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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -44.200980 0.0000000) to (54.134924 44.200980 8.9604763) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1910201 5.4494359 5.9736509 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -44.200980 0.0000000) to (54.134924 44.200980 8.9604763) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1910201 5.4494359 5.9736509 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -44.200980 0.0000000) to (54.134924 44.200980 8.9604763) create_atoms CPU = 0.002 seconds 1757 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 25 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 11 atoms, new total = 3497 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 15 25 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) = 6.566 | 6.566 | 6.566 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12558.565 0 -12558.565 70261.091 662 0 -13758.755 0 -13758.755 -53147.478 Loop time of 30.3885 on 1 procs for 662 steps with 3497 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12558.564602914 -13758.7419219213 -13758.7552914538 Force two-norm initial, final = 1431.3196 0.35747712 Force max component initial, final = 263.23454 0.033758336 Final line search alpha, max atom move = 0.88286205 0.029803953 Iterations, force evaluations = 662 1292 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 29.534 | 29.534 | 29.534 | 0.0 | 97.19 Neigh | 0.51824 | 0.51824 | 0.51824 | 0.0 | 1.71 Comm | 0.13356 | 0.13356 | 0.13356 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2032 | | | 0.67 Nlocal: 3497.00 ave 3497 max 3497 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10028.0 ave 10028 max 10028 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: 482198.0 ave 482198 max 482198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 482198 Ave neighs/atom = 137.88905 Neighbor list builds = 16 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 25 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 : 662 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.564 | 6.564 | 6.564 Mbytes Step Temp E_pair E_mol TotEng Press Volume 662 0 -13758.755 0 -13758.755 -53147.478 42881.555 704 0 -13823.485 0 -13823.485 -6.5644744 41439.206 Loop time of 1.12939 on 1 procs for 42 steps with 3497 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 = -13758.755291454 -13823.4749084266 -13823.4851055009 Force two-norm initial, final = 2974.3366 7.3565307 Force max component initial, final = 2235.3244 1.7409245 Final line search alpha, max atom move = 4.6988983e-05 8.1804270e-05 Iterations, force evaluations = 42 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.99511 | 0.99511 | 0.99511 | 0.0 | 88.11 Neigh | 0.10121 | 0.10121 | 0.10121 | 0.0 | 8.96 Comm | 0.0045583 | 0.0045583 | 0.0045583 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02851 | | | 2.52 Nlocal: 3497.00 ave 3497 max 3497 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9925.00 ave 9925 max 9925 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: 493284.0 ave 493284 max 493284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 493284 Ave neighs/atom = 141.05919 Neighbor list builds = 3 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 = 15 24 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) = 7.082 | 7.082 | 7.082 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13823.485 0 -13823.485 -6.5644744 Loop time of 2.037e-06 on 1 procs for 0 steps with 3497 atoms 196.4% 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 | | 2.037e-06 | | |100.00 Nlocal: 3497.00 ave 3497 max 3497 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9897.00 ave 9897 max 9897 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: 493374.0 ave 493374 max 493374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 493374 Ave neighs/atom = 141.08493 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 = 15 24 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) = 7.082 | 7.082 | 7.082 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 -13823.485 -13823.485 52.763637 85.351261 9.2016722 -6.5644744 -6.5644744 3.4286372 45.999658 -69.121718 2.2384823 7688.2489 Loop time of 2.813e-06 on 1 procs for 0 steps with 3497 atoms 177.7% 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 | | 2.813e-06 | | |100.00 Nlocal: 3497.00 ave 3497 max 3497 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9897.00 ave 9897 max 9897 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 246687.0 ave 246687 max 246687 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 493374.0 ave 493374 max 493374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 493374 Ave neighs/atom = 141.08493 Neighbor list builds = 0 Dangerous builds = 0 3497 -13328.9336866763 eV 2.23848230964119 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:32