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 = 3.5242205 3.5242205 3.5242205 Created orthogonal box = (0.0000000 -66.494858 0.0000000) to (33.247429 66.494858 3.5242205) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8563661 4.8563661 3.5242205 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -66.494858 0.0000000) to (33.247429 66.494858 3.5242205) create_atoms CPU = 0.003 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8563661 4.8563661 3.5242205 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -66.494858 0.0000000) to (33.247429 66.494858 3.5242205) create_atoms CPU = 0.002 seconds 714 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 11 43 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, cut 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1416 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_769632475533_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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 11 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5937.6334 0 -5937.6334 62511.682 183 0 -6296.3536 0 -6296.3536 3601.2308 Loop time of 5.10235 on 1 procs for 183 steps with 1416 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 = -5937.6334130912 -6296.34807097006 -6296.35355851828 Force two-norm initial, final = 955.36042 0.29004096 Force max component initial, final = 330.09141 0.057940236 Final line search alpha, max atom move = 1.0000000 0.057940236 Iterations, force evaluations = 183 349 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9078 | 4.9078 | 4.9078 | 0.0 | 96.19 Neigh | 0.062456 | 0.062456 | 0.062456 | 0.0 | 1.22 Comm | 0.073921 | 0.073921 | 0.073921 | 0.0 | 1.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05821 | | | 1.14 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9244.00 ave 9244 max 9244 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: 121392.0 ave 121392 max 121392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121392 Ave neighs/atom = 85.728814 Neighbor list builds = 3 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 11 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 183 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.097 | 5.097 | 5.097 Mbytes Step Temp E_pair E_mol TotEng Press Volume 183 0 -6296.3536 0 -6296.3536 3601.2308 15582.574 187 0 -6296.4453 0 -6296.4453 -18.478519 15611.541 Loop time of 0.10345 on 1 procs for 4 steps with 1416 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 = -6296.35355851829 -6296.44067693656 -6296.44525400683 Force two-norm initial, final = 74.280115 2.1400428 Force max component initial, final = 68.551126 1.5344104 Final line search alpha, max atom move = 7.3656029e-05 0.00011301857 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.097173 | 0.097173 | 0.097173 | 0.0 | 93.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015226 | 0.0015226 | 0.0015226 | 0.0 | 1.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004755 | | | 4.60 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9264.00 ave 9264 max 9264 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: 121336.0 ave 121336 max 121336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121336 Ave neighs/atom = 85.689266 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 11 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 5.235 | 5.235 | 5.235 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6296.4453 0 -6296.4453 -18.478519 Loop time of 6.695e-06 on 1 procs for 0 steps with 1416 atoms 209.1% 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 | | 6.695e-06 | | |100.00 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9264.00 ave 9264 max 9264 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: 121312.0 ave 121312 max 121312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121312 Ave neighs/atom = 85.672316 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 11 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 5.235 | 5.235 | 5.235 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 -6296.4453 -6296.4453 33.275164 133.34138 3.5185249 -18.478519 -18.478519 143.57912 -157.8894 -41.125268 2.3028983 418.40568 Loop time of 7.237e-06 on 1 procs for 0 steps with 1416 atoms 262.5% 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 | | 7.237e-06 | | |100.00 Nlocal: 1416.00 ave 1416 max 1416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9264.00 ave 9264 max 9264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60656.0 ave 60656 max 60656 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 121312.0 ave 121312 max 121312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 121312 Ave neighs/atom = 85.672316 Neighbor list builds = 0 Dangerous builds = 0 1416 -6296.44525400683 eV 2.30289828241687 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05