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 = 2.8638485 2.8638485 2.8638485 Created orthogonal box = (0.0000000 -33.397926 0.0000000) to (11.807950 33.397926 4.0500934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8620970 4.9114597 4.0500934 Created 136 atoms using lattice units in orthogonal box = (0.0000000 -33.397926 0.0000000) to (11.807950 33.397926 4.0500934) create_atoms CPU = 0.001 seconds 136 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8620970 4.9114597 4.0500934 Created 138 atoms using lattice units in orthogonal box = (0.0000000 -33.397926 0.0000000) to (11.807950 33.397926 4.0500934) create_atoms CPU = 0.000 seconds 138 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 12 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 270 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 4.920 | 4.920 | 4.920 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1071.0266 0 -1071.0266 35436.368 76 0 -1119.7862 0 -1119.7862 -4347.1569 Loop time of 1.09335 on 1 procs for 76 steps with 270 atoms 96.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1071.02662797283 -1119.78532288077 -1119.78616156534 Force two-norm initial, final = 99.805638 0.12224885 Force max component initial, final = 34.370359 0.019590662 Final line search alpha, max atom move = 1.0000000 0.019590662 Iterations, force evaluations = 76 138 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0661 | 1.0661 | 1.0661 | 0.0 | 97.51 Neigh | 0.016064 | 0.016064 | 0.016064 | 0.0 | 1.47 Comm | 0.0078184 | 0.0078184 | 0.0078184 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003324 | | | 0.30 Nlocal: 270.000 ave 270 max 270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6937.00 ave 6937 max 6937 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: 163104.0 ave 163104 max 163104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163104 Ave neighs/atom = 604.08889 Neighbor list builds = 2 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.920 | 4.920 | 4.920 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -1119.7862 0 -1119.7862 -4347.1569 3194.3981 82 0 -1119.9379 0 -1119.9379 -17.475873 3185.9501 Loop time of 0.132878 on 1 procs for 6 steps with 270 atoms 51.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1119.78616156534 -1119.93781366349 -1119.93792521933 Force two-norm initial, final = 44.011661 0.42947801 Force max component initial, final = 28.675052 0.15479711 Final line search alpha, max atom move = 0.0012455565 0.00019280856 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13082 | 0.13082 | 0.13082 | 0.0 | 98.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044868 | 0.00044868 | 0.00044868 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00161 | | | 1.21 Nlocal: 270.000 ave 270 max 270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6913.00 ave 6913 max 6913 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: 163084.0 ave 163084 max 163084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163084 Ave neighs/atom = 604.01481 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.058 | 5.058 | 5.058 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1119.9379 0 -1119.9379 -17.475873 Loop time of 1.726e-06 on 1 procs for 0 steps with 270 atoms 173.8% 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 | | 1.726e-06 | | |100.00 Nlocal: 270.000 ave 270 max 270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6880.00 ave 6880 max 6880 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: 163428.0 ave 163428 max 163428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163428 Ave neighs/atom = 605.28889 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.058 | 5.058 | 5.058 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 -1119.9379 -1119.9379 11.863903 66.565006 4.0342741 -17.475873 -17.475873 -8.4940199 -77.576597 33.642997 2.3051395 232.09058 Loop time of 1.848e-06 on 1 procs for 0 steps with 270 atoms 216.5% 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 | | 1.848e-06 | | |100.00 Nlocal: 270.000 ave 270 max 270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6880.00 ave 6880 max 6880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81714.0 ave 81714 max 81714 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 163428.0 ave 163428 max 163428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163428 Ave neighs/atom = 605.28889 Neighbor list builds = 0 Dangerous builds = 0 270 -1119.93792521933 eV 2.30513945171433 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01