1 2.5 -1 2 #C:C:C:C Both C atom hybridization considered as sp2 dihedral_coeff 2 2.5 -1 2 #C:C:C:H Both C atom hybridization considered as sp2 dihedral_coeff 3 2.5 -1 2 #H:C:C:H Both C atom hybridization considered as sp2 dihedral_coeff 4 2.5 -1 2 #O:C:C:C Both C atom hybridization considered as sp2 dihedral_coeff 5 2.5 -1 2 #O:C:C:H Both C atom hybridization considered as sp2 dihedral_coeff 6 0.5 -1 6 #O:O:Zr:C #O considered as sp2 and Zr as sp3 dihedral_coeff 7 0.5 -1 6 #O:O:Zr:H #O considered as sp2 and Zr as sp3 dihedral_coeff 8 0.5 -1 6 #O:Zr:O:C #O considered as sp2 and Zr as sp3 dihedral_coeff 9 0.5 -1 6 #O:Zr:O:H #O considered as sp2 and Zr as sp3 dihedral_coeff 10 22.5 -1 2 #Zr:C:O:C the dihedrals should checked because Zr and C are not connected in MOF-801 dihedral_coeff 11 22.5 -1 2 #Zr:C:O:O dihedral_coeff 12 22.5 -1 2 #Zr:O:C:C dihedral_coeff 13 22.5 -1 2 #Zr:O:C:O dihedral_coeff 14 0.5 -1 6 #Zr:O:Zr:O dihedral_coeff 15 0.5 -1 6 #Zr:Zr:O:O group MOF type 1 2 3 4 group H2O type 5 6 molecule water_mol water-TIP4P-2005-2.mol variable oxygen atom "type==5" group oxygen dynamic all var oxygen variable numADS equal count(oxygen) comm_modify cutoff 14.0 reset_timestep 0 timestep 1.0 velocity all create 300.0 546987 mom yes rot yes dist gaussian compute mdtemp H2O temp compute_modify mdtemp dynamic/dof yes fix MOF_rigid MOF setforce 0.0 0.0 0.0 fix H2O_rigid H2O shake 1.0e-4 200 0 b 1 a 1 mol water_mol fix mygcmc H2O gcmc 10 100 100 0 654321 300 0.0 0.5 mol water_mol pressure 0.1 group H2O full_energy #assuming water vapor at low pressure as ideal gas fix mynvt H2O nvt temp 300.0 300.0 100.0 fix_modify mynvt temp mdtemp thermo 20 thermo_style custom step v_numADS press temp dump dump-GCMC all xyz 100 dump.xyz ############# #### Run #### ############# run 100000 write_data gcmc_data.data