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 = 4.0320734 4.0320734 4.0320734 Created orthogonal box = (0.0000000 -79.830980 0.0000000) to (48.886292 79.830980 9.8765224) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6535167 5.7022129 6.5843483 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -79.830980 0.0000000) to (48.886292 79.830980 9.8765224) create_atoms CPU = 0.009 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6535167 5.7022129 6.5843483 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -79.830980 0.0000000) to (48.886292 79.830980 9.8765224) create_atoms CPU = 0.009 seconds 2358 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 42 3 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 4710 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 11.40 | 11.40 | 11.40 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15532.375 0 -15532.375 7483.5185 82 0 -15797.473 0 -15797.473 3888.7406 Loop time of 8.38757 on 1 procs for 82 steps with 4710 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 = -15532.3752194603 -15797.4596000522 -15797.47272957 Force two-norm initial, final = 78.442417 0.33540143 Force max component initial, final = 5.7209094 0.048448634 Final line search alpha, max atom move = 1.0000000 0.048448634 Iterations, force evaluations = 82 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.0788 | 8.0788 | 8.0788 | 0.0 | 96.32 Neigh | 0.18708 | 0.18708 | 0.18708 | 0.0 | 2.23 Comm | 0.046636 | 0.046636 | 0.046636 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07508 | | | 0.90 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12711.0 ave 12711 max 12711 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: 621852.0 ave 621852 max 621852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621852 Ave neighs/atom = 132.02803 Neighbor list builds = 2 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.40 | 11.40 | 11.40 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -15797.473 0 -15797.473 3888.7406 77089.034 88 0 -15798.3 0 -15798.3 -180.93014 77474.417 Loop time of 0.428076 on 1 procs for 6 steps with 4710 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 = -15797.4727295702 -15798.2941985902 -15798.2997998022 Force two-norm initial, final = 359.16208 17.157808 Force max component initial, final = 309.79610 12.249017 Final line search alpha, max atom move = 4.3163186e-05 0.00052870660 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41472 | 0.41472 | 0.41472 | 0.0 | 96.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021924 | 0.0021924 | 0.0021924 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01117 | | | 2.61 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12484.0 ave 12484 max 12484 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: 622368.0 ave 622368 max 622368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 622368 Ave neighs/atom = 132.13758 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 42 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 10.91 | 10.91 | 10.91 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15798.3 0 -15798.3 -180.93014 Loop time of 6.765e-06 on 1 procs for 0 steps with 4710 atoms 206.9% 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 | | 6.765e-06 | | |100.00 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12485.0 ave 12485 max 12485 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: 621780.0 ave 621780 max 621780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621780 Ave neighs/atom = 132.01274 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 13 42 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 10.91 | 10.91 | 10.91 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 -15798.3 -15798.3 48.906227 160.5363 9.8678129 -180.93014 -180.93014 -253.41385 -45.483145 -243.89342 2.5766329 2373.916 Loop time of 6.886e-06 on 1 procs for 0 steps with 4710 atoms 275.9% 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 | | 6.886e-06 | | |100.00 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12485.0 ave 12485 max 12485 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 310890.0 ave 310890 max 310890 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 621780.0 ave 621780 max 621780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 621780 Ave neighs/atom = 132.01274 Neighbor list builds = 0 Dangerous builds = 0 4710 -15798.2997998022 eV 2.57663291532967 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10