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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -57.589025 0.0000000) to (40.721590 57.589025 5.7021631) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3877004 5.0813845 5.7021631 Created 811 atoms using lattice units in orthogonal box = (0.0000000 -57.589025 0.0000000) to (40.721590 57.589025 5.7021631) create_atoms CPU = 0.007 seconds 811 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3877004 5.0813845 5.7021631 Created 819 atoms using lattice units in orthogonal box = (0.0000000 -57.589025 0.0000000) to (40.721590 57.589025 5.7021631) create_atoms CPU = 0.005 seconds 819 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 10 27 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1628 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_019873715786_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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.557 | 5.557 | 5.557 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5326.2935 0 -5326.2935 4925.4102 74 0 -5458.0577 0 -5458.0577 2529.3854 Loop time of 4.3174 on 1 procs for 74 steps with 1628 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5326.29347420249 -5458.05256664215 -5458.05766582539 Force two-norm initial, final = 42.597469 0.17906577 Force max component initial, final = 6.7577380 0.024222592 Final line search alpha, max atom move = 1.0000000 0.024222592 Iterations, force evaluations = 74 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2187 | 4.2187 | 4.2187 | 0.0 | 97.71 Neigh | 0.040553 | 0.040553 | 0.040553 | 0.0 | 0.94 Comm | 0.031423 | 0.031423 | 0.031423 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02669 | | | 0.62 Nlocal: 1628.00 ave 1628 max 1628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9399.00 ave 9399 max 9399 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: 281586.0 ave 281586 max 281586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281586 Ave neighs/atom = 172.96437 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.552 | 5.552 | 5.552 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -5458.0577 0 -5458.0577 2529.3854 26744.475 77 0 -5458.1355 0 -5458.1355 -2.7531529 26825.865 Loop time of 0.197523 on 1 procs for 3 steps with 1628 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 = -5458.05766582538 -5458.13111991271 -5458.13549739366 Force two-norm initial, final = 75.070414 0.89933166 Force max component initial, final = 53.218495 0.75547829 Final line search alpha, max atom move = 8.8457349e-05 6.6827606e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19197 | 0.19197 | 0.19197 | 0.0 | 97.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013838 | 0.0013838 | 0.0013838 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004167 | | | 2.11 Nlocal: 1628.00 ave 1628 max 1628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9068.00 ave 9068 max 9068 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: 283236.0 ave 283236 max 283236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283236 Ave neighs/atom = 173.97789 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.690 | 5.690 | 5.690 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5458.1355 0 -5458.1355 -2.7531529 Loop time of 6.455e-06 on 1 procs for 0 steps with 1628 atoms 185.9% 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 | | 6.455e-06 | | |100.00 Nlocal: 1628.00 ave 1628 max 1628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9068.00 ave 9068 max 9068 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: 283044.0 ave 283044 max 283044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283044 Ave neighs/atom = 173.85995 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.690 | 5.690 | 5.690 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 -5458.1355 -5458.1355 40.71246 115.42035 5.7087889 -2.7531529 -2.7531529 14.583341 22.330619 -45.173419 2.6712959 1119.1837 Loop time of 6.866e-06 on 1 procs for 0 steps with 1628 atoms 305.9% 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 | | 6.866e-06 | | |100.00 Nlocal: 1628.00 ave 1628 max 1628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9068.00 ave 9068 max 9068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 141522.0 ave 141522 max 141522 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 283044.0 ave 283044 max 283044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283044 Ave neighs/atom = 173.85995 Neighbor list builds = 0 Dangerous builds = 0 1628 -5458.13549739366 eV 2.67129592836171 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05