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 = 4.2107185 4.2107185 4.2107185 Created orthogonal box = (0.0000000 -71.952790 0.0000000) to (35.976395 71.952790 4.2107185) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4211006 5.4211006 4.2107185 Created 584 atoms using lattice units in orthogonal box = (0.0000000 -71.952790 0.0000000) to (35.976395 71.952790 4.2107185) create_atoms CPU = 0.002 seconds 584 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4211006 5.4211006 4.2107185 Created 586 atoms using lattice units in orthogonal box = (0.0000000 -71.952790 0.0000000) to (35.976395 71.952790 4.2107185) create_atoms CPU = 0.002 seconds 586 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 8 32 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1170 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_137572817842_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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.460 | 5.460 | 5.460 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4760.4068 0 -4760.4068 -101442.28 22 0 -16280.049 0 -16280.049 -189811.72 Loop time of 4.19638 on 1 procs for 22 steps with 1170 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -4760.40675590062 -16280.0487826376 -16280.0487826376 Force two-norm initial, final = 1894.8785 6218.0902 Force max component initial, final = 722.76040 3070.5346 Final line search alpha, max atom move = 2.5151199e-15 7.7227628e-12 Iterations, force evaluations = 22 170 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1366 | 4.1366 | 4.1366 | 0.0 | 98.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.039241 | 0.039241 | 0.039241 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0205 | | | 0.49 Nlocal: 1170.00 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9688.00 ave 9688 max 9688 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: 205364.0 ave 205364 max 205364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205364 Ave neighs/atom = 175.52479 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.460 | 5.460 | 5.460 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -16280.049 0 -16280.049 -189811.72 21799.749 1022 0 -78760.399 0 -78760.399 161510.17 8495.0118 Loop time of 50.5875 on 1 procs for 1000 steps with 1170 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -16280.0487826352 -78599.2929315502 -78760.3990964601 Force two-norm initial, final = 8033.6262 13658.988 Force max component initial, final = 4008.6150 1982.4819 Final line search alpha, max atom move = 4.6322189e-07 0.00091832901 Iterations, force evaluations = 1000 1000 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 44.971 | 44.971 | 44.971 | 0.0 | 88.90 Neigh | 4.4277 | 4.4277 | 4.4277 | 0.0 | 8.75 Comm | 0.32428 | 0.32428 | 0.32428 | 0.0 | 0.64 Output | 0.00013411 | 0.00013411 | 0.00013411 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.8645 | | | 1.71 Nlocal: 1170.00 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13503.0 ave 13503 max 13503 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: 476296.0 ave 476296 max 476296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 476296 Ave neighs/atom = 407.09060 Neighbor list builds = 104 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 15 11 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 6.406 | 6.406 | 6.406 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -78760.399 0 -78760.399 161510.17 Loop time of 6.626e-06 on 1 procs for 0 steps with 1170 atoms 196.2% 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 | | 6.626e-06 | | |100.00 Nlocal: 1170.00 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13503.0 ave 13503 max 13503 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: 475196.0 ave 475196 max 475196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 475196 Ave neighs/atom = 406.15043 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 15 11 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 6.406 | 6.406 | 6.406 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 -78760.399 -78760.399 63.475069 45.094769 2.9678001 161510.17 161510.17 617316.03 -3221.0393 -129564.49 0.0046588302 873.43541 Loop time of 6.745e-06 on 1 procs for 0 steps with 1170 atoms 311.3% 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 | | 6.745e-06 | | |100.00 Nlocal: 1170.00 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13503.0 ave 13503 max 13503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 237598.0 ave 237598 max 237598 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 475196.0 ave 475196 max 475196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 475196 Ave neighs/atom = 406.15043 Neighbor list builds = 0 Dangerous builds = 0 1170 -78648.0215558605 eV 0.00465883019932131 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:55