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 = 3.5240105 3.5240105 3.5240105 Created orthogonal box = (0.0000000 -43.589603 0.0000000) to (20.548336 43.589603 4.9837035) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0436282 5.9828866 4.9837035 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -43.589603 0.0000000) to (20.548336 43.589603 4.9837035) create_atoms CPU = 0.004 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0436282 5.9828866 4.9837035 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -43.589603 0.0000000) to (20.548336 43.589603 4.9837035) create_atoms CPU = 0.003 seconds 412 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 23 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 816 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_535504325462_003#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 4.987 | 4.987 | 4.987 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3596.4038 0 -3596.4038 11225.822 58 0 -3682.4129 0 -3682.4129 10304.659 Loop time of 1.79783 on 1 procs for 58 steps with 816 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3596.40383948573 -3682.40943089477 -3682.41290595426 Force two-norm initial, final = 36.650411 0.20254596 Force max component initial, final = 6.4472637 0.022635575 Final line search alpha, max atom move = 1.0000000 0.022635575 Iterations, force evaluations = 58 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7471 | 1.7471 | 1.7471 | 0.0 | 97.18 Neigh | 0.022158 | 0.022158 | 0.022158 | 0.0 | 1.23 Comm | 0.015885 | 0.015885 | 0.015885 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01265 | | | 0.70 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6237.00 ave 6237 max 6237 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: 142168.0 ave 142168 max 142168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142168 Ave neighs/atom = 174.22549 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.987 | 4.987 | 4.987 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -3682.4129 0 -3682.4129 10304.659 8927.7445 64 0 -3682.7118 0 -3682.7118 240.82193 8977.8938 Loop time of 0.132803 on 1 procs for 6 steps with 816 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 = -3682.41290595426 -3682.70828885929 -3682.71180305113 Force two-norm initial, final = 116.37201 2.4749210 Force max component initial, final = 105.81578 1.6806554 Final line search alpha, max atom move = 0.00014333082 0.00024088971 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12822 | 0.12822 | 0.12822 | 0.0 | 96.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010674 | 0.0010674 | 0.0010674 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003518 | | | 2.65 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6295.00 ave 6295 max 6295 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: 142272.0 ave 142272 max 142272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142272 Ave neighs/atom = 174.35294 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.125 | 5.125 | 5.125 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3682.7118 0 -3682.7118 240.82193 Loop time of 6.455e-06 on 1 procs for 0 steps with 816 atoms 154.9% 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 | | 6.455e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6295.00 ave 6295 max 6295 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: 141984.0 ave 141984 max 141984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141984 Ave neighs/atom = 174.00000 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.125 | 5.125 | 5.125 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 -3682.7118 -3682.7118 20.540714 87.658977 4.9861177 240.82193 240.82193 290.63155 301.57689 130.25734 2.3793637 473.17104 Loop time of 7.026e-06 on 1 procs for 0 steps with 816 atoms 242.0% 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 | | 7.026e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6295.00 ave 6295 max 6295 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70992.0 ave 70992 max 70992 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 141984.0 ave 141984 max 141984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141984 Ave neighs/atom = 174.00000 Neighbor list builds = 0 Dangerous builds = 0 816 -3682.71180305113 eV 2.37936372438802 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02