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 = 3.6284422 3.6284422 3.6284422 Created orthogonal box = (0.0000000 -37.707877 0.0000000) to (26.663496 37.707877 5.1313921) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9252213 4.8880582 5.1313921 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -37.707877 0.0000000) to (26.663496 37.707877 5.1313921) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9252213 4.8880582 5.1313921 Created 440 atoms using lattice units in orthogonal box = (0.0000000 -37.707877 0.0000000) to (26.663496 37.707877 5.1313921) create_atoms CPU = 0.001 seconds 440 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 8 20 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 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 872 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_681088298208_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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 8 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 4.968 | 4.968 | 4.968 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1222.3429 0 -1222.3429 514411.88 461 0 -3677.0881 0 -3677.0881 -1780.5004 Loop time of 6.34218 on 1 procs for 461 steps with 872 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1222.34286596926 -3677.08446732653 -3677.08809015541 Force two-norm initial, final = 3461.2678 0.22552414 Force max component initial, final = 448.49964 0.057475981 Final line search alpha, max atom move = 1.0000000 0.057475981 Iterations, force evaluations = 461 873 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1571 | 6.1571 | 6.1571 | 0.0 | 97.08 Neigh | 0.086367 | 0.086367 | 0.086367 | 0.0 | 1.36 Comm | 0.053962 | 0.053962 | 0.053962 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04471 | | | 0.70 Nlocal: 872.000 ave 872 max 872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5573.00 ave 5573 max 5573 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: 134344.0 ave 134344 max 134344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134344 Ave neighs/atom = 154.06422 Neighbor list builds = 9 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 8 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 461 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.971 | 4.971 | 4.971 Mbytes Step Temp E_pair E_mol TotEng Press Volume 461 0 -3677.0881 0 -3677.0881 -1780.5004 10318.448 482 0 -3680.9562 0 -3680.9562 -8.14082 10291.208 Loop time of 0.181999 on 1 procs for 21 steps with 872 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 = -3677.08809015541 -3680.95380711881 -3680.95621267692 Force two-norm initial, final = 279.06154 2.0778734 Force max component initial, final = 216.41505 0.50802842 Final line search alpha, max atom move = 0.00018368949 9.3319483e-05 Iterations, force evaluations = 21 22 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1661 | 0.1661 | 0.1661 | 0.0 | 91.26 Neigh | 0.0085529 | 0.0085529 | 0.0085529 | 0.0 | 4.70 Comm | 0.0013251 | 0.0013251 | 0.0013251 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006024 | | | 3.31 Nlocal: 872.000 ave 872 max 872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5632.00 ave 5632 max 5632 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: 134436.0 ave 134436 max 134436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134436 Ave neighs/atom = 154.16972 Neighbor list builds = 1 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 5.110 | 5.110 | 5.110 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3680.9562 0 -3680.9562 -8.14082 Loop time of 1.967e-06 on 1 procs for 0 steps with 872 atoms 203.4% 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 | | 1.967e-06 | | |100.00 Nlocal: 872.000 ave 872 max 872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5664.00 ave 5664 max 5664 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: 136104.0 ave 136104 max 136104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136104 Ave neighs/atom = 156.08257 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 5.110 | 5.110 | 5.110 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 -3680.9562 -3680.9562 26.651118 76.78319 5.0290361 -8.14082 -8.14082 -30.280372 -71.656342 77.514255 2.3176252 2581.2671 Loop time of 2.171e-06 on 1 procs for 0 steps with 872 atoms 230.3% 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 | | 2.171e-06 | | |100.00 Nlocal: 872.000 ave 872 max 872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5664.00 ave 5664 max 5664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68052.0 ave 68052 max 68052 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 136104.0 ave 136104 max 136104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136104 Ave neighs/atom = 156.08257 Neighbor list builds = 0 Dangerous builds = 0 872 -3680.95621267692 eV 2.317625168934 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06