LAMMPS (30 Jul 2021) 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 Lattice spacing in x,y,z = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -40.445396 0.0000000) to (28.596725 40.445396 4.9780508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3328371 5.5148013 4.9780508 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.445396 0.0000000) to (28.596725 40.445396 4.9780508) create_atoms CPU = 0.003 seconds 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3328371 5.5148013 4.9780508 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.445396 0.0000000) to (28.596725 40.445396 4.9780508) create_atoms CPU = 0.003 seconds 532 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 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 kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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/MO_871937946490_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:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.431 | 5.431 | 5.431 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4617.9007 0 -4617.9007 4610.3338 34 0 -4641.8679 0 -4641.8679 -1052.4271 Loop time of 1.46796 on 1 procs for 34 steps with 1048 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4617.90069968233 -4641.86332017116 -4641.86786505905 Force two-norm initial, final = 24.944907 0.22205863 Force max component initial, final = 4.1195782 0.016308023 Final line search alpha, max atom move = 1.0000000 0.016308023 Iterations, force evaluations = 34 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4186 | 1.4186 | 1.4186 | 0.0 | 96.64 Neigh | 0.030662 | 0.030662 | 0.030662 | 0.0 | 2.09 Comm | 0.010327 | 0.010327 | 0.010327 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008353 | | | 0.57 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7526.00 ave 7526 max 7526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 234008.0 ave 234008 max 234008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234008 Ave neighs/atom = 223.29008 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.431 | 5.431 | 5.431 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -4641.8679 0 -4641.8679 -1052.4271 11515.286 36 0 -4641.8825 0 -4641.8825 1415.7358 11499.32 Loop time of 0.123605 on 1 procs for 2 steps with 1048 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4641.86786505905 -4641.88183894745 -4641.88254289464 Force two-norm initial, final = 29.159577 0.23144619 Force max component initial, final = 21.789923 0.044029784 Final line search alpha, max atom move = 0.00035613022 1.5680336e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12052 | 0.12052 | 0.12052 | 0.0 | 97.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00075402 | 0.00075402 | 0.00075402 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00233 | | | 1.88 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7501.00 ave 7501 max 7501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 233792.0 ave 233792 max 233792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233792 Ave neighs/atom = 223.08397 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/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 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.569 | 5.569 | 5.569 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4641.8825 0 -4641.8825 1415.7358 Loop time of 6.295e-06 on 1 procs for 0 steps with 1048 atoms 174.7% 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 | | 6.295e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7501.00 ave 7501 max 7501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 233816.0 ave 233816 max 233816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233816 Ave neighs/atom = 223.10687 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/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 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.569 | 5.569 | 5.569 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 -4641.8825 -4641.8825 28.568035 80.890793 4.9761411 1415.7358 1415.7358 -1.0234648 4254.3631 -6.1322255 2.2514322 517.47697 Loop time of 6.365e-06 on 1 procs for 0 steps with 1048 atoms 298.5% 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 | | 6.365e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7501.00 ave 7501 max 7501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116908.0 ave 116908 max 116908 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 233816.0 ave 233816 max 233816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233816 Ave neighs/atom = 223.10687 Neighbor list builds = 0 Dangerous builds = 0 1048 -4613.31259385857 eV 2.25143221192981 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02