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 -44.277584 0) to (44.277584 44.277584 4.1652847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8775554 5.8775554 4.1652847 Created 451 atoms using lattice units in orthogonal box = (0 -44.277584 0) to (44.277584 44.277584 4.1652847) create_atoms CPU = 0.000 seconds 451 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8775554 5.8775554 4.1652847 Created 453 atoms using lattice units in orthogonal box = (0 -44.277584 0) to (44.277584 44.277584 4.1652847) create_atoms CPU = 0.000 seconds 453 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-XXXXXX2XTarJ/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 = 8 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 0 atoms, new total = 904 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 = 8 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) = 400.4 | 400.4 | 400.4 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -64957.552 0 -64957.552 70599.593 81 0 -77809.598 0 -77809.598 6934.2117 Loop time of 14.345 on 1 procs for 81 steps with 904 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 = -64957.5518473769 -77809.5392585731 -77809.5976521498 Force two-norm initial, final = 14505.322 4.4651208 Force max component initial, final = 3787.7291 0.93448594 Final line search alpha, max atom move = 0.14398497 0.13455193 Iterations, force evaluations = 81 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.281 | 11.281 | 11.281 | 0.0 | 78.64 Neigh | 0.11073 | 0.11073 | 0.11073 | 0.0 | 0.77 Comm | 0.0097662 | 0.0097662 | 0.0097662 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 2.9381 | 2.9381 | 2.9381 | 0.0 | 20.48 Other | | 0.00507 | | | 0.04 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10611 ave 10611 max 10611 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 309480 ave 309480 max 309480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309480 Ave neighs/atom = 342.34513 Neighbor list builds = 2 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 : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 400.3 | 400.3 | 400.3 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -77809.598 0 -77809.598 6934.2117 16332.119 87 0 -77817.275 0 -77817.275 -145.8876 16415.425 Loop time of 0.76769 on 1 procs for 6 steps with 904 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 = -77809.5976521214 -77817.2652473718 -77817.2750973155 Force two-norm initial, final = 3438.9186 69.552153 Force max component initial, final = 3093.695 58.305076 Final line search alpha, max atom move = 1.6123716e-05 0.0009400945 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66853 | 0.66853 | 0.66853 | 0.0 | 87.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037527 | 0.00037527 | 0.00037527 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0.097501 | 0.097501 | 0.097501 | 0.0 | 12.70 Other | | 0.001289 | | | 0.17 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10590 ave 10590 max 10590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 308268 ave 308268 max 308268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 308268 Ave neighs/atom = 341.00442 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 = 8 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) = 399.7 | 399.7 | 399.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -77817.275 0 -77817.275 -145.8876 Loop time of 1.273e-06 on 1 procs for 0 steps with 904 atoms 235.7% 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 | | 1.273e-06 | | |100.00 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10602 ave 10602 max 10602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 307161 ave 307161 max 307161 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 = 307161 Ave neighs/atom = 339.77987 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) = 399.7 | 399.7 | 399.7 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 -3374.4764 -77817.275 44.254344 88.976488 4.1688952 -145.8876 -147.82061 -44.569425 -151.90702 -246.98537 2.6774054 197.89968 Loop time of 1.182e-06 on 1 procs for 0 steps with 904 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: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10602 ave 10602 max 10602 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 307161 ave 307161 max 307161 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 344948 ave 344948 max 344948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 344948 Ave neighs/atom = 381.57965 Neighbor list builds = 0 Dangerous builds = 0 904 -3374.47640258618 eV 2.67740543238935 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15