LAMMPS (4 Jan 2019) using 1 OpenMP thread(s) per MPI task units real atom_style full # Interaction potential definition pair_style lj/class2/coul/long 9.5 pair_modify mix sixthpower bond_style class2 angle_style class2 dihedral_style class2 improper_style class2 special_bonds lj/coul 0 0 1 kspace_style pppm 1e-5 # read data & and add extra atoms for reaction read_data phenol.data extra/special/per/atom 4 extra/bond/per/atom 1 extra/angle/per/atom 1 extra/dihedral/per/atom 2 Reading data file ... orthogonal box = (0 0 0) to (30.721 30.721 30.721) 2 by 2 by 4 MPI processor grid reading atoms ... 14 atoms reading velocities ... 14 velocities scanning bonds ... 4 = max bonds/atom scanning angles ... 4 = max angles/atom scanning dihedrals ... 7 = max dihedrals/atom scanning impropers ... 1 = max impropers/atom reading bonds ... 13 bonds reading angles ... 19 angles reading dihedrals ... 26 dihedrals reading impropers ... 6 impropers Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 1 special bond factors coul: 0 0 1 3 = max # of 1-2 neighbors 5 = max # of 1-3 neighbors 12 = max # of special neighbors reset_ids Resetting atom IDs ... PPPM initialization ... WARNING: System is not charge neutral, net charge = -0.053 (src/kspace.cpp:302) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.22883 grid = 10 10 10 stencil order = 5 estimated absolute RMS force accuracy = 0.0023184 estimated relative force accuracy = 6.98178e-06 using double precision FFTs 3d grid and FFT values/proc = 800 90 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.5 ghost atom cutoff = 11.5 binsize = 5.75, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 1 special bond factors coul: 0 0 1 3 = max # of 1-2 neighbors 5 = max # of 1-3 neighbors 12 = max # of special neighbors velocity all create 300.0 6659 dist gaussian # Integration conditions (check) #timestep 0.5 molecule rxn1a_unreacted rxn1a.unreacted.template Read molecule rxn1a_unreacted: 10 atoms with max type 7 8 bonds with max type 6 10 angles with max type 7 10 dihedrals with max type 11 3 impropers with max type 3 molecule rxn1a_reacted rxn1a.reacted.template Read molecule rxn1a_reacted: 10 atoms with max type 6 9 bonds with max type 6 11 angles with max type 7 12 dihedrals with max type 9 3 impropers with max type 3 #variable variable prob equal 0.5+step/400 fix rxn all bond/react stabilization yes nvt_grp 0.1 react rxn1a all 5 0 6.5 rxn1a_unreacted rxn1a_reacted rxn1a.map prob v_prob 1234 update_edges custom stabilize_steps 0 max_rxn 20 react rxn1a_r all 5 0 6.5 rxn1a_reacted rxn1a_unreacted rxn1a.map prob 1.0 6512 update_edges custom stabilize_steps 0 max_rxn 5 dynamic group bond_react_MASTER_group defined dynamic group nvt_grp_REACT defined #fix rxn all bond/react stabilization no # react rxn1a all 5 0 6.5 rxn1a_unreacted rxn1a_reacted rxn1a.map prob v_prob 1234 update_edges custom max_rxn 20 # react rxn1a_r all 5 0 6.5 rxn1a_reacted rxn1a_unreacted rxn1a.map prob 1.0 6512 update_edges custom max_rxn 5 variable f3 equal f_rxn[1]-f_rxn[2] # basically reaction is on or off thermo 5 thermo_style custom step temp f_rxn[1] f_rxn[2] v_f3 v_prob # dump mydump all custom 5 dump id type x y z run 200 PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.22883 grid = 10 10 10 stencil order = 5 estimated absolute RMS force accuracy = 0.0023184 estimated relative force accuracy = 6.98178e-06 using double precision FFTs 3d grid and FFT values/proc = 800 90 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.5 ghost atom cutoff = 11.5 binsize = 5.75, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) pair lj/class2/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard (2) fix bond/react, occasional, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 11.36 | 11.46 | 12.14 Mbytes Step Temp f_rxn[1] f_rxn[2] v_f3 v_prob 0 300 0 0 0 0.5 5 300 0 0 0 0.5125 10 7927.7013 1 0 1 0.525 15 7863.5298 1 1 0 0.5375 20 7793.044 1 1 0 0.55 25 7922.917 2 1 1 0.5625 30 7703.6122 2 2 0 0.575 35 7986.219 3 2 1 0.5875 40 7715.4566 3 3 0 0.6 45 7434.0633 3 3 0 0.6125 50 8295.1796 4 3 1 0.625 55 7925.4639 4 4 0 0.6375 60 7520.2382 4 4 0 0.65 65 8959.5524 5 4 1 0.6625 70 8042.3627 5 5 0 0.675