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 -53.574730 0.0000000) to (43.740628 53.574730 8.8671532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3926802 5.1369557 5.9114354 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -53.574730 0.0000000) to (43.740628 53.574730 8.8671532) create_atoms CPU = 0.002 seconds 1757 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3926802 5.1369557 5.9114354 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -53.574730 0.0000000) to (43.740628 53.574730 8.8671532) create_atoms CPU = 0.002 seconds 1757 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 42 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_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 = 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) = 7.397 | 7.397 | 7.397 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12182.076 0 -12182.076 1599.5638 55 0 -12251.254 0 -12251.254 -5851.9136 Loop time of 2.86056 on 1 procs for 55 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 = -12182.0759820616 -12251.244844313 -12251.2544008259 Force two-norm initial, final = 49.812444 0.36247241 Force max component initial, final = 6.1306444 0.057555833 Final line search alpha, max atom move = 0.98347371 0.056604648 Iterations, force evaluations = 55 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8011 | 2.8011 | 2.8011 | 0.0 | 97.92 Neigh | 0.034428 | 0.034428 | 0.034428 | 0.0 | 1.20 Comm | 0.0105 | 0.0105 | 0.0105 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0145 | | | 0.51 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11340.0 ave 11340 max 11340 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: 603244.0 ave 603244 max 603244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603244 Ave neighs/atom = 173.74539 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 : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.398 | 7.398 | 7.398 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -12251.254 0 -12251.254 -5851.9136 41558.437 59 0 -12251.604 0 -12251.604 -366.85116 41387.817 Loop time of 0.188657 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 = -12251.254400826 -12251.5988522711 -12251.6040105505 Force two-norm initial, final = 225.81247 0.40428043 Force max component initial, final = 182.11948 0.051030205 Final line search alpha, max atom move = 5.5648787e-05 2.8397690e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18487 | 0.18487 | 0.18487 | 0.0 | 97.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057607 | 0.00057607 | 0.00057607 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003213 | | | 1.70 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11335.0 ave 11335 max 11335 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: 603570.0 ave 603570 max 603570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603570 Ave neighs/atom = 173.83929 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) = 7.536 | 7.536 | 7.536 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12251.604 0 -12251.604 -366.85116 Loop time of 1.979e-06 on 1 procs for 0 steps with 3472 atoms 151.6% 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 | | 1.979e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11350.0 ave 11350 max 11350 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: 603864.0 ave 603864 max 603864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603864 Ave neighs/atom = 173.92396 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) = 7.536 | 7.536 | 7.536 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 -12251.604 -12251.604 43.604684 107.14946 8.8582799 -366.85116 -366.85116 1.7225531 -1103.0908 0.81472836 2.3112319 1567.5327 Loop time of 2.947e-06 on 1 procs for 0 steps with 3472 atoms 169.7% 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 | | 2.947e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11350.0 ave 11350 max 11350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 301932.0 ave 301932 max 301932 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 603864.0 ave 603864 max 603864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603864 Ave neighs/atom = 173.92396 Neighbor list builds = 0 Dangerous builds = 0 3472 -12251.6040105505 eV 2.31123187481749 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03