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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -49.555184 0.0000000) to (12.387817 49.555184 3.9173716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9551267 4.9551267 3.9173716 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -49.555184 0.0000000) to (12.387817 49.555184 3.9173716) create_atoms CPU = 0.001 seconds 162 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9551267 4.9551267 3.9173716 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -49.555184 0.0000000) to (12.387817 49.555184 3.9173716) create_atoms CPU = 0.001 seconds 162 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 319 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_070797404269_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.433 | 4.433 | 4.433 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1795.9104 0 -1795.9104 31081.447 44 0 -1831.7116 0 -1831.7116 6475.9683 Loop time of 1.096 on 1 procs for 44 steps with 319 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1795.91040613006 -1831.71046053811 -1831.71164101873 Force two-norm initial, final = 83.392264 0.14116802 Force max component initial, final = 23.243445 0.048326835 Final line search alpha, max atom move = 1.0000000 0.048326835 Iterations, force evaluations = 44 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0862 | 1.0862 | 1.0862 | 0.0 | 99.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.005081 | 0.005081 | 0.005081 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004731 | | | 0.43 Nlocal: 319.000 ave 319 max 319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2641.00 ave 2641 max 2641 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: 24754.0 ave 24754 max 24754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24754 Ave neighs/atom = 77.598746 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.433 | 4.433 | 4.433 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -1831.7116 0 -1831.7116 6475.9683 4809.5964 46 0 -1831.7266 0 -1831.7266 2396.7038 4820.4798 Loop time of 0.0554667 on 1 procs for 2 steps with 319 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1831.71164101873 -1831.72638782964 -1831.72659110967 Force two-norm initial, final = 18.871397 0.55690391 Force max component initial, final = 13.352398 0.47453524 Final line search alpha, max atom move = 0.00054571096 0.00025895908 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.054464 | 0.054464 | 0.054464 | 0.0 | 98.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022899 | 0.00022899 | 0.00022899 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007738 | | | 1.40 Nlocal: 319.000 ave 319 max 319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2637.00 ave 2637 max 2637 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: 24660.0 ave 24660 max 24660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24660 Ave neighs/atom = 77.304075 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.571 | 4.571 | 4.571 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1831.7266 0 -1831.7266 2396.7038 Loop time of 6.555e-06 on 1 procs for 0 steps with 319 atoms 0.0% 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 | | 6.555e-06 | | |100.00 Nlocal: 319.000 ave 319 max 319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2637.00 ave 2637 max 2637 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: 24656.0 ave 24656 max 24656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24656 Ave neighs/atom = 77.291536 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.571 | 4.571 | 4.571 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 -1831.7266 -1831.7266 12.401358 99.110368 3.921949 2396.7038 2396.7038 -157.89305 7266.3151 81.689376 2.4630613 214.80647 Loop time of 6.846e-06 on 1 procs for 0 steps with 319 atoms 204.5% 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: 319.000 ave 319 max 319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2637.00 ave 2637 max 2637 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12328.0 ave 12328 max 12328 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24656.0 ave 24656 max 24656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24656 Ave neighs/atom = 77.291536 Neighbor list builds = 0 Dangerous builds = 0 319 -1831.72659110967 eV 2.46306130679524 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01