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 = 2.8553126 2.8553126 2.8553126 Created orthogonal box = (0.0000000 -56.532305 0.0000000) to (34.618825 56.532305 6.9940589) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0035376 4.0380218 4.6627059 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -56.532305 0.0000000) to (34.618825 56.532305 6.9940589) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0035376 4.0380218 4.6627059 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -56.532305 0.0000000) to (34.618825 56.532305 6.9940589) create_atoms CPU = 0.001 seconds 1182 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 27 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2352 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_577453891941_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.914 | 6.914 | 6.914 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6357.4375 0 -6357.4375 252590.61 75 0 -9397.8501 0 -9397.8501 7475.6122 Loop time of 3.90309 on 1 procs for 75 steps with 2352 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 = -6357.43747898772 -9397.8408748576 -9397.85012398952 Force two-norm initial, final = 5046.3563 0.36419488 Force max component initial, final = 702.83526 0.038912387 Final line search alpha, max atom move = 1.0000000 0.038912387 Iterations, force evaluations = 75 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8379 | 3.8379 | 3.8379 | 0.0 | 98.33 Neigh | 0.029584 | 0.029584 | 0.029584 | 0.0 | 0.76 Comm | 0.018781 | 0.018781 | 0.018781 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01679 | | | 0.43 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11724.0 ave 11724 max 11724 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: 533196.0 ave 533196 max 533196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 533196 Ave neighs/atom = 226.69898 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.909 | 6.909 | 6.909 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -9397.8501 0 -9397.8501 7475.6122 27375.893 81 0 -9398.4331 0 -9398.4331 -308.44598 27498.886 Loop time of 0.22377 on 1 procs for 6 steps with 2352 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 = -9397.85012398953 -9398.43029215896 -9398.43311823401 Force two-norm initial, final = 255.39561 10.386235 Force max component initial, final = 231.03643 8.6159699 Final line search alpha, max atom move = 7.4424846e-05 0.00064124223 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21981 | 0.21981 | 0.21981 | 0.0 | 98.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066356 | 0.00066356 | 0.00066356 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003297 | | | 1.47 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11141.0 ave 11141 max 11141 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: 531744.0 ave 531744 max 531744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 531744 Ave neighs/atom = 226.08163 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.046 | 7.046 | 7.046 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9398.4331 0 -9398.4331 -308.44598 Loop time of 1.887e-06 on 1 procs for 0 steps with 2352 atoms 159.0% 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 | | 1.887e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11087.0 ave 11087 max 11087 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: 530544.0 ave 530544 max 530544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 530544 Ave neighs/atom = 225.57143 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.046 | 7.046 | 7.046 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 -9398.4331 -9398.4331 34.603602 113.67012 6.9911315 -308.44598 -308.44598 -501.77429 -104.28457 -319.27907 2.2271413 1023.2145 Loop time of 2.259e-06 on 1 procs for 0 steps with 2352 atoms 221.3% 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 | | 2.259e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11087.0 ave 11087 max 11087 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 265272.0 ave 265272 max 265272 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 530544.0 ave 530544 max 530544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 530544 Ave neighs/atom = 225.57143 Neighbor list builds = 0 Dangerous builds = 0 2352 -9398.43311823401 eV 2.22714127117964 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05