LAMMPS (23 Jun 2022) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_KeithFantauzziJacob_2010_AuO__SM_974345878378_001 # For Simulator : LAMMPS 28 Feb 2019 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 4.1652847 4.1652847 4.1652847 Created orthogonal box = (0 -58.906022 0) to (29.453011 58.906022 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7124817 4.7124817 4.1652847 Created 400 atoms using lattice units in orthogonal box = (0 -58.906022 0) to (29.453011 58.906022 4.1652847) create_atoms CPU = 0.000 seconds 400 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7124817 4.7124817 4.1652847 Created 402 atoms using lattice units in orthogonal box = (0 -58.906022 0) to (29.453011 58.906022 4.1652847) create_atoms CPU = 0.000 seconds 402 atoms in group lower Displacing atoms ... WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:98) WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:98) Reading potential file /tmp/kim-shared-library-parameter-file-directory-XXXXXXjBlxh7/ffield.reax.AuO with DATE: 2011-02-18 System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 2 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (3) fix qeq/reax, perpetual, copy from (2) attributes: half, newton off pair build: copy stencil: none bin: none Deleted 6 atoms, new total = 796 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/SM_974345878378_001#item-citation - pair reaxff command: - fix qeq/reaxff command: The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 5 20 1 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off pair build: copy stencil: none bin: none Setting up cg style minimization ... Unit style : real Current step : 0 Per MPI rank memory allocation (min/avg/max) = 362.4 | 362.4 | 362.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -62376.099 0 -62376.099 35087.046 75 0 -68439.889 0 -68439.889 4010.777 Loop time of 13.9638 on 1 procs for 75 steps with 796 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -62376.0991568765 -68439.8305139058 -68439.888921895 Force two-norm initial, final = 10135.706 4.2704878 Force max component initial, final = 3403.6836 0.5486005 Final line search alpha, max atom move = 0.086066186 0.047215953 Iterations, force evaluations = 75 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.306 | 11.306 | 11.306 | 0.0 | 80.97 Neigh | 0.057785 | 0.057785 | 0.057785 | 0.0 | 0.41 Comm | 0.0088768 | 0.0088768 | 0.0088768 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 2.5864 | 2.5864 | 2.5864 | 0.0 | 18.52 Other | | 0.004532 | | | 0.03 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10497 ave 10497 max 10497 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 270993 ave 270993 max 270993 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 270993 Ave neighs/atom = 340.44347 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) Setting up cg style minimization ... Unit style : real Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 362.4 | 362.4 | 362.4 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -68439.889 0 -68439.889 4010.777 14453.202 77 0 -68441.12 0 -68441.12 -125.74532 14496.586 Loop time of 0.342233 on 1 procs for 2 steps with 796 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -68439.8889218247 -68441.1134591001 -68441.120104798 Force two-norm initial, final = 1466.1211 55.083114 Force max component initial, final = 897.43525 49.49197 Final line search alpha, max atom move = 1.656225e-05 0.00081969837 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29817 | 0.29817 | 0.29817 | 0.0 | 87.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016976 | 0.00016976 | 0.00016976 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.043411 | 0.043411 | 0.043411 | 0.0 | 12.68 Other | | 0.0004868 | | | 0.14 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10460 ave 10460 max 10460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 271480 ave 271480 max 271480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271480 Ave neighs/atom = 341.05528 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 4000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 5 20 1 4 neighbor lists, perpetual/occasional/extra = 2 2 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: full/ghost/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard (4) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off 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) = 362.5 | 362.5 | 362.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -68441.12 0 -68441.12 -125.74532 Loop time of 9.72e-07 on 1 procs for 0 steps with 796 atoms 411.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.72e-07 | | |100.00 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10460 ave 10460 max 10460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 271283 ave 271283 max 271283 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 271283 Ave neighs/atom = 340.80779 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) Setting up Verlet run ... Unit style : real Current step : 0 Time step : 1 Per MPI rank memory allocation (min/avg/max) = 362.5 | 362.5 | 362.5 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -2967.8878 -68441.12 29.482937 117.9486 4.1687149 -125.74532 -127.41145 -107.40259 -37.43911 -237.39263 2.7587356 353.41712 Loop time of 8.92e-07 on 1 procs for 0 steps with 796 atoms 336.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 8.92e-07 | | |100.00 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10460 ave 10460 max 10460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 271283 ave 271283 max 271283 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 302496 ave 302496 max 302496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 302496 Ave neighs/atom = 380.0201 Neighbor list builds = 0 Dangerous builds = 0 796 -2967.88784329014 eV 2.75873557120275 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15