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 = 3.6473074 3.6473074 3.6473074 Created orthogonal box = (0.0000000 -44.070583 0.0000000) to (53.975220 44.070583 8.9340421) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1757061 5.4333595 5.9560280 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -44.070583 0.0000000) to (53.975220 44.070583 8.9340421) create_atoms CPU = 0.003 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1757061 5.4333595 5.9560280 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -44.070583 0.0000000) to (53.975220 44.070583 8.9340421) create_atoms CPU = 0.003 seconds 1754 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 = 21 33 4 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 24 atoms, new total = 3478 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 = 21 33 4 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) = 6.353 | 6.353 | 6.353 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12518.361 0 -12518.361 95818.224 131 0 -14377.779 0 -14377.779 -8600.9065 Loop time of 44.693 on 1 procs for 131 steps with 3478 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 = -12518.3608045355 -14377.7651139871 -14377.7789941451 Force two-norm initial, final = 2503.4940 0.44412055 Force max component initial, final = 483.11827 0.037292139 Final line search alpha, max atom move = 1.0000000 0.037292139 Iterations, force evaluations = 131 230 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 44.45 | 44.45 | 44.45 | 0.0 | 99.46 Neigh | 0.18296 | 0.18296 | 0.18296 | 0.0 | 0.41 Comm | 0.020093 | 0.020093 | 0.020093 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04008 | | | 0.09 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6672.00 ave 6672 max 6672 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: 186806.0 ave 186806 max 186806 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186806 Ave neighs/atom = 53.710753 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 21 33 4 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 : 131 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.350 | 6.350 | 6.350 Mbytes Step Temp E_pair E_mol TotEng Press Volume 131 0 -14377.779 0 -14377.779 -8600.9065 42503.159 136 0 -14378.537 0 -14378.537 27.15045 42280.196 Loop time of 1.48352 on 1 procs for 5 steps with 3478 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 = -14377.7789941451 -14378.5350785003 -14378.5366972433 Force two-norm initial, final = 411.62271 4.7755906 Force max component initial, final = 302.02942 4.3735211 Final line search alpha, max atom move = 4.9644921e-05 0.00021712311 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4796 | 1.4796 | 1.4796 | 0.0 | 99.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043636 | 0.00043636 | 0.00043636 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003504 | | | 0.24 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6667.00 ave 6667 max 6667 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: 187054.0 ave 187054 max 187054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187054 Ave neighs/atom = 53.782059 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 = 21 33 4 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) = 6.488 | 6.488 | 6.488 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14378.537 0 -14378.537 27.15045 Loop time of 2.116e-06 on 1 procs for 0 steps with 3478 atoms 141.8% 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 | | 2.116e-06 | | |100.00 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6684.00 ave 6684 max 6684 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: 187232.0 ave 187232 max 187232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187232 Ave neighs/atom = 53.833237 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 = 21 33 4 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) = 6.488 | 6.488 | 6.488 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 -14378.537 -14378.537 53.875726 87.816899 8.936465 27.15045 27.15045 165.42582 -19.302577 -64.671897 2.3484896 1473.9204 Loop time of 2.389e-06 on 1 procs for 0 steps with 3478 atoms 251.2% 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 | | 2.389e-06 | | |100.00 Nlocal: 3478.00 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6684.00 ave 6684 max 6684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93616.0 ave 93616 max 93616 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 187232.0 ave 187232 max 187232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187232 Ave neighs/atom = 53.833237 Neighbor list builds = 0 Dangerous builds = 0 3478 -14378.5366972433 eV 2.34848956963342 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:47