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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -37.441127 0.0000000) to (21.616645 37.441127 5.0032811) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6321382 4.4572771 5.0032811 Created 336 atoms using lattice units in orthogonal box = (0.0000000 -37.441127 0.0000000) to (21.616645 37.441127 5.0032811) create_atoms CPU = 0.003 seconds 336 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6321382 4.4572771 5.0032811 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -37.441127 0.0000000) to (21.616645 37.441127 5.0032811) create_atoms CPU = 0.002 seconds 339 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 = 9 28 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 3 atoms, new total = 672 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 = 9 28 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) = 4.884 | 4.884 | 4.884 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2738.6792 0 -2738.6792 25587.742 27 0 -2791.0992 0 -2791.0992 5421.1133 Loop time of 6.10924 on 1 procs for 27 steps with 672 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 = -2738.6792396281 -2791.09693068683 -2791.09915863323 Force two-norm initial, final = 80.452320 0.22919056 Force max component initial, final = 18.083169 0.050982839 Final line search alpha, max atom move = 1.0000000 0.050982839 Iterations, force evaluations = 27 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1006 | 6.1006 | 6.1006 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0039998 | 0.0039998 | 0.0039998 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004604 | | | 0.08 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2994.00 ave 2994 max 2994 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: 38760.0 ave 38760 max 38760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38760 Ave neighs/atom = 57.678571 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 = 9 28 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 : 27 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.884 | 4.884 | 4.884 Mbytes Step Temp E_pair E_mol TotEng Press Volume 27 0 -2791.0992 0 -2791.0992 5421.1133 8098.8266 31 0 -2791.1742 0 -2791.1742 44.688679 8121.7578 Loop time of 0.951148 on 1 procs for 4 steps with 672 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 = -2791.09915863323 -2791.17415281205 -2791.17418525999 Force two-norm initial, final = 55.522788 0.59700399 Force max component initial, final = 50.192228 0.39554368 Final line search alpha, max atom move = 0.0011477064 0.00045396802 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94829 | 0.94829 | 0.94829 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054655 | 0.00054655 | 0.00054655 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002317 | | | 0.24 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2975.00 ave 2975 max 2975 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: 38640.0 ave 38640 max 38640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38640 Ave neighs/atom = 57.500000 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 = 9 29 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) = 5.022 | 5.022 | 5.022 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2791.1742 0 -2791.1742 44.688679 Loop time of 6.094e-06 on 1 procs for 0 steps with 672 atoms 164.1% 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 | | 6.094e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2975.00 ave 2975 max 2975 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: 38632.0 ave 38632 max 38632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38632 Ave neighs/atom = 57.488095 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 = 9 29 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) = 5.022 | 5.022 | 5.022 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 -2791.1742 -2791.1742 21.604706 75.09869 5.0057519 44.688679 44.688679 24.930993 31.067737 78.067307 2.306034 424.29798 Loop time of 6.936e-06 on 1 procs for 0 steps with 672 atoms 273.9% 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 | | 6.936e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2975.00 ave 2975 max 2975 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19316.0 ave 19316 max 19316 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 38632.0 ave 38632 max 38632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38632 Ave neighs/atom = 57.488095 Neighbor list builds = 0 Dangerous builds = 0 672 -2791.17418525999 eV 2.30603402837081 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07