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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -43.623885 0.0000000) to (21.809917 43.623885 4.0500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2644628 5.2644628 4.0500000 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -43.623885 0.0000000) to (21.809917 43.623885 4.0500000) create_atoms CPU = 0.002 seconds 233 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2644628 5.2644628 4.0500000 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -43.623885 0.0000000) to (21.809917 43.623885 4.0500000) create_atoms CPU = 0.001 seconds 233 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 25 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 459 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_971738391444_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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1522.1315 0 -1522.1315 778.7829 40 0 -1530.678 0 -1530.678 -5978.0998 Loop time of 4.16024 on 1 procs for 40 steps with 459 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 = -1522.13146136085 -1530.67696447022 -1530.67795891787 Force two-norm initial, final = 9.6802731 0.21782849 Force max component initial, final = 2.5748749 0.072863414 Final line search alpha, max atom move = 0.78571693 0.057250018 Iterations, force evaluations = 40 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1415 | 4.1415 | 4.1415 | 0.0 | 99.55 Neigh | 0.0061587 | 0.0061587 | 0.0061587 | 0.0 | 0.15 Comm | 0.0067753 | 0.0067753 | 0.0067753 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005781 | | | 0.14 Nlocal: 459.000 ave 459 max 459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3486.00 ave 3486 max 3486 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: 36234.0 ave 36234 max 36234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36234 Ave neighs/atom = 78.941176 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -1530.678 0 -1530.678 -5978.0998 7706.61 44 0 -1530.735 0 -1530.735 -2064.6274 7666.3539 Loop time of 0.446465 on 1 procs for 4 steps with 459 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 = -1530.67795891788 -1530.73492387365 -1530.7349975852 Force two-norm initial, final = 30.736142 0.61043544 Force max component initial, final = 21.957622 0.37871464 Final line search alpha, max atom move = 0.0077687307 0.0029421320 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4437 | 0.4437 | 0.4437 | 0.0 | 99.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059294 | 0.00059294 | 0.00059294 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002175 | | | 0.49 Nlocal: 459.000 ave 459 max 459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3504.00 ave 3504 max 3504 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: 36278.0 ave 36278 max 36278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36278 Ave neighs/atom = 79.037037 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1530.735 0 -1530.735 -2064.6274 Loop time of 6.445e-06 on 1 procs for 0 steps with 459 atoms 170.7% 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 | | 6.445e-06 | | |100.00 Nlocal: 459.000 ave 459 max 459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3508.00 ave 3508 max 3508 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: 36868.0 ave 36868 max 36868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36868 Ave neighs/atom = 80.322440 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 ghost atom cutoff = 7 binsize = 3.5, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.600 | 4.600 | 4.600 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 -1530.735 -1530.735 21.749893 87.24777 4.0399631 -2064.6274 -2064.6274 77.387653 -6192.3193 -78.950697 1.8894957 345.48759 Loop time of 6.966e-06 on 1 procs for 0 steps with 459 atoms 315.8% 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 | | 6.966e-06 | | |100.00 Nlocal: 459.000 ave 459 max 459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3508.00 ave 3508 max 3508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18434.0 ave 18434 max 18434 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 36868.0 ave 36868 max 36868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36868 Ave neighs/atom = 80.322440 Neighbor list builds = 0 Dangerous builds = 0 459 -1530.7349975852 eV 1.88949566214253 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05