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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -38.484749 0.0000000) to (38.481129 38.484749 3.6200001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1081145 5.1081145 3.6200001 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.484749 0.0000000) to (38.481129 38.484749 3.6200001) create_atoms CPU = 0.001 seconds 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1081145 5.1081145 3.6200001 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.484749 0.0000000) to (38.481129 38.484749 3.6200001) create_atoms CPU = 0.001 seconds 454 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 20 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 900 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.984 | 4.984 | 4.984 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3130.5439 0 -3130.5439 12309.81 71 0 -3178.6185 0 -3178.6185 -2914.2817 Loop time of 1.06291 on 1 procs for 71 steps with 900 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 = -3130.54392932088 -3178.61596228418 -3178.61851070331 Force two-norm initial, final = 31.449406 0.18137652 Force max component initial, final = 7.2293122 0.042933381 Final line search alpha, max atom move = 1.0000000 0.042933381 Iterations, force evaluations = 71 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0202 | 1.0202 | 1.0202 | 0.0 | 95.98 Neigh | 0.028088 | 0.028088 | 0.028088 | 0.0 | 2.64 Comm | 0.0084499 | 0.0084499 | 0.0084499 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00621 | | | 0.58 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7480.00 ave 7480 max 7480 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: 154592.0 ave 154592 max 154592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154592 Ave neighs/atom = 171.76889 Neighbor list builds = 3 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.984 | 4.984 | 4.984 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -3178.6185 0 -3178.6185 -2914.2817 10721.981 74 0 -3178.6378 0 -3178.6378 -626.66269 10703.452 Loop time of 0.0416058 on 1 procs for 3 steps with 900 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 = -3178.61851070331 -3178.63765708021 -3178.63778193298 Force two-norm initial, final = 23.049662 0.20977527 Force max component initial, final = 20.288949 0.088626955 Final line search alpha, max atom move = 0.00048723058 4.3181763e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040262 | 0.040262 | 0.040262 | 0.0 | 96.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029164 | 0.00029164 | 0.00029164 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001052 | | | 2.53 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7468.00 ave 7468 max 7468 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: 155220.0 ave 155220 max 155220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155220 Ave neighs/atom = 172.46667 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.122 | 5.122 | 5.122 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3178.6378 0 -3178.6378 -626.66269 Loop time of 1.8e-06 on 1 procs for 0 steps with 900 atoms 166.7% 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 | | 1.8e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7468.00 ave 7468 max 7468 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: 155224.0 ave 155224 max 155224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155224 Ave neighs/atom = 172.47111 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.122 | 5.122 | 5.122 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 -3178.6378 -3178.6378 38.495608 76.969498 3.6123851 -626.66269 -626.66269 13.271368 -1889.8283 -3.4311291 2.348812 134.16534 Loop time of 2.117e-06 on 1 procs for 0 steps with 900 atoms 188.9% 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 | | 2.117e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7468.00 ave 7468 max 7468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 77612.0 ave 77612 max 77612 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 155224.0 ave 155224 max 155224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155224 Ave neighs/atom = 172.47111 Neighbor list builds = 0 Dangerous builds = 0 900 -3178.63778193297 eV 2.34881197740477 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01