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 = 3.5273294 3.5273294 3.5273294 Created orthogonal box = (0.0000000 -45.171857 0.0000000) to (31.941326 45.171857 4.9883971) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4533972 6.0596393 4.9883971 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -45.171857 0.0000000) to (31.941326 45.171857 4.9883971) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4533972 6.0596393 4.9883971 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -45.171857 0.0000000) to (31.941326 45.171857 4.9883971) create_atoms CPU = 0.002 seconds 660 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 7 18 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 10.13295 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_758825945924_004#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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 7 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 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) = 6.727 | 6.727 | 6.727 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5097.1586 0 -5097.1586 43253.737 65 0 -5443.0019 0 -5443.0019 -5356.3846 Loop time of 2.56526 on 1 procs for 65 steps with 1304 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5097.15861538956 -5442.99675851644 -5443.00185776758 Force two-norm initial, final = 481.79895 0.33042210 Force max component initial, final = 117.14690 0.040471769 Final line search alpha, max atom move = 1.0000000 0.040471769 Iterations, force evaluations = 65 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5107 | 2.5107 | 2.5107 | 0.0 | 97.87 Neigh | 0.026103 | 0.026103 | 0.026103 | 0.0 | 1.02 Comm | 0.017295 | 0.017295 | 0.017295 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01113 | | | 0.43 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12340.0 ave 12340 max 12340 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: 497320.0 ave 497320 max 497320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 497320 Ave neighs/atom = 381.38037 Neighbor list builds = 1 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 7 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.726 | 6.726 | 6.726 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -5443.0019 0 -5443.0019 -5356.3846 14395.008 77 0 -5444.8763 0 -5444.8763 16.059881 14350.743 Loop time of 0.305186 on 1 procs for 12 steps with 1304 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5443.00185776761 -5444.87619513429 -5444.87629770101 Force two-norm initial, final = 291.70623 1.1746676 Force max component initial, final = 240.64430 0.52399285 Final line search alpha, max atom move = 0.00075863794 0.00039752085 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29758 | 0.29758 | 0.29758 | 0.0 | 97.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014157 | 0.0014157 | 0.0014157 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006193 | | | 2.03 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12340.0 ave 12340 max 12340 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: 498560.0 ave 498560 max 498560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498560 Ave neighs/atom = 382.33129 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 7 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 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) = 6.864 | 6.864 | 6.864 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5444.8763 0 -5444.8763 16.059881 Loop time of 2.11e-06 on 1 procs for 0 steps with 1304 atoms 189.6% 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 | | 2.11e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12362.0 ave 12362 max 12362 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: 498952.0 ave 498952 max 498952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498952 Ave neighs/atom = 382.63190 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 = 10.13295 ghost atom cutoff = 10.13295 binsize = 5.066475, bins = 7 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.13295 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) = 6.864 | 6.864 | 6.864 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 -5444.8763 -5444.8763 31.59506 91.001279 4.9912315 16.059881 16.059881 16.285406 58.926531 -27.032294 2.2909861 1008.6102 Loop time of 2.283e-06 on 1 procs for 0 steps with 1304 atoms 262.8% 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 | | 2.283e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12362.0 ave 12362 max 12362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 249476.0 ave 249476 max 249476 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 498952.0 ave 498952 max 498952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498952 Ave neighs/atom = 382.63190 Neighbor list builds = 0 Dangerous builds = 0 1304 -5444.87629770101 eV 2.29098614613111 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03