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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -37.583316 0.0000000) to (26.575417 37.583316 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1285893 5.9342077 4.9780318 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -37.583316 0.0000000) to (26.575417 37.583316 4.9780318) create_atoms CPU = 0.003 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1285893 5.9342077 4.9780318 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.583316 0.0000000) to (26.575417 37.583316 4.9780318) create_atoms CPU = 0.003 seconds 458 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 7 18 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 908 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_826591359508_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.394 | 5.394 | 5.394 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3982.9034 0 -3982.9034 2997.317 98 0 -4019.6814 0 -4019.6814 6297.1852 Loop time of 4.26292 on 1 procs for 98 steps with 908 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 = -3982.90342129013 -4019.67810584696 -4019.68143879737 Force two-norm initial, final = 22.591138 0.19287443 Force max component initial, final = 5.0692397 0.035749943 Final line search alpha, max atom move = 1.0000000 0.035749943 Iterations, force evaluations = 98 184 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1287 | 4.1287 | 4.1287 | 0.0 | 96.85 Neigh | 0.080106 | 0.080106 | 0.080106 | 0.0 | 1.88 Comm | 0.030459 | 0.030459 | 0.030459 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02364 | | | 0.55 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7037.00 ave 7037 max 7037 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: 203580.0 ave 203580 max 203580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203580 Ave neighs/atom = 224.20705 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.394 | 5.394 | 5.394 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -4019.6814 0 -4019.6814 6297.1852 9944.0396 103 0 -4019.8643 0 -4019.8643 263.17478 9978.3663 Loop time of 0.159813 on 1 procs for 5 steps with 908 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4019.68143879737 -4019.86114456616 -4019.86427973412 Force two-norm initial, final = 88.383607 3.5523012 Force max component initial, final = 85.390255 3.2203740 Final line search alpha, max atom move = 0.00014904489 0.00047998029 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15544 | 0.15544 | 0.15544 | 0.0 | 97.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001042 | 0.001042 | 0.001042 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003327 | | | 2.08 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6864.00 ave 6864 max 6864 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: 203340.0 ave 203340 max 203340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203340 Ave neighs/atom = 223.94273 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.532 | 5.532 | 5.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4019.8643 0 -4019.8643 263.17478 Loop time of 6.334e-06 on 1 procs for 0 steps with 908 atoms 173.7% 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 | | 6.334e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6864.00 ave 6864 max 6864 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: 203064.0 ave 203064 max 203064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203064 Ave neighs/atom = 223.63877 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.532 | 5.532 | 5.532 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 -4019.8643 -4019.8643 26.557306 75.50017 4.9765399 263.17478 263.17478 41.089807 231.51012 516.92442 2.2834959 634.24646 Loop time of 6.506e-06 on 1 procs for 0 steps with 908 atoms 261.3% 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 | | 6.506e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6864.00 ave 6864 max 6864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101532.0 ave 101532 max 101532 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 203064.0 ave 203064 max 203064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203064 Ave neighs/atom = 223.63877 Neighbor list builds = 0 Dangerous builds = 0 908 -4019.86427973412 eV 2.2834959169295 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05