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 -42.477736 0) to (21.238868 42.477736 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9012773 4.9012773 4.1652847 Created 208 atoms using lattice units in orthogonal box = (0 -42.477736 0) to (21.238868 42.477736 4.1652847) create_atoms CPU = 0.000 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9012773 4.9012773 4.1652847 Created 210 atoms using lattice units in orthogonal box = (0 -42.477736 0) to (21.238868 42.477736 4.1652847) create_atoms CPU = 0.000 seconds 210 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-XXXXXXHwe2R0/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 = 4 15 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 = 412 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 = 4 15 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) = 232.4 | 232.4 | 232.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -33834.301 0 -33834.301 22221.397 65 0 -35327.884 0 -35327.884 3908.9118 Loop time of 6.59581 on 1 procs for 65 steps with 412 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -33834.3010412461 -35327.8509029395 -35327.8836011975 Force two-norm initial, final = 3130.9526 3.1800583 Force max component initial, final = 1098.9308 0.53036378 Final line search alpha, max atom move = 0.1188337 0.06302509 Iterations, force evaluations = 65 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3985 | 5.3985 | 5.3985 | 0.0 | 81.85 Neigh | 0.03451 | 0.03451 | 0.03451 | 0.0 | 0.52 Comm | 0.0046204 | 0.0046204 | 0.0046204 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 1.1559 | 1.1559 | 1.1559 | 0.0 | 17.52 Other | | 0.002288 | | | 0.03 Nlocal: 412 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6910 ave 6910 max 6910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 141454 ave 141454 max 141454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141454 Ave neighs/atom = 343.33495 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 : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 232.4 | 232.4 | 232.4 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -35327.884 0 -35327.884 3908.9118 7515.6652 68 0 -35328.578 0 -35328.578 6.385646 7537.1629 Loop time of 0.301479 on 1 procs for 3 steps with 412 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -35327.8836012166 -35328.5526596615 -35328.5777930591 Force two-norm initial, final = 754.69857 6.1592363 Force max component initial, final = 540.20367 4.5003751 Final line search alpha, max atom move = 1.4776822e-05 6.6501243e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26714 | 0.26714 | 0.26714 | 0.0 | 88.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016414 | 0.00016414 | 0.00016414 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.033635 | 0.033635 | 0.033635 | 0.0 | 11.16 Other | | 0.0005345 | | | 0.18 Nlocal: 412 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6911 ave 6911 max 6911 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 141615 ave 141615 max 141615 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141615 Ave neighs/atom = 343.72573 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 = 4 15 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) = 232.6 | 232.6 | 232.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -35328.578 0 -35328.578 6.3856457 Loop time of 1.352e-06 on 1 procs for 0 steps with 412 atoms 147.9% 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 | | 1.352e-06 | | |100.00 Nlocal: 412 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6911 ave 6911 max 6911 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 141551 ave 141551 max 141551 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 = 141551 Ave neighs/atom = 343.57039 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) = 232.6 | 232.6 | 232.6 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 -1531.9921 -35328.578 21.250935 85.121561 4.1666813 6.3856456 6.4702554 41.507655 -7.8829479 -14.213941 2.7721228 314.14131 Loop time of 9.82e-07 on 1 procs for 0 steps with 412 atoms 305.5% 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 | | 9.82e-07 | | |100.00 Nlocal: 412 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6911 ave 6911 max 6911 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 141551 ave 141551 max 141551 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156128 ave 156128 max 156128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156128 Ave neighs/atom = 378.95146 Neighbor list builds = 0 Dangerous builds = 0 412 -1531.99211807547 eV 2.77212283157719 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07