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 = 3.3901167 3.3901167 3.3901167 Created orthogonal box = (0.0000000 -36.196541 0.0000000) to (25.594820 36.196541 4.7943490) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8374150 5.7152433 4.7943490 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -36.196541 0.0000000) to (25.594820 36.196541 4.7943490) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8374150 5.7152433 4.7943490 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -36.196541 0.0000000) to (25.594820 36.196541 4.7943490) create_atoms CPU = 0.001 seconds 230 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 3 8 1 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 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 452 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_959249795837_003#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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 3 8 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 11.69 | 11.69 | 11.69 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 722608.68 0 722608.68 5.3556981e+08 389 0 -16476.065 0 -16476.065 -395256.97 Loop time of 7.39216 on 1 procs for 389 steps with 452 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 = 722608.680588157 -16476.0499291823 -16476.0645353276 Force two-norm initial, final = 4923819.3 1.8932694 Force max component initial, final = 1740812.9 0.17505548 Final line search alpha, max atom move = 0.15938397 0.027901038 Iterations, force evaluations = 389 719 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.7258 | 6.7258 | 6.7258 | 0.0 | 90.99 Neigh | 0.50512 | 0.50512 | 0.50512 | 0.0 | 6.83 Comm | 0.12378 | 0.12378 | 0.12378 | 0.0 | 1.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03743 | | | 0.51 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17039.0 ave 17039 max 17039 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: 826792.0 ave 826792 max 826792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 826792 Ave neighs/atom = 1829.1858 Neighbor list builds = 15 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 3 8 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 389 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.69 | 11.69 | 11.69 Mbytes Step Temp E_pair E_mol TotEng Press Volume 389 0 -16476.065 0 -16476.065 -395256.97 8883.391 423 0 -16599.359 0 -16599.359 -600.28281 8696.3843 Loop time of 0.480923 on 1 procs for 34 steps with 452 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 = -16476.0645353276 -16599.3536139212 -16599.3589209012 Force two-norm initial, final = 6685.5988 25.393294 Force max component initial, final = 5612.5901 9.7712283 Final line search alpha, max atom move = 3.9390591e-05 0.00038489446 Iterations, force evaluations = 34 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38225 | 0.38225 | 0.38225 | 0.0 | 79.48 Neigh | 0.073976 | 0.073976 | 0.073976 | 0.0 | 15.38 Comm | 0.0058343 | 0.0058343 | 0.0058343 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01886 | | | 3.92 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17245.0 ave 17245 max 17245 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: 849456.0 ave 849456 max 849456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 849456 Ave neighs/atom = 1879.3274 Neighbor list builds = 2 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 3 7 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 11.20 | 11.20 | 11.20 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16599.359 0 -16599.359 -600.28281 Loop time of 1.893e-06 on 1 procs for 0 steps with 452 atoms 211.3% 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 | | 1.893e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17245.0 ave 17245 max 17245 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: 849834.0 ave 849834 max 849834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 849834 Ave neighs/atom = 1880.1637 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.26535, bins = 3 7 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 11.20 | 11.20 | 11.20 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 -16599.359 -16599.359 25.38019 70.256861 4.8770264 -600.28281 -600.28281 1262.0266 -1231.6309 -1831.2442 2.8508983 3196.786 Loop time of 2.447e-06 on 1 procs for 0 steps with 452 atoms 245.2% 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 | | 2.447e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17245.0 ave 17245 max 17245 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 424917.0 ave 424917 max 424917 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 849834.0 ave 849834 max 849834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 849834 Ave neighs/atom = 1880.1637 Neighbor list builds = 0 Dangerous builds = 0 452 -16599.358920901 eV 2.85089827251162 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08