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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -38.504775 0.0000000) to (27.226987 38.504775 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2096638 6.0797013 5.1000820 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.504775 0.0000000) to (27.226987 38.504775 5.1000820) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2096638 6.0797013 5.1000820 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.504775 0.0000000) to (27.226987 38.504775 5.1000820) create_atoms CPU = 0.001 seconds 458 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 914 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_147603128437_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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.647 | 6.647 | 6.647 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3622.4919 0 -3622.4919 51397.025 89 0 -3822.7039 0 -3822.7039 9520.0673 Loop time of 4.0954 on 1 procs for 89 steps with 914 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 = -3622.49186833129 -3822.70061564805 -3822.70387848508 Force two-norm initial, final = 238.03698 0.24152953 Force max component initial, final = 61.374121 0.031475023 Final line search alpha, max atom move = 1.0000000 0.031475023 Iterations, force evaluations = 89 169 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0433 | 4.0433 | 4.0433 | 0.0 | 98.73 Neigh | 0.025487 | 0.025487 | 0.025487 | 0.0 | 0.62 Comm | 0.017756 | 0.017756 | 0.017756 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008809 | | | 0.22 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12008.0 ave 12008 max 12008 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: 563684.0 ave 563684 max 563684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 563684 Ave neighs/atom = 616.72210 Neighbor list builds = 1 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.647 | 6.647 | 6.647 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -3822.7039 0 -3822.7039 9520.0673 10693.536 96 0 -3823.1964 0 -3823.1964 105.91937 10751.206 Loop time of 0.218237 on 1 procs for 7 steps with 914 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 = -3822.70387848512 -3823.19573192267 -3823.19644244848 Force two-norm initial, final = 158.68975 1.3940979 Force max component initial, final = 151.82134 1.0479519 Final line search alpha, max atom move = 0.00021369155 0.00022393847 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21451 | 0.21451 | 0.21451 | 0.0 | 98.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076689 | 0.00076689 | 0.00076689 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002956 | | | 1.35 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11937.0 ave 11937 max 11937 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: 564304.0 ave 564304 max 564304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 564304 Ave neighs/atom = 617.40044 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.785 | 6.785 | 6.785 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3823.1964 0 -3823.1964 105.91937 Loop time of 1.715e-06 on 1 procs for 0 steps with 914 atoms 174.9% 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 | | 1.715e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11935.0 ave 11935 max 11935 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: 559756.0 ave 559756 max 559756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 559756 Ave neighs/atom = 612.42451 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 5 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.785 | 6.785 | 6.785 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 -3823.1964 -3823.1964 27.393482 76.879635 5.1050339 105.91937 105.91937 157.12388 44.395434 116.2388 2.3994304 1133.1604 Loop time of 2.365e-06 on 1 procs for 0 steps with 914 atoms 211.4% 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 | | 2.365e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11935.0 ave 11935 max 11935 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 279878.0 ave 279878 max 279878 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 559756.0 ave 559756 max 559756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 559756 Ave neighs/atom = 612.42451 Neighbor list builds = 0 Dangerous builds = 0 914 -3823.19644244848 eV 2.39943042992408 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04