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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -42.059316 0.0000000) to (21.029658 42.059316 2.8886457) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5710740 3.5710740 2.8886457 Created 212 atoms using lattice units in orthogonal box = (0.0000000 -42.059316 0.0000000) to (21.029658 42.059316 2.8886457) create_atoms CPU = 0.002 seconds 212 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5710740 3.5710740 2.8886457 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -42.059316 0.0000000) to (21.029658 42.059316 2.8886457) create_atoms CPU = 0.001 seconds 213 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 32 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 425 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.817 | 4.817 | 4.817 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1693.453 0 -1693.453 46971.859 46 0 -1766.3384 0 -1766.3384 11226.671 Loop time of 6.45599 on 1 procs for 46 steps with 425 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1693.4529833195 -1766.33680670706 -1766.33837450215 Force two-norm initial, final = 206.04787 0.24924303 Force max component initial, final = 135.34101 0.10860375 Final line search alpha, max atom move = 1.0000000 0.10860375 Iterations, force evaluations = 46 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.445 | 6.445 | 6.445 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0055136 | 0.0055136 | 0.0055136 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005525 | | | 0.09 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2822.00 ave 2822 max 2822 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: 24574.0 ave 24574 max 24574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24574 Ave neighs/atom = 57.821176 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.817 | 4.817 | 4.817 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -1766.3384 0 -1766.3384 11226.671 5109.9739 58 0 -1766.6847 0 -1766.6847 -175.24877 5140.8287 Loop time of 1.05689 on 1 procs for 12 steps with 425 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 = -1766.33837450215 -1766.68425211492 -1766.6847444977 Force two-norm initial, final = 75.618813 1.3687248 Force max component initial, final = 70.974831 0.98115664 Final line search alpha, max atom move = 0.0011310122 0.0011097001 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0525 | 1.0525 | 1.0525 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0009482 | 0.0009482 | 0.0009482 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003426 | | | 0.32 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2822.00 ave 2822 max 2822 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: 24422.0 ave 24422 max 24422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24422 Ave neighs/atom = 57.463529 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.955 | 4.955 | 4.955 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1766.6847 0 -1766.6847 -175.24877 Loop time of 5.703e-06 on 1 procs for 0 steps with 425 atoms 192.9% 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 | | 5.703e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2818.00 ave 2818 max 2818 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: 24396.0 ave 24396 max 24396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24396 Ave neighs/atom = 57.402353 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.955 | 4.955 | 4.955 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 -1766.6847 -1766.6847 21.036462 85.029838 2.8740153 -175.24877 -175.24877 -305.88351 -133.42603 -86.436761 2.3524197 240.88028 Loop time of 6.515e-06 on 1 procs for 0 steps with 425 atoms 230.2% 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 | | 6.515e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2818.00 ave 2818 max 2818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12198.0 ave 12198 max 12198 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24396.0 ave 24396 max 24396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24396 Ave neighs/atom = 57.402353 Neighbor list builds = 0 Dangerous builds = 0 425 -1766.6847444977 eV 2.35241974971599 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08