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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -41.649211 0.0000000) to (51.009657 41.649211 8.6222058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8296751 5.3548985 5.7481372 Created 1661 atoms using lattice units in orthogonal box = (0.0000000 -41.649211 0.0000000) to (51.009657 41.649211 8.6222058) create_atoms CPU = 0.003 seconds 1661 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8296751 5.3548985 5.7481372 Created 1685 atoms using lattice units in orthogonal box = (0.0000000 -41.649211 0.0000000) to (51.009657 41.649211 8.6222058) create_atoms CPU = 0.003 seconds 1685 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 29 atoms, new total = 3317 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.013 | 7.013 | 7.013 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14564.47 0 -14564.47 -2956.8152 246 0 -14684.378 0 -14684.378 -13731.725 Loop time of 13.5089 on 1 procs for 246 steps with 3317 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 = -14564.4699776227 -14684.3628623214 -14684.3775439394 Force two-norm initial, final = 51.606902 0.64631802 Force max component initial, final = 7.1612509 0.24547282 Final line search alpha, max atom move = 0.44801604 0.10997576 Iterations, force evaluations = 246 471 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.086 | 13.086 | 13.086 | 0.0 | 96.87 Neigh | 0.28818 | 0.28818 | 0.28818 | 0.0 | 2.13 Comm | 0.055911 | 0.055911 | 0.055911 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07928 | | | 0.59 Nlocal: 3317.00 ave 3317 max 3317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11285.0 ave 11285 max 11285 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: 583238.0 ave 583238 max 583238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 583238 Ave neighs/atom = 175.83298 Neighbor list builds = 8 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 246 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.014 | 7.014 | 7.014 Mbytes Step Temp E_pair E_mol TotEng Press Volume 246 0 -14684.378 0 -14684.378 -13731.725 36635.959 252 0 -14685.744 0 -14685.744 33.788461 36370.298 Loop time of 0.245947 on 1 procs for 6 steps with 3317 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 = -14684.3775439394 -14685.7442818085 -14685.7444643566 Force two-norm initial, final = 564.64469 2.2905741 Force max component initial, final = 436.05161 1.9680558 Final line search alpha, max atom move = 0.00022122276 0.00043537875 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24022 | 0.24022 | 0.24022 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0008264 | 0.0008264 | 0.0008264 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004897 | | | 1.99 Nlocal: 3317.00 ave 3317 max 3317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11279.0 ave 11279 max 11279 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: 583028.0 ave 583028 max 583028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 583028 Ave neighs/atom = 175.76967 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.152 | 7.152 | 7.152 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14685.744 0 -14685.744 33.788461 Loop time of 2.355e-06 on 1 procs for 0 steps with 3317 atoms 169.9% 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 | | 2.355e-06 | | |100.00 Nlocal: 3317.00 ave 3317 max 3317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11291.0 ave 11291 max 11291 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: 584910.0 ave 584910 max 584910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 584910 Ave neighs/atom = 176.33705 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.152 | 7.152 | 7.152 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 -14685.744 -14685.744 50.964091 82.89415 8.6091187 33.788461 33.788461 -15.301868 30.102473 86.564778 2.2143697 1654.1359 Loop time of 2.223e-06 on 1 procs for 0 steps with 3317 atoms 269.9% 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 | | 2.223e-06 | | |100.00 Nlocal: 3317.00 ave 3317 max 3317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11291.0 ave 11291 max 11291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 292455.0 ave 292455 max 292455 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 584910.0 ave 584910 max 584910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 584910 Ave neighs/atom = 176.33705 Neighbor list builds = 0 Dangerous builds = 0 3317 -14685.7444643566 eV 2.21436967923859 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14