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 -53.109245 0.0000000) to (26.552799 53.109245 3.6473074) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5089658 4.5089658 3.6473074 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -53.109245 0.0000000) to (26.552799 53.109245 3.6473074) create_atoms CPU = 0.003 seconds 426 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5089658 4.5089658 3.6473074 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -53.109245 0.0000000) to (26.552799 53.109245 3.6473074) create_atoms CPU = 0.002 seconds 426 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 = 10 40 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 12 atoms, new total = 840 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 = 10 40 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) = 5.305 | 5.305 | 5.305 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3449.9058 0 -3449.9058 789.67161 84 0 -3470.2678 0 -3470.2678 -8169.9152 Loop time of 19.8117 on 1 procs for 84 steps with 840 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 = -3449.90579851368 -3470.26489350656 -3470.2678469244 Force two-norm initial, final = 31.645152 0.22196190 Force max component initial, final = 9.6059684 0.041006390 Final line search alpha, max atom move = 1.0000000 0.041006390 Iterations, force evaluations = 84 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.775 | 19.775 | 19.775 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018018 | 0.018018 | 0.018018 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01834 | | | 0.09 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4344.00 ave 4344 max 4344 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: 44872.0 ave 44872 max 44872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44872 Ave neighs/atom = 53.419048 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 = 10 40 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 : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.304 | 5.304 | 5.304 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -3470.2678 0 -3470.2678 -8169.9152 10286.859 89 0 -3470.3809 0 -3470.3809 -1796.3658 10245.93 Loop time of 1.08871 on 1 procs for 5 steps with 840 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 = -3470.2678469244 -3470.38081260854 -3470.38090952712 Force two-norm initial, final = 67.679626 1.1631804 Force max component initial, final = 56.811265 1.0980646 Final line search alpha, max atom move = 0.00078395727 0.00086083573 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0843 | 1.0843 | 1.0843 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00087549 | 0.00087549 | 0.00087549 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003551 | | | 0.33 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4332.00 ave 4332 max 4332 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: 44992.0 ave 44992 max 44992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44992 Ave neighs/atom = 53.561905 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 = 10 40 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) = 5.442 | 5.442 | 5.442 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3470.3809 0 -3470.3809 -1796.3658 Loop time of 6.235e-06 on 1 procs for 0 steps with 840 atoms 192.5% 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 | | 6.235e-06 | | |100.00 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4340.00 ave 4340 max 4340 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: 44996.0 ave 44996 max 44996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44996 Ave neighs/atom = 53.566667 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 = 10 40 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) = 5.442 | 5.442 | 5.442 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 -3470.3809 -3470.3809 26.453467 106.21849 3.6464366 -1796.3658 -1796.3658 -171.06421 -5172.5424 -45.490944 2.321468 155.32684 Loop time of 6.715e-06 on 1 procs for 0 steps with 840 atoms 253.2% 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 | | 6.715e-06 | | |100.00 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4340.00 ave 4340 max 4340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22498.0 ave 22498 max 22498 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44996.0 ave 44996 max 44996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44996 Ave neighs/atom = 53.566667 Neighbor list builds = 0 Dangerous builds = 0 840 -3470.38090952712 eV 2.32146803983097 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21