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### lammps filename: input_23.txt units real dimension 3 boundary p p p atom_style charge region simbox prism 0.0 13.914108 0.0 12.9327 0.0 35 6.258126 0.0 0.0 region bottom_fixed prism 0.0 13.914108 0.0 12.9327 0.0 4.6 6.258126 0.0 0.0 # the last three values are copied from region simbox create_box 7 simbox ### define a water molecule read_data data_slab.txt add append read_data data_pfoa_water.txt add append offset 2 0 0 0 0 group waterpfoa type 3:7 group bottom region bottom_fixed pair_style reax/c ../../lmp_control pair_coeff * * ../../reaxff/TiOCHNCl.ff Ti O H O C F O neighbor 2 bin neigh_modify every 10 delay 0 check no fix 1 all nvt temp 298 298 100 fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c fix 4 bottom setforce 0.0 0.0 0.0 fix 5 waterpfoa efield 0 0 0.03 timestep 0.25 thermo 10 minimize 1.0e-6 1.0e-6 1000 100000 dump 1 all atom 100 output_23.trj dump 2 all custom 100 output_23.trj id x y z thermo 1000 run 2000 write_data neb_initial_org.txt run 300 write_data neb_final_org.txt run 1000 ################################## ### neb filename: input_neb_23.txt units real dimension 3 boundary p p p atom_style charge atom_modify map array sort 0 0.0 region simbox prism 0.0 13.914108 0.0 12.9327 0.0 35 6.258126 0.0 0.0 region bottom_fixed prism 0.0 13.914108 0.0 12.9327 0.0 4.6 6.258126 0.0 0.0 # the last three values are copied from region simbox ### define a water molecule read_data neb_initial.txt group waterpfoa type 3:7 group bottom region bottom_fixed group nebatoms subtract all bottom pair_style reax/c ../../lmp_control pair_coeff * * ../../reaxff/TiOCHNCl.ff Ti O H O C F O neighbor 2 bin neigh_modify every 10 delay 0 check no fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c fix 4 bottom setforce 0.0 0.0 0.0 timestep 0.25 thermo 10 minimize 1.0e-6 1.0e-4 1000 10000 fix 6 nebatoms neb 1.0 parallel ideal min_style quickmin neb 0.0 0.1 1000 1000 100 final neb_final.txt default ################## ### in the command line, you type: mpirun -np 3 ../../lmp_reaxc_neb -partition 3x1 -in input_neb_23.txt

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