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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -55.263046 0.0000000) to (31.906134 55.263046 5.0032811) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7074624 4.2277740 5.0032811 Created 732 atoms using lattice units in orthogonal box = (0.0000000 -55.263046 0.0000000) to (31.906134 55.263046 5.0032811) create_atoms CPU = 0.005 seconds 732 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7074624 4.2277740 5.0032811 Created 734 atoms using lattice units in orthogonal box = (0.0000000 -55.263046 0.0000000) to (31.906134 55.263046 5.0032811) create_atoms CPU = 0.005 seconds 734 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 42 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 1466 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 5.820 | 5.820 | 5.820 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5834.4529 0 -5834.4529 44522.827 42 0 -6105.9814 0 -6105.9814 5846.5255 Loop time of 20.2512 on 1 procs for 42 steps with 1466 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 = -5834.45287613478 -6105.97546135489 -6105.98138795529 Force two-norm initial, final = 735.80946 0.31210410 Force max component initial, final = 330.49426 0.043564520 Final line search alpha, max atom move = 1.0000000 0.043564520 Iterations, force evaluations = 42 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.228 | 20.228 | 20.228 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011033 | 0.011033 | 0.011033 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01249 | | | 0.06 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5329.00 ave 5329 max 5329 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: 84744.0 ave 84744 max 84744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84744 Ave neighs/atom = 57.806276 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.820 | 5.820 | 5.820 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -6105.9814 0 -6105.9814 5846.5255 17643.872 46 0 -6106.1663 0 -6106.1663 182.94158 17699.532 Loop time of 1.53675 on 1 procs for 4 steps with 1466 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 = -6105.98138795529 -6106.16465404893 -6106.16632306256 Force two-norm initial, final = 127.65154 5.1136058 Force max component initial, final = 114.98722 4.7225666 Final line search alpha, max atom move = 9.8149944e-05 0.00046351965 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5327 | 1.5327 | 1.5327 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072123 | 0.00072123 | 0.00072123 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003291 | | | 0.21 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5319.00 ave 5319 max 5319 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: 84716.0 ave 84716 max 84716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84716 Ave neighs/atom = 57.787176 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 5.958 | 5.958 | 5.958 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6106.1663 0 -6106.1663 182.94158 Loop time of 5.673e-06 on 1 procs for 0 steps with 1466 atoms 211.5% 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 | | 5.673e-06 | | |100.00 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5319.00 ave 5319 max 5319 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: 84696.0 ave 84696 max 84696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84696 Ave neighs/atom = 57.773533 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 12 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 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) = 5.958 | 5.958 | 5.958 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 -6106.1663 -6106.1663 31.900902 110.86065 5.0047388 182.94158 182.94158 -46.13758 428.78467 166.17764 2.3277013 494.21692 Loop time of 6.505e-06 on 1 procs for 0 steps with 1466 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 | | 6.505e-06 | | |100.00 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5319.00 ave 5319 max 5319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42348.0 ave 42348 max 42348 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 84696.0 ave 84696 max 84696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 84696 Ave neighs/atom = 57.773533 Neighbor list builds = 0 Dangerous builds = 0 1466 -6106.16632306256 eV 2.32770132527635 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23