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 = 4.0248454 4.0248454 4.0248454 Created orthogonal box = (0.0000000 -71.092944 0.0000000) to (41.045530 71.092944 6.9712367) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3146970 6.3801360 6.9712367 Created 1247 atoms using lattice units in orthogonal box = (0.0000000 -71.092944 0.0000000) to (41.045530 71.092944 6.9712367) create_atoms CPU = 0.008 seconds 1247 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3146970 6.3801360 6.9712367 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -71.092944 0.0000000) to (41.045530 71.092944 6.9712367) create_atoms CPU = 0.007 seconds 1251 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 10 34 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2490 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_149316865608_005#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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.132 | 6.132 | 6.132 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6487.6477 0 -6487.6477 7351.2791 83 0 -6572.4655 0 -6572.4655 2185.5415 Loop time of 6.55271 on 1 procs for 83 steps with 2490 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 = -6487.64765593084 -6572.45940979817 -6572.4655049286 Force two-norm initial, final = 94.421379 0.21859301 Force max component initial, final = 17.545401 0.068948362 Final line search alpha, max atom move = 1.0000000 0.068948362 Iterations, force evaluations = 83 151 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3109 | 6.3109 | 6.3109 | 0.0 | 96.31 Neigh | 0.16126 | 0.16126 | 0.16126 | 0.0 | 2.46 Comm | 0.040772 | 0.040772 | 0.040772 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03978 | | | 0.61 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10566.0 ave 10566 max 10566 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: 348588.0 ave 348588 max 348588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 348588 Ave neighs/atom = 139.99518 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.131 | 6.131 | 6.131 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -6572.4655 0 -6572.4655 2185.5415 40684.801 89 0 -6572.7907 0 -6572.7907 5.830812 40794.985 Loop time of 0.334693 on 1 procs for 6 steps with 2490 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6572.46550492861 -6572.78832160904 -6572.79070992079 Force two-norm initial, final = 131.22779 0.49691584 Force max component initial, final = 126.64124 0.34126819 Final line search alpha, max atom move = 0.00014493079 4.9460267e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32557 | 0.32557 | 0.32557 | 0.0 | 97.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019141 | 0.0019141 | 0.0019141 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007205 | | | 2.15 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10552.0 ave 10552 max 10552 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: 348576.0 ave 348576 max 348576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 348576 Ave neighs/atom = 139.99036 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.270 | 6.270 | 6.270 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6572.7907 0 -6572.7907 5.830812 Loop time of 6.866e-06 on 1 procs for 0 steps with 2490 atoms 174.8% 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 | | 6.866e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10552.0 ave 10552 max 10552 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: 348364.0 ave 348364 max 348364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 348364 Ave neighs/atom = 139.90522 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 6.270 | 6.270 | 6.270 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 -6572.7907 -6572.7907 41.021727 142.96146 6.9562287 5.830812 5.830812 -1.8228916 5.9412629 13.374065 2.584652 1255.3723 Loop time of 6.846e-06 on 1 procs for 0 steps with 2490 atoms 277.5% 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 | | 6.846e-06 | | |100.00 Nlocal: 2490.00 ave 2490 max 2490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10552.0 ave 10552 max 10552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 174182.0 ave 174182 max 174182 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 348364.0 ave 348364 max 348364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 348364 Ave neighs/atom = 139.90522 Neighbor list builds = 0 Dangerous builds = 0 2490 -6496.26239478897 eV 2.58465197188533 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07