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 = 2.8665000 2.8665000 2.8665000 Created orthogonal box = (0.0000000 -37.593796 0.0000000) to (26.582828 37.593796 4.0538432) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9456424 4.8085087 4.0538432 Created 343 atoms using lattice units in orthogonal box = (0.0000000 -37.593796 0.0000000) to (26.582828 37.593796 4.0538432) create_atoms CPU = 0.001 seconds 343 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9456424 4.8085087 4.0538432 Created 345 atoms using lattice units in orthogonal box = (0.0000000 -37.593796 0.0000000) to (26.582828 37.593796 4.0538432) create_atoms CPU = 0.001 seconds 345 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 7 20 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 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 688 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_960699513424_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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 4.916 | 4.916 | 4.916 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 57822.841 0 57822.841 42955659 123 0 -2931.5325 0 -2931.5325 5874.6378 Loop time of 1.33993 on 1 procs for 123 steps with 688 atoms 97.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 57822.8408633288 -2931.52968868604 -2931.5325384392 Force two-norm initial, final = 432215.74 0.25187425 Force max component initial, final = 134323.41 0.068200510 Final line search alpha, max atom move = 1.0000000 0.068200510 Iterations, force evaluations = 123 231 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.301 | 1.301 | 1.301 | 0.0 | 97.10 Neigh | 0.020744 | 0.020744 | 0.020744 | 0.0 | 1.55 Comm | 0.0099854 | 0.0099854 | 0.0099854 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008153 | | | 0.61 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5195.00 ave 5195 max 5195 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: 114422.0 ave 114422 max 114422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114422 Ave neighs/atom = 166.31105 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 123 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.918 | 4.918 | 4.918 Mbytes Step Temp E_pair E_mol TotEng Press Volume 123 0 -2931.5325 0 -2931.5325 5874.6378 8102.4115 127 0 -2931.62 0 -2931.62 232.85626 8127.5921 Loop time of 0.0322586 on 1 procs for 4 steps with 688 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 = -2931.53253843923 -2931.61899303951 -2931.61997183409 Force two-norm initial, final = 59.735941 2.7198877 Force max component initial, final = 54.443762 2.5419042 Final line search alpha, max atom move = 0.00021567800 0.00054823281 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.031098 | 0.031098 | 0.031098 | 0.0 | 96.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002202 | 0.0002202 | 0.0002202 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009406 | | | 2.92 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5195.00 ave 5195 max 5195 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: 114562.0 ave 114562 max 114562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114562 Ave neighs/atom = 166.51453 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 5.056 | 5.056 | 5.056 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2931.62 0 -2931.62 232.85626 Loop time of 1.669e-06 on 1 procs for 0 steps with 688 atoms 119.8% 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 | | 1.669e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5195.00 ave 5195 max 5195 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: 114486.0 ave 114486 max 114486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114486 Ave neighs/atom = 166.40407 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 5.056 | 5.056 | 5.056 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 -2931.62 -2931.62 26.583321 75.418855 4.0538972 232.85626 232.85626 180.63726 502.62189 15.309637 2.3328474 424.7101 Loop time of 1.938e-06 on 1 procs for 0 steps with 688 atoms 258.0% 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 | | 1.938e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5195.00 ave 5195 max 5195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57243.0 ave 57243 max 57243 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114486.0 ave 114486 max 114486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114486 Ave neighs/atom = 166.40407 Neighbor list builds = 0 Dangerous builds = 0 688 -2931.61997183409 eV 2.33284740772873 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01