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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -39.354797 0.0000000) to (19.279834 39.354797 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1412891 4.7225756 5.7481360 Created 600 atoms using lattice units in orthogonal box = (0.0000000 -39.354797 0.0000000) to (19.279834 39.354797 8.6222040) create_atoms CPU = 0.001 seconds 600 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1412891 4.7225756 5.7481360 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -39.354797 0.0000000) to (19.279834 39.354797 8.6222040) create_atoms CPU = 0.001 seconds 612 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1200 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_101214310689_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.926 | 5.926 | 5.926 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5274.7124 0 -5274.7124 6123.4398 15 0 -5310.4547 0 -5310.4547 16564.534 Loop time of 0.5077 on 1 procs for 15 steps with 1200 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 = -5274.71237923729 -5310.45148966204 -5310.45468254814 Force two-norm initial, final = 30.894561 0.19227171 Force max component initial, final = 4.4395365 0.0092605649 Final line search alpha, max atom move = 1.0000000 0.0092605649 Iterations, force evaluations = 15 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50278 | 0.50278 | 0.50278 | 0.0 | 99.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026448 | 0.0026448 | 0.0026448 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002279 | | | 0.45 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7521.00 ave 7521 max 7521 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: 298368.0 ave 298368 max 298368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 298368 Ave neighs/atom = 248.64000 Neighbor list builds = 0 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.925 | 5.925 | 5.925 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -5310.4547 0 -5310.4547 16564.534 13084.263 28 0 -5311.8836 0 -5311.8836 33.658705 13205.689 Loop time of 0.258279 on 1 procs for 13 steps with 1200 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 = -5310.45468254813 -5311.88316176092 -5311.8836451154 Force two-norm initial, final = 277.87290 1.0624959 Force max component initial, final = 255.98114 0.48566779 Final line search alpha, max atom move = 0.00037310233 0.00018120378 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25252 | 0.25252 | 0.25252 | 0.0 | 97.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00093619 | 0.00093619 | 0.00093619 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004824 | | | 1.87 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7377.00 ave 7377 max 7377 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: 295200.0 ave 295200 max 295200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295200 Ave neighs/atom = 246.00000 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 6.063 | 6.063 | 6.063 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5311.8836 0 -5311.8836 33.658705 Loop time of 2.326e-06 on 1 procs for 0 steps with 1200 atoms 215.0% 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 | | 2.326e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7377.00 ave 7377 max 7377 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: 294624.0 ave 294624 max 294624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294624 Ave neighs/atom = 245.52000 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 6.063 | 6.063 | 6.063 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 -5311.8836 -5311.8836 19.246671 79.665187 8.6126509 33.658705 33.658705 58.822155 56.437032 -14.283072 2.2384388 731.52223 Loop time of 2.433e-06 on 1 procs for 0 steps with 1200 atoms 205.5% 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 | | 2.433e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7377.00 ave 7377 max 7377 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 147312.0 ave 147312 max 147312 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 294624.0 ave 294624 max 294624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294624 Ave neighs/atom = 245.52000 Neighbor list builds = 0 Dangerous builds = 0 1200 -5284.82406493049 eV 2.2384387737758 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01