# D2020 HOPI Combined Run File # Variables variable timestep index 0.33333 # integration time step variable annealtime index 10000 variable name index D2020_Pt variable dtdump index 1 variable nrestart index 0 variable restartminusone equal ${nrestart}-1 variable temp index 353 variable mu index -8.1 variable data index after_anneal.data # Box Settings units real atom_style full boundary p p f pair_style lj/cut/coul/long 22.5 22.5 pair_modify mix sixthpower dielectric 1.0 special_bonds lj 0.000000 0.000000 1.000000 coul 0.000000 0.000000 1.000000 bond_style harmonic angle_style harmonic dihedral_style charmm read_data ${data} # Include Parameter File include D2020_1.8_Pt_dreiding.params # Kspace Commands kspace_style pppm 0.00001 kspace_modify slab 10.0 # Modify Log/Thermo Output thermo_style custom etotal ke pe ebond eangle edihed eimp evdwl ecoul elong temp press vol thermo_modify line multi flush yes thermo 1000 log log.lammps # Create Groups and Freeze Selected atoms group pt type 1 group ox type 8 group notpt type != 1 fix frpt pt setforce 0.0 0.0 0.0 # Set Harmonic wall fix wallhi all wall/harmonic zlo EDGE 622.609 0.000 4.0000 units box timestep ${timestep} # GCMC molecule oxygen oxygen.mol # Molecule File region polyregion block 2.0 31.0 2.0 26.0 -4.12 50.37 # Region for GCMC insertion fix oxgcmc notpt gcmc 100 100 0 0 54341 ${temp} ${mu} 0.5 mol oxygen & region polyregion charge 0.0 delete_atoms overlap 0.5 all all # Set Integrator and modify to allow for variable number of atoms fix int notpt nvt temp ${temp} ${temp} 100 compute_modify int_temp dynamic/dof yes compute_modify thermo_temp dynamic/dof yes run 2000000 write_data ${name}_run.data