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 = 3.6150000 3.6150000 3.6150000 Created orthogonal box = (0.0000000 -38.597638 0.0000000) to (27.292651 38.597638 5.1123820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2670029 6.0943639 5.1123820 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.597638 0.0000000) to (27.292651 38.597638 5.1123820) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2670029 6.0943639 5.1123820 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.597638 0.0000000) to (27.292651 38.597638 5.1123820) create_atoms CPU = 0.001 seconds 458 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 7 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 7.995011000293092 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 908 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_128703483589_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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 4.998 | 4.998 | 4.998 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2887.7807 0 -2887.7807 88016.872 90 0 -3199.8257 0 -3199.8257 2147.7799 Loop time of 1.53816 on 1 procs for 90 steps with 908 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 = -2887.78070108376 -3199.82284116382 -3199.82570365637 Force two-norm initial, final = 841.92315 0.17898789 Force max component initial, final = 265.11925 0.032138313 Final line search alpha, max atom move = 1.0000000 0.032138313 Iterations, force evaluations = 90 173 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4871 | 1.4871 | 1.4871 | 0.0 | 96.68 Neigh | 0.031591 | 0.031591 | 0.031591 | 0.0 | 2.05 Comm | 0.011101 | 0.011101 | 0.011101 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00836 | | | 0.54 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6483.00 ave 6483 max 6483 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: 159844.0 ave 159844 max 159844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159844 Ave neighs/atom = 176.03965 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.998 | 4.998 | 4.998 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -3199.8257 0 -3199.8257 2147.7799 10771.092 93 0 -3199.8525 0 -3199.8525 53.940312 10787.402 Loop time of 0.0488323 on 1 procs for 3 steps with 908 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3199.82570365637 -3199.85243576188 -3199.8524703467 Force two-norm initial, final = 30.581795 0.77503856 Force max component initial, final = 28.311625 0.61677167 Final line search alpha, max atom move = 0.0010926635 0.00067392387 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.047426 | 0.047426 | 0.047426 | 0.0 | 97.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002834 | 0.0002834 | 0.0002834 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001123 | | | 2.30 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6467.00 ave 6467 max 6467 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: 159804.0 ave 159804 max 159804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159804 Ave neighs/atom = 175.99559 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 5.136 | 5.136 | 5.136 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3199.8525 0 -3199.8525 53.940312 Loop time of 1.7e-06 on 1 procs for 0 steps with 908 atoms 176.5% 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 | | 1.7e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6431.00 ave 6431 max 6431 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: 159732.0 ave 159732 max 159732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159732 Ave neighs/atom = 175.91630 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 5.136 | 5.136 | 5.136 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 -3199.8525 -3199.8525 27.294331 77.343665 5.1099854 53.940312 53.940312 7.3683303 62.890815 91.561791 2.3525565 665.18688 Loop time of 1.811e-06 on 1 procs for 0 steps with 908 atoms 165.7% 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 | | 1.811e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6431.00 ave 6431 max 6431 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79866.0 ave 79866 max 79866 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 159732.0 ave 159732 max 159732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159732 Ave neighs/atom = 175.91630 Neighbor list builds = 0 Dangerous builds = 0 908 -3199.85228790178 eV 2.35255648840905 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01