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 = 4.0452705 4.0452705 4.0452705 Created orthogonal box = (0.0000000 -63.704983 0.0000000) to (39.011176 63.704983 9.9088485) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2921251 6.1649984 6.6058990 Created 1486 atoms using lattice units in orthogonal box = (0.0000000 -63.704983 0.0000000) to (39.011176 63.704983 9.9088485) create_atoms CPU = 0.002 seconds 1486 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2921251 6.1649984 6.6058990 Created 1492 atoms using lattice units in orthogonal box = (0.0000000 -63.704983 0.0000000) to (39.011176 63.704983 9.9088485) create_atoms CPU = 0.002 seconds 1492 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 27 3 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2976 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_658278549784_005#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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 7.408 | 7.408 | 7.408 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9341.1322 0 -9341.1322 42613.187 79 0 -10128.404 0 -10128.404 3765.0039 Loop time of 4.80076 on 1 procs for 79 steps with 2976 atoms 96.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9341.1321593572 -10128.3945174716 -10128.4039198866 Force two-norm initial, final = 877.02096 0.21645570 Force max component initial, final = 152.19889 0.033596674 Final line search alpha, max atom move = 1.0000000 0.033596674 Iterations, force evaluations = 79 135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6362 | 4.6362 | 4.6362 | 0.0 | 96.57 Neigh | 0.1165 | 0.1165 | 0.1165 | 0.0 | 2.43 Comm | 0.021804 | 0.021804 | 0.021804 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02629 | | | 0.55 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11834.0 ave 11834 max 11834 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: 647284.0 ave 647284 max 647284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 647284 Ave neighs/atom = 217.50134 Neighbor list builds = 3 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.408 | 7.408 | 7.408 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -10128.404 0 -10128.404 3765.0039 49251.065 86 0 -10129.017 0 -10129.017 -6.5768038 49480.219 Loop time of 0.300343 on 1 procs for 7 steps with 2976 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10128.4039198865 -10129.0127920926 -10129.016705926 Force two-norm initial, final = 231.40878 0.48942693 Force max component initial, final = 209.09813 0.32658949 Final line search alpha, max atom move = 0.00010266707 3.3529987e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29342 | 0.29342 | 0.29342 | 0.0 | 97.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00096024 | 0.00096024 | 0.00096024 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005962 | | | 1.99 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11858.0 ave 11858 max 11858 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: 656292.0 ave 656292 max 656292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 656292 Ave neighs/atom = 220.52823 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 7.546 | 7.546 | 7.546 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10129.017 0 -10129.017 -6.5768038 Loop time of 2.306e-06 on 1 procs for 0 steps with 2976 atoms 173.5% 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 | | 2.306e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11858.0 ave 11858 max 11858 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: 651500.0 ave 651500 max 651500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 651500 Ave neighs/atom = 218.91801 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 7.546 | 7.546 | 7.546 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 -10129.017 -10129.017 38.996602 128.24449 9.8938684 -6.5768038 -6.5768038 -10.571063 -6.80254 -2.3568079 2.5346315 1170.2489 Loop time of 3.4e-06 on 1 procs for 0 steps with 2976 atoms 235.3% 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 | | 3.4e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11858.0 ave 11858 max 11858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 325750.0 ave 325750 max 325750 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 651500.0 ave 651500 max 651500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 651500 Ave neighs/atom = 218.91801 Neighbor list builds = 0 Dangerous builds = 0 2976 -10129.016705926 eV 2.53463154475229 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05