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 = 3.6461252 3.6461252 3.6461252 Created orthogonal box = (0.0000000 -57.419238 0.0000000) to (35.161958 57.419238 8.9311464) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6712836 5.5567004 5.9540976 Created 1483 atoms using lattice units in orthogonal box = (0.0000000 -57.419238 0.0000000) to (35.161958 57.419238 8.9311464) create_atoms CPU = 0.003 seconds 1483 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6712836 5.5567004 5.9540976 Created 1489 atoms using lattice units in orthogonal box = (0.0000000 -57.419238 0.0000000) to (35.161958 57.419238 8.9311464) create_atoms CPU = 0.002 seconds 1489 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 9 27 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 2965 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_331285495617_004#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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 9 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 7.440 | 7.440 | 7.440 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11147.671 0 -11147.671 21984.804 68 0 -11533.455 0 -11533.455 -2992.6112 Loop time of 2.51076 on 1 procs for 68 steps with 2965 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11147.6711391061 -11533.4456809963 -11533.4554447878 Force two-norm initial, final = 378.42998 0.42176206 Force max component initial, final = 67.491646 0.072998288 Final line search alpha, max atom move = 0.50356032 0.036759041 Iterations, force evaluations = 68 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3251 | 2.3251 | 2.3251 | 0.0 | 92.61 Neigh | 0.15027 | 0.15027 | 0.15027 | 0.0 | 5.99 Comm | 0.015924 | 0.015924 | 0.015924 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01947 | | | 0.78 Nlocal: 2965.00 ave 2965 max 2965 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12266.0 ave 12266 max 12266 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: 660692.0 ave 660692 max 660692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 660692 Ave neighs/atom = 222.83035 Neighbor list builds = 4 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 9 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.441 | 7.441 | 7.441 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -11533.455 0 -11533.455 -2992.6112 36063.484 72 0 -11533.782 0 -11533.782 101.83205 35995.36 Loop time of 0.12287 on 1 procs for 4 steps with 2965 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 = -11533.4554447878 -11533.7808567994 -11533.7816451252 Force two-norm initial, final = 191.19401 4.3330999 Force max component initial, final = 172.41892 3.1848844 Final line search alpha, max atom move = 0.00011532936 0.00036731069 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11891 | 0.11891 | 0.11891 | 0.0 | 96.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058491 | 0.00058491 | 0.00058491 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003372 | | | 2.74 Nlocal: 2965.00 ave 2965 max 2965 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12266.0 ave 12266 max 12266 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: 660670.0 ave 660670 max 660670 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 660670 Ave neighs/atom = 222.82293 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 9 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 7.579 | 7.579 | 7.579 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11533.782 0 -11533.782 101.83205 Loop time of 2.023e-06 on 1 procs for 0 steps with 2965 atoms 197.7% 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 | | 2.023e-06 | | |100.00 Nlocal: 2965.00 ave 2965 max 2965 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12277.0 ave 12277 max 12277 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: 661056.0 ave 661056 max 661056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 661056 Ave neighs/atom = 222.95312 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.329525, bins = 9 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 7.579 | 7.579 | 7.579 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 -11533.782 -11533.782 35.223108 114.47489 8.9270634 101.83205 101.83205 142.00778 42.863284 120.62509 2.2605559 997.8516 Loop time of 5.449e-06 on 1 procs for 0 steps with 2965 atoms 201.9% 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 | | 5.449e-06 | | |100.00 Nlocal: 2965.00 ave 2965 max 2965 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12277.0 ave 12277 max 12277 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 330528.0 ave 330528 max 330528 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 661056.0 ave 661056 max 661056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 661056 Ave neighs/atom = 222.95312 Neighbor list builds = 0 Dangerous builds = 0 2965 -11533.7816451252 eV 2.26055594984602 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03