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 -53.574729 0.0000000) to (43.740627 53.574729 8.8671530) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3926800 5.1369556 5.9114353 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -53.574729 0.0000000) to (43.740627 53.574729 8.8671530) create_atoms CPU = 0.003 seconds 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3926800 5.1369556 5.9114353 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -53.574729 0.0000000) to (43.740627 53.574729 8.8671530) create_atoms CPU = 0.002 seconds 1756 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 = 12 28 3 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 40 atoms, new total = 3472 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_803527979660_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 = 12 28 3 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) = 7.420 | 7.420 | 7.420 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12183.302 0 -12183.302 1140.2524 56 0 -12251.258 0 -12251.258 -5852.0059 Loop time of 3.12386 on 1 procs for 56 steps with 3472 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12183.3021799437 -12251.2461526215 -12251.257581736 Force two-norm initial, final = 46.339071 0.40220594 Force max component initial, final = 6.1306447 0.062062187 Final line search alpha, max atom move = 1.0000000 0.062062187 Iterations, force evaluations = 56 105 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0579 | 3.0579 | 3.0579 | 0.0 | 97.89 Neigh | 0.035308 | 0.035308 | 0.035308 | 0.0 | 1.13 Comm | 0.012899 | 0.012899 | 0.012899 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0177 | | | 0.57 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11339.0 ave 11339 max 11339 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: 603288.0 ave 603288 max 603288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603288 Ave neighs/atom = 173.75806 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 28 3 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.420 | 7.420 | 7.420 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -12251.258 0 -12251.258 -5852.0059 41558.435 60 0 -12251.607 0 -12251.607 -367.55166 41387.839 Loop time of 0.209519 on 1 procs for 4 steps with 3472 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 = -12251.2575817359 -12251.6019898589 -12251.6071537306 Force two-norm initial, final = 225.79298 0.46093222 Force max component initial, final = 182.12141 0.074386423 Final line search alpha, max atom move = 5.5605946e-05 4.1363274e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20464 | 0.20464 | 0.20464 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067781 | 0.00067781 | 0.00067781 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004204 | | | 2.01 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11333.0 ave 11333 max 11333 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: 603582.0 ave 603582 max 603582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603582 Ave neighs/atom = 173.84274 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 = 12 28 3 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) = 7.559 | 7.559 | 7.559 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12251.607 0 -12251.607 -367.55166 Loop time of 1.913e-06 on 1 procs for 0 steps with 3472 atoms 156.8% 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 | | 1.913e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11351.0 ave 11351 max 11351 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: 603862.0 ave 603862 max 603862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603862 Ave neighs/atom = 173.92339 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 = 12 28 3 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) = 7.559 | 7.559 | 7.559 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 -12251.607 -12251.607 43.604668 107.14946 8.858288 -367.55166 -367.55166 1.7550264 -1105.1154 0.70542152 2.3114285 1570.7851 Loop time of 2.363e-06 on 1 procs for 0 steps with 3472 atoms 296.2% 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 | | 2.363e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11351.0 ave 11351 max 11351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 301931.0 ave 301931 max 301931 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 603862.0 ave 603862 max 603862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603862 Ave neighs/atom = 173.92339 Neighbor list builds = 0 Dangerous builds = 0 3472 -12251.6071537306 eV 2.31142854490866 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04