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 -67.163198 0) to (33.581599 67.163198 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6830399 5.6830399 4.1652847 Created 520 atoms using lattice units in orthogonal box = (0 -67.163198 0) to (33.581599 67.163198 4.1652847) create_atoms CPU = 0.000 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6830399 5.6830399 4.1652847 Created 522 atoms using lattice units in orthogonal box = (0 -67.163198 0) to (33.581599 67.163198 4.1652847) create_atoms CPU = 0.000 seconds 522 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-XXXXXXSFbrQI/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 = 6 23 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 2 atoms, new total = 1040 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 = 6 23 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) = 471.8 | 471.8 | 471.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -76877.806 0 -76877.806 54660.271 106 0 -89429.56 0 -89429.56 10173.252 Loop time of 23.5332 on 1 procs for 106 steps with 1040 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -76877.8062074035 -89429.4796850599 -89429.5595232856 Force two-norm initial, final = 16562.27 4.9251786 Force max component initial, final = 4659.9241 0.91732436 Final line search alpha, max atom move = 0.10628879 0.097501298 Iterations, force evaluations = 106 188 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.748 | 18.748 | 18.748 | 0.0 | 79.67 Neigh | 0.28365 | 0.28365 | 0.28365 | 0.0 | 1.21 Comm | 0.017199 | 0.017199 | 0.017199 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 4.4771 | 4.4771 | 4.4771 | 0.0 | 19.02 Other | | 0.007529 | | | 0.03 Nlocal: 1040 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13639 ave 13639 max 13639 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 352442 ave 352442 max 352442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 352442 Ave neighs/atom = 338.88654 Neighbor list builds = 4 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 : 106 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 471.8 | 471.8 | 471.8 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -89429.56 0 -89429.56 10173.252 18789.163 114 0 -89447.837 0 -89447.837 23.268585 18926.685 Loop time of 1.17127 on 1 procs for 8 steps with 1040 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 = -89429.5595231441 -89447.751582105 -89447.8371916022 Force two-norm initial, final = 5587.3661 60.389261 Force max component initial, final = 5014.727 52.049035 Final line search alpha, max atom move = 6.0539954e-06 0.00031510462 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.97209 | 0.97209 | 0.97209 | 0.0 | 82.99 Neigh | 0.070181 | 0.070181 | 0.070181 | 0.0 | 5.99 Comm | 0.0006636 | 0.0006636 | 0.0006636 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.12656 | 0.12656 | 0.12656 | 0.0 | 10.80 Other | | 0.001785 | | | 0.15 Nlocal: 1040 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13639 ave 13639 max 13639 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 351871 ave 351871 max 351871 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 351871 Ave neighs/atom = 338.3375 Neighbor list builds = 1 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 = 6 23 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) = 471.9 | 471.9 | 471.9 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -89447.837 0 -89447.837 23.268585 Loop time of 1.032e-06 on 1 procs for 0 steps with 1040 atoms 290.7% 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 | | 1.032e-06 | | |100.00 Nlocal: 1040 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13653 ave 13653 max 13653 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 351854 ave 351854 max 351854 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 = 351854 Ave neighs/atom = 338.32115 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) = 471.9 | 471.9 | 471.9 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 -3878.8253 -89447.837 33.577382 135.33123 4.1651409 23.268584 23.576893 191.04 -102.52519 -17.784134 2.6778619 612.7918 Loop time of 1.182e-06 on 1 procs for 0 steps with 1040 atoms 253.8% 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 | | 1.182e-06 | | |100.00 Nlocal: 1040 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13653 ave 13653 max 13653 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 351854 ave 351854 max 351854 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 394216 ave 394216 max 394216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 394216 Ave neighs/atom = 379.05385 Neighbor list builds = 0 Dangerous builds = 0 1040 -3878.82530565061 eV 2.67786194467318 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:25