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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -52.686751 0.0000000) to (43.015645 52.686751 8.7201838) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3032987 5.0518128 5.8134559 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -52.686751 0.0000000) to (43.015645 52.686751 8.7201838) create_atoms CPU = 0.002 seconds 1759 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3032987 5.0518128 5.8134559 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -52.686751 0.0000000) to (43.015645 52.686751 8.7201838) create_atoms CPU = 0.002 seconds 1759 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 28 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, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 62 atoms, new total = 3456 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_803527979660_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.404 | 7.404 | 7.404 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15012.643 0 -15012.643 -9301.4695 127 0 -15136.066 0 -15136.066 -11867.848 Loop time of 6.74837 on 1 procs for 127 steps with 3456 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15012.6425627874 -15136.0520112763 -15136.0661353673 Force two-norm initial, final = 48.201113 0.58967248 Force max component initial, final = 4.7129528 0.085763436 Final line search alpha, max atom move = 1.0000000 0.085763436 Iterations, force evaluations = 127 240 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5856 | 6.5856 | 6.5856 | 0.0 | 97.59 Neigh | 0.10504 | 0.10504 | 0.10504 | 0.0 | 1.56 Comm | 0.024408 | 0.024408 | 0.024408 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03333 | | | 0.49 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11382.0 ave 11382 max 11382 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: 603604.0 ave 603604 max 603604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603604 Ave neighs/atom = 174.65394 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 127 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.406 | 7.406 | 7.406 Mbytes Step Temp E_pair E_mol TotEng Press Volume 127 0 -15136.066 0 -15136.066 -11867.848 39526.057 132 0 -15137.14 0 -15137.14 -206.2351 39275.847 Loop time of 0.21304 on 1 procs for 5 steps with 3456 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 = -15136.0661353673 -15137.1287444624 -15137.139529643 Force two-norm initial, final = 452.31771 1.2696059 Force max component initial, final = 345.05036 0.47490730 Final line search alpha, max atom move = 4.0707651e-05 1.9332361e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20874 | 0.20874 | 0.20874 | 0.0 | 97.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063044 | 0.00063044 | 0.00063044 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003675 | | | 1.72 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11545.0 ave 11545 max 11545 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: 603566.0 ave 603566 max 603566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603566 Ave neighs/atom = 174.64294 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.543 | 7.543 | 7.543 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15137.14 0 -15137.14 -206.2351 Loop time of 2.115e-06 on 1 procs for 0 steps with 3456 atoms 141.8% 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 | | 2.115e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11601.0 ave 11601 max 11601 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: 603982.0 ave 603982 max 603982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603982 Ave neighs/atom = 174.76331 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.543 | 7.543 | 7.543 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 -15137.14 -15137.14 42.828132 105.3735 8.7029205 -206.2351 -206.2351 19.288406 -649.08225 11.088544 2.3047838 1533.6241 Loop time of 2.31e-06 on 1 procs for 0 steps with 3456 atoms 216.5% 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 | | 2.31e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11601.0 ave 11601 max 11601 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 301991.0 ave 301991 max 301991 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 603982.0 ave 603982 max 603982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603982 Ave neighs/atom = 174.76331 Neighbor list builds = 0 Dangerous builds = 0 3456 -15137.139529643 eV 2.30478383110462 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07