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 = 3.6284422 3.6284422 3.6284422 Created orthogonal box = (0.0000000 -37.002995 0.0000000) to (32.045534 37.002995 6.2846462) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7517624 5.6927684 6.2846462 Created 622 atoms using lattice units in orthogonal box = (0.0000000 -37.002995 0.0000000) to (32.045534 37.002995 6.2846462) create_atoms CPU = 0.001 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7517624 5.6927684 6.2846462 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -37.002995 0.0000000) to (32.045534 37.002995 6.2846462) create_atoms CPU = 0.001 seconds 629 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 9 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 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1249 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_681088298208_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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 5.059 | 5.059 | 5.059 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4092.5549 0 -4092.5549 196771.74 466 0 -5267.9869 0 -5267.9869 -6634.1719 Loop time of 8.82115 on 1 procs for 466 steps with 1249 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4092.55491218224 -5267.98202181991 -5267.98693696647 Force two-norm initial, final = 1826.9872 0.27810629 Force max component initial, final = 749.79253 0.10901923 Final line search alpha, max atom move = 1.0000000 0.10901923 Iterations, force evaluations = 466 874 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.5272 | 8.5272 | 8.5272 | 0.0 | 96.67 Neigh | 0.16206 | 0.16206 | 0.16206 | 0.0 | 1.84 Comm | 0.068145 | 0.068145 | 0.068145 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0637 | | | 0.72 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6292.00 ave 6292 max 6292 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: 193344.0 ave 193344 max 193344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193344 Ave neighs/atom = 154.79904 Neighbor list builds = 12 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 9 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 466 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.061 | 5.061 | 5.061 Mbytes Step Temp E_pair E_mol TotEng Press Volume 466 0 -5267.9869 0 -5267.9869 -6634.1719 14904.425 478 0 -5269.6687 0 -5269.6687 0.62883678 14839.968 Loop time of 0.136182 on 1 procs for 12 steps with 1249 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 = -5267.98693696646 -5269.66749651564 -5269.66868470065 Force two-norm initial, final = 238.45905 1.4391524 Force max component initial, final = 194.69667 0.30850340 Final line search alpha, max atom move = 0.00021518343 6.6384820e-05 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13138 | 0.13138 | 0.13138 | 0.0 | 96.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076248 | 0.00076248 | 0.00076248 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004043 | | | 2.97 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6288.00 ave 6288 max 6288 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: 193328.0 ave 193328 max 193328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193328 Ave neighs/atom = 154.78623 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 5.198 | 5.198 | 5.198 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5269.6687 0 -5269.6687 0.62883678 Loop time of 2.734e-06 on 1 procs for 0 steps with 1249 atoms 146.3% 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 | | 2.734e-06 | | |100.00 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6268.00 ave 6268 max 6268 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: 194344.0 ave 194344 max 194344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194344 Ave neighs/atom = 155.59968 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 9 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 5.198 | 5.198 | 5.198 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 -5269.6687 -5269.6687 31.720073 73.722369 6.3459918 0.62883678 0.62883678 32.968866 -4.9657118 -26.116644 2.2570424 2999.4338 Loop time of 2.459e-06 on 1 procs for 0 steps with 1249 atoms 325.3% 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 | | 2.459e-06 | | |100.00 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6268.00 ave 6268 max 6268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 97172.0 ave 97172 max 97172 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 194344.0 ave 194344 max 194344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194344 Ave neighs/atom = 155.59968 Neighbor list builds = 0 Dangerous builds = 0 1249 -5269.66868470065 eV 2.25704241885695 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09