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 = 4.0500004 4.0500004 4.0500004 Created orthogonal box = (0.0000000 -52.960627 0.0000000) to (24.965879 52.960627 5.7275655) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2559746 6.5039367 5.7275655 Created 450 atoms using lattice units in orthogonal box = (0.0000000 -52.960627 0.0000000) to (24.965879 52.960627 5.7275655) create_atoms CPU = 0.003 seconds 450 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2559746 6.5039367 5.7275655 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -52.960627 0.0000000) to (24.965879 52.960627 5.7275655) 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 28 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 898 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_820335782779_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 = 7 28 2 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) = 4.982 | 4.982 | 4.982 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2994.0093 0 -2994.0093 43.216524 46 0 -3009.0499 0 -3009.0499 -5239.0982 Loop time of 1.13961 on 1 procs for 46 steps with 898 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 = -2994.00934026258 -3009.04777686337 -3009.04990236552 Force two-norm initial, final = 18.291562 0.16583242 Force max component initial, final = 8.1873419 0.054160928 Final line search alpha, max atom move = 1.0000000 0.054160928 Iterations, force evaluations = 46 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1013 | 1.1013 | 1.1013 | 0.0 | 96.64 Neigh | 0.015851 | 0.015851 | 0.015851 | 0.0 | 1.39 Comm | 0.011974 | 0.011974 | 0.011974 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01052 | | | 0.92 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5347.00 ave 5347 max 5347 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: 118116.0 ave 118116 max 118116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118116 Ave neighs/atom = 131.53229 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 = 7 28 2 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 : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.982 | 4.982 | 4.982 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -3009.0499 0 -3009.0499 -5239.0982 15146.073 50 0 -3009.221 0 -3009.221 3.8643111 15046.224 Loop time of 0.0920886 on 1 procs for 4 steps with 898 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3009.04990236552 -3009.21889726127 -3009.2209814947 Force two-norm initial, final = 86.309500 0.43427667 Force max component initial, final = 57.280799 0.27794287 Final line search alpha, max atom move = 0.00025344829 7.0444145e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.08833 | 0.08833 | 0.08833 | 0.0 | 95.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00086209 | 0.00086209 | 0.00086209 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002897 | | | 3.15 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5347.00 ave 5347 max 5347 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: 118072.0 ave 118072 max 118072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118072 Ave neighs/atom = 131.48330 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 = 7 28 2 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) = 5.120 | 5.120 | 5.120 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3009.221 0 -3009.221 3.8643111 Loop time of 6.455e-06 on 1 procs for 0 steps with 898 atoms 185.9% 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: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5347.00 ave 5347 max 5347 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: 118128.0 ave 118128 max 118128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118128 Ave neighs/atom = 131.54566 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 = 7 28 2 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) = 5.120 | 5.120 | 5.120 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 -3009.221 -3009.221 24.9277 105.75194 5.7076455 3.8643111 3.8643111 29.551104 -25.861727 7.903556 2.6532673 708.97938 Loop time of 6.746e-06 on 1 procs for 0 steps with 898 atoms 237.2% 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 | | 6.746e-06 | | |100.00 Nlocal: 898.000 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5347.00 ave 5347 max 5347 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59064.0 ave 59064 max 59064 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 118128.0 ave 118128 max 118128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118128 Ave neighs/atom = 131.54566 Neighbor list builds = 0 Dangerous builds = 0 898 -3009.2209814947 eV 2.65326727091347 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01