#Purpose: Energy Barrier Calculation (NEB), CO2 in rigid Structure ########################################################################## # #Initialization dimension 3 newton on # periodic boundries boundary p p p units real atom_style full #Read atom cinfigurations read_data data.initial # Nonbonded Potential Parameters (Lennard Jones & Coulombic Potential) pair_style hybrid/overlay lj/cut 18.0 coul/long 18.0 kspace_style ewald/disp 1.0E-06 pair_modify shift yes # L-J pair interactions # atom1 (C1)= carbon in CO2, atom2(O)=Oxygen in CO2, atom3(C)=Solid Carbon pair_coeff 1 1 lj/cut 0.0570 2.820 # i j epsilon(kcal/mol) sigma(A) for C1 - C1 pair_coeff 2 2 lj/cut 0.1630 3.030 # i j epsilon(kcal/mol) sigma(A) for O - O pair_coeff 3 3 lj/cut 0.0 3.4 #0.0725 3.40 # i j epsilon(kcal/mol) sigma(A) for C - C # pair_coeff 1 2 lj/cut 0.0964 2.925 # i j epsilon(kcal/mol) sigma(A) for C1 - O pair_coeff 1 3 lj/cut 0.0643 3.110 # i j epsilon(kcal/mol) sigma(A) for C1 - C # pair_coeff 2 3 lj/cut 0.1087 3.215 # i j epsilon(kcal/mol) sigma(A) for O - C # # Coulombic pair interactions pair_coeff * * coul/long # bond Interaction bond_style harmonic bond_coeff 1 6724.8804 1.162 # bond_type bond_force bond_distance (for C1-O bond) # angle_style harmonic angle_coeff 1 34.4498 180.00 # bond_type bond_force bond_angle (for O-C1-O bond) #Group definitions group adsorbent molecule 297 # the solid structure group sorbate molecule <> 2 296 # all fluid molecule group neb_mol molecule 1 # The NEB molecule # #Neighbor list parameters neigh_modify every 1 delay 0 check yes # fix 1 neb_mol rigid molecule fix 2 sorbate rigid molecule #Storing the coordinates of the transition state variable u uloop 32 dump 1 all custom 100 dump.$u id mol type x y z #Minimization dynamic algorithm choice (quickmin and fire "work the best" with NEB), these methods need a timestep min_style fire timestep 1.0 #Spatial sorting/reordering of atoms within each processor's sub-domain (0=sorting off), you need this command to get NEB to work atom_modify sort 0 0.0 #Sets all the forces on the framework atoms to zero fix 3 adsorbent setforce 0.0 0.0 0.0 fix 4 sorbate setforce 0.0 0.0 0.0 #NEB calculation parameters fix neb_calc neb_mol neb 100.0 neb 0.000000001 0.00 1000000000 1000000000 100 final final_neb_coord.dat