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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -33.207227 0.0000000) to (16.602072 33.207227 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0073967 4.0073967 3.0829274 Created 117 atoms using lattice units in orthogonal box = (0.0000000 -33.207227 0.0000000) to (16.602072 33.207227 3.0829274) create_atoms CPU = 0.000 seconds 117 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0073967 4.0073967 3.0829274 Created 117 atoms using lattice units in orthogonal box = (0.0000000 -33.207227 0.0000000) to (16.602072 33.207227 3.0829274) create_atoms CPU = 0.000 seconds 117 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 232 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.788 | 4.788 | 4.788 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1388.4875 0 -1388.4875 121971.86 56 0 -1502.9276 0 -1502.9276 13263.727 Loop time of 2.7524 on 1 procs for 56 steps with 232 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 = -1388.48754816617 -1502.92619474536 -1502.9275980584 Force two-norm initial, final = 297.32076 0.16545623 Force max component initial, final = 93.251253 0.053872864 Final line search alpha, max atom move = 1.0000000 0.053872864 Iterations, force evaluations = 56 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7495 | 2.7495 | 2.7495 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020677 | 0.0020677 | 0.0020677 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008312 | | | 0.03 Nlocal: 232.000 ave 232 max 232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2519.00 ave 2519 max 2519 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: 15298.0 ave 15298 max 15298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15298 Ave neighs/atom = 65.939655 Neighbor list builds = 0 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.786 | 4.786 | 4.786 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -1502.9276 0 -1502.9276 13263.727 3399.2898 61 0 -1502.9522 0 -1502.9522 9964.7092 3405.1402 Loop time of 0.191349 on 1 procs for 5 steps with 232 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 = -1502.9275980584 -1502.95193993956 -1502.95217800322 Force two-norm initial, final = 10.197610 0.75378013 Force max component initial, final = 10.059902 0.60790843 Final line search alpha, max atom move = 0.0012270581 0.00074593899 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.191 | 0.191 | 0.191 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.1e-05 | 8.1e-05 | 8.1e-05 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002685 | | | 0.14 Nlocal: 232.000 ave 232 max 232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2298.00 ave 2298 max 2298 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: 17748.0 ave 17748 max 17748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17748 Ave neighs/atom = 76.500000 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.924 | 4.924 | 4.924 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1502.9522 0 -1502.9522 9964.7092 Loop time of 2e-06 on 1 procs for 0 steps with 232 atoms 150.0% 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 | | 2e-06 | | |100.00 Nlocal: 232.000 ave 232 max 232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2298.00 ave 2298 max 2298 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: 17726.0 ave 17726 max 17726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17726 Ave neighs/atom = 76.405172 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.924 | 4.924 | 4.924 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 -1502.9522 -1502.9522 16.557179 66.414454 3.0966067 9964.7092 9964.7092 -285.25783 30357.508 -178.12267 2.5352451 409.32406 Loop time of 1.8e-06 on 1 procs for 0 steps with 232 atoms 111.1% 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: 232.000 ave 232 max 232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2298.00 ave 2298 max 2298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8863.00 ave 8863 max 8863 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17726.0 ave 17726 max 17726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17726 Ave neighs/atom = 76.405172 Neighbor list builds = 0 Dangerous builds = 0 232 -1502.95217800322 eV 2.53524508184375 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03