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_ADP_WangXuQian_2021_AuRh__SM_066295357485_000 # For Simulator : LAMMPS 30 Jul 2021 # Running on : LAMMPS 23 Jun 2022 # Lattice spacing in x,y,z = 3.7999997 3.7999997 3.7999997 Created orthogonal box = (0 -76.189756 0) to (43.988176 76.189756 6.5817925) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9088595 6.0648562 6.5817925 Created 1608 atoms using lattice units in orthogonal box = (0 -76.189756 0) to (43.988176 76.189756 6.5817925) create_atoms CPU = 0.002 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9088595 6.0648562 6.5817925 Created 1610 atoms using lattice units in orthogonal box = (0 -76.189756 0) to (43.988176 76.189756 6.5817925) create_atoms CPU = 0.001 seconds 1610 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.3498742 ghost atom cutoff = 9.3498742 binsize = 4.6749371, bins = 10 33 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Deleted 2 atoms, new total = 3216 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_066295357485_000#item-citation 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: 2000, page size: 100000 master list distance cutoff = 9.3498742 ghost atom cutoff = 9.3498742 binsize = 4.6749371, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 16.1 | 16.1 | 16.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16028.872 0 -16028.872 118368.25 107 0 -18433.817 0 -18433.817 12521.815 Loop time of 4.76319 on 1 procs for 107 steps with 3216 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 = -16028.8723807827 -18433.7985982098 -18433.8168137352 Force two-norm initial, final = 1831.5209 0.68528171 Force max component initial, final = 356.80226 0.1730896 Final line search alpha, max atom move = 0.57420114 0.099388246 Iterations, force evaluations = 107 192 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7213 | 4.7213 | 4.7213 | 0.0 | 99.12 Neigh | 0.018854 | 0.018854 | 0.018854 | 0.0 | 0.40 Comm | 0.013207 | 0.013207 | 0.013207 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009866 | | | 0.21 Nlocal: 3216 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17328 ave 17328 max 17328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 396516 ave 396516 max 396516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 396516 Ave neighs/atom = 123.29478 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 : metal Current step : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 16.1 | 16.1 | 16.1 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -18433.817 0 -18433.817 12521.815 44117.076 113 0 -18435.726 0 -18435.726 275.39155 44319.306 Loop time of 0.196104 on 1 procs for 6 steps with 3216 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 = -18433.8168137352 -18435.712191398 -18435.7258768429 Force two-norm initial, final = 759.05439 13.865801 Force max component initial, final = 716.28247 9.6513139 Final line search alpha, max atom move = 2.8020893e-05 0.00027043843 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19364 | 0.19364 | 0.19364 | 0.0 | 98.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004857 | 0.0004857 | 0.0004857 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001979 | | | 1.01 Nlocal: 3216 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17320 ave 17320 max 17320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 396162 ave 396162 max 396162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 396162 Ave neighs/atom = 123.1847 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: 2000, page size: 100000 master list distance cutoff = 9.3498742 ghost atom cutoff = 9.3498742 binsize = 4.6749371, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair adp, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/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, copy from (1) attributes: half, newton on pair build: copy stencil: none bin: none Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 14.98 | 14.98 | 14.98 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18435.726 0 -18435.726 275.39155 Loop time of 8.62e-07 on 1 procs for 0 steps with 3216 atoms 348.0% 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 | | 8.62e-07 | | |100.00 Nlocal: 3216 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17308 ave 17308 max 17308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 395784 ave 395784 max 395784 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 = 395784 Ave neighs/atom = 123.06716 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 : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 14.98 | 14.98 | 14.98 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 -18435.726 -18435.726 43.995243 153.19635 6.5756519 275.39155 275.39155 151.69933 350.77262 323.70271 2.4376533 1271.3189 Loop time of 3.5e-07 on 1 procs for 0 steps with 3216 atoms 571.4% 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 | | 3.5e-07 | | |100.00 Nlocal: 3216 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17308 ave 17308 max 17308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 395784 ave 395784 max 395784 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 791568 ave 791568 max 791568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 791568 Ave neighs/atom = 246.13433 Neighbor list builds = 0 Dangerous builds = 0 3216 -18435.7258768429 eV 2.43765327129608 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05