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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -43.286830 0.0000000) to (53.015323 43.286830 8.9612251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0588940 5.5654495 5.9741501 Created 1666 atoms using lattice units in orthogonal box = (0.0000000 -43.286830 0.0000000) to (53.015323 43.286830 8.9612251) create_atoms CPU = 0.003 seconds 1666 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0588940 5.5654495 5.9741501 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -43.286830 0.0000000) to (53.015323 43.286830 8.9612251) create_atoms CPU = 0.003 seconds 1690 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 24 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3356 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_249706810527_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.538 | 6.538 | 6.538 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12331.652 0 -12331.652 62802.101 1031 0 -13249.059 0 -13249.059 -74659.676 Loop time of 47.7686 on 1 procs for 1031 steps with 3356 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 = -12331.6515560187 -13249.0464877101 -13249.0585866508 Force two-norm initial, final = 867.32501 0.61983519 Force max component initial, final = 282.59172 0.36048473 Final line search alpha, max atom move = 0.51810157 0.18676771 Iterations, force evaluations = 1031 1988 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 46.324 | 46.324 | 46.324 | 0.0 | 96.98 Neigh | 0.88714 | 0.88714 | 0.88714 | 0.0 | 1.86 Comm | 0.22665 | 0.22665 | 0.22665 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3307 | | | 0.69 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9827.00 ave 9827 max 9827 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: 463396.0 ave 463396 max 463396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463396 Ave neighs/atom = 138.07986 Neighbor list builds = 26 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1031 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.537 | 6.537 | 6.537 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1031 0 -13249.059 0 -13249.059 -74659.676 41129.608 1092 0 -13381.061 0 -13381.061 -23.814479 39316.993 Loop time of 1.5968 on 1 procs for 61 steps with 3356 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 = -13249.0585866508 -13381.0582596431 -13381.0608640246 Force two-norm initial, final = 4101.4372 9.4812731 Force max component initial, final = 2956.8381 5.4784408 Final line search alpha, max atom move = 0.00018446790 0.0010105965 Iterations, force evaluations = 61 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.418 | 1.418 | 1.418 | 0.0 | 88.80 Neigh | 0.13326 | 0.13326 | 0.13326 | 0.0 | 8.35 Comm | 0.0062717 | 0.0062717 | 0.0062717 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03929 | | | 2.46 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9730.00 ave 9730 max 9730 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: 479020.0 ave 479020 max 479020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 479020 Ave neighs/atom = 142.73540 Neighbor list builds = 4 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.672 | 6.672 | 6.672 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13381.061 0 -13381.061 -23.814479 Loop time of 2.487e-06 on 1 procs for 0 steps with 3356 atoms 160.8% 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 | | 2.487e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9671.00 ave 9671 max 9671 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: 478470.0 ave 478470 max 478470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478470 Ave neighs/atom = 142.57151 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.672 | 6.672 | 6.672 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 -13381.061 -13381.061 50.946107 82.611475 9.3417645 -23.814479 -23.814479 157.84737 3.4371494 -232.72796 2.0839087 3954.8155 Loop time of 3.163e-06 on 1 procs for 0 steps with 3356 atoms 252.9% 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 | | 3.163e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9671.00 ave 9671 max 9671 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 239235.0 ave 239235 max 239235 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 478470.0 ave 478470 max 478470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 478470 Ave neighs/atom = 142.57151 Neighbor list builds = 0 Dangerous builds = 0 3356 -13381.0608640246 eV 2.08390874244277 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:50