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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -31.977957 0.0000000) to (15.665936 31.977957 7.0060194) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1775828 3.8373549 4.6706796 Created 300 atoms using lattice units in orthogonal box = (0.0000000 -31.977957 0.0000000) to (15.665936 31.977957 7.0060194) create_atoms CPU = 0.001 seconds 300 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1775828 3.8373549 4.6706796 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -31.977957 0.0000000) to (15.665936 31.977957 7.0060194) create_atoms CPU = 0.000 seconds 306 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 = 6 24 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 6 atoms, new total = 600 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_137964310702_004#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 = 6 24 3 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) = 4.829 | 4.829 | 4.829 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2518.0243 0 -2518.0243 20499.695 24 0 -2551.4677 0 -2551.4677 8794.023 Loop time of 1.72818 on 1 procs for 24 steps with 600 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 = -2518.02433053882 -2551.46528247185 -2551.46770057149 Force two-norm initial, final = 42.168134 0.18923465 Force max component initial, final = 6.3270673 0.025899699 Final line search alpha, max atom move = 1.0000000 0.025899699 Iterations, force evaluations = 24 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7249 | 1.7249 | 1.7249 | 0.0 | 99.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013033 | 0.0013033 | 0.0013033 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001928 | | | 0.11 Nlocal: 600.000 ave 600 max 600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2384.00 ave 2384 max 2384 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: 34560.0 ave 34560 max 34560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34560 Ave neighs/atom = 57.600000 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 = 6 24 3 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 : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.829 | 4.829 | 4.829 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -2551.4677 0 -2551.4677 8794.023 7019.5357 37 0 -2552.1631 0 -2552.1631 22.031723 7052.144 Loop time of 0.544041 on 1 procs for 13 steps with 600 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 = -2551.46770057149 -2552.16295529698 -2552.16313882672 Force two-norm initial, final = 117.09341 1.1473330 Force max component initial, final = 116.94845 0.55964087 Final line search alpha, max atom move = 0.0012326456 0.00068983887 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54216 | 0.54216 | 0.54216 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029346 | 0.00029346 | 0.00029346 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001588 | | | 0.29 Nlocal: 600.000 ave 600 max 600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2442.00 ave 2442 max 2442 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: 34404.0 ave 34404 max 34404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34404 Ave neighs/atom = 57.340000 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 = 6 25 3 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) = 4.968 | 4.968 | 4.968 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2552.1631 0 -2552.1631 22.031723 Loop time of 2.118e-06 on 1 procs for 0 steps with 600 atoms 141.6% 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 | | 2.118e-06 | | |100.00 Nlocal: 600.000 ave 600 max 600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2463.00 ave 2463 max 2463 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: 34380.0 ave 34380 max 34380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34380 Ave neighs/atom = 57.300000 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 = 6 25 3 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) = 4.968 | 4.968 | 4.968 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 -2552.1631 -2552.1631 15.593181 64.725395 6.9873377 22.031723 22.031723 126.55433 52.559863 -113.01902 2.3956742 415.91884 Loop time of 1.469e-06 on 1 procs for 0 steps with 600 atoms 204.2% 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 | | 1.469e-06 | | |100.00 Nlocal: 600.000 ave 600 max 600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2463.00 ave 2463 max 2463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17190.0 ave 17190 max 17190 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34380.0 ave 34380 max 34380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34380 Ave neighs/atom = 57.300000 Neighbor list builds = 0 Dangerous builds = 0 600 -2552.16313882672 eV 2.39567421326642 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02