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 = 3.5242205 3.5242205 3.5242205 Created orthogonal box = (0.0000000 -36.962336 0.0000000) to (45.269431 36.962336 8.6325418) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7615640 5.3763398 5.7550279 Created 1316 atoms using lattice units in orthogonal box = (0.0000000 -36.962336 0.0000000) to (45.269431 36.962336 8.6325418) create_atoms CPU = 0.008 seconds 1316 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7615640 5.3763398 5.7550279 Created 1322 atoms using lattice units in orthogonal box = (0.0000000 -36.962336 0.0000000) to (45.269431 36.962336 8.6325418) create_atoms CPU = 0.007 seconds 1322 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 15 24 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 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2630 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_769632475533_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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 5.572 | 5.572 | 5.572 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8881.5799 0 -8881.5799 233760.44 103 0 -11667.022 0 -11667.022 17026.01 Loop time of 4.3861 on 1 procs for 103 steps with 2630 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 = -8881.57993613456 -11667.011034067 -11667.0224057194 Force two-norm initial, final = 3538.1961 0.46270127 Force max component initial, final = 484.31708 0.10094577 Final line search alpha, max atom move = 1.0000000 0.10094577 Iterations, force evaluations = 103 173 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1367 | 4.1367 | 4.1367 | 0.0 | 94.31 Neigh | 0.16906 | 0.16906 | 0.16906 | 0.0 | 3.85 Comm | 0.031553 | 0.031553 | 0.031553 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04879 | | | 1.11 Nlocal: 2630.00 ave 2630 max 2630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7174.00 ave 7174 max 7174 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: 225718.0 ave 225718 max 225718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225718 Ave neighs/atom = 85.824335 Neighbor list builds = 4 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.572 | 5.572 | 5.572 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -11667.022 0 -11667.022 17026.01 28889.042 112 0 -11669.226 0 -11669.226 -139.67046 29121.405 Loop time of 0.24975 on 1 procs for 9 steps with 2630 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 = -11667.0224057195 -11669.2234174552 -11669.2263005292 Force two-norm initial, final = 612.85290 4.5236189 Force max component initial, final = 554.88972 2.9158627 Final line search alpha, max atom move = 7.3327488e-05 0.00021381289 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23927 | 0.23927 | 0.23927 | 0.0 | 95.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017488 | 0.0017488 | 0.0017488 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008727 | | | 3.49 Nlocal: 2630.00 ave 2630 max 2630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7195.00 ave 7195 max 7195 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: 225600.0 ave 225600 max 225600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225600 Ave neighs/atom = 85.779468 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 5.709 | 5.709 | 5.709 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11669.226 0 -11669.226 -139.67046 Loop time of 6.325e-06 on 1 procs for 0 steps with 2630 atoms 173.9% 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 | | 6.325e-06 | | |100.00 Nlocal: 2630.00 ave 2630 max 2630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7176.00 ave 7176 max 7176 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: 225166.0 ave 225166 max 225166 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225166 Ave neighs/atom = 85.614449 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 = 6.3171695 ghost atom cutoff = 6.3171695 binsize = 3.1585848, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.3171695 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) = 5.709 | 5.709 | 5.709 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 -11669.226 -11669.226 45.284704 74.541102 8.6271032 -139.67046 -139.67046 -147.18974 -111.50028 -160.32136 2.2706076 1405.6856 Loop time of 7.146e-06 on 1 procs for 0 steps with 2630 atoms 251.9% 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 | | 7.146e-06 | | |100.00 Nlocal: 2630.00 ave 2630 max 2630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7176.00 ave 7176 max 7176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112583.0 ave 112583 max 112583 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 225166.0 ave 225166 max 225166 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225166 Ave neighs/atom = 85.614449 Neighbor list builds = 0 Dangerous builds = 0 2630 -11669.2263005292 eV 2.27060761171028 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05