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 -42.728902 0.0000000) to (34.888003 42.728902 8.6325418) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9840004 4.9414377 5.7550279 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -42.728902 0.0000000) to (34.888003 42.728902 8.6325418) create_atoms CPU = 0.004 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9840004 4.9414377 5.7550279 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -42.728902 0.0000000) to (34.888003 42.728902 8.6325418) create_atoms CPU = 0.004 seconds 1184 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 = 12 28 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 24 atoms, new total = 2336 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 = 12 28 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) = 5.538 | 5.538 | 5.538 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9577.7004 0 -9577.7004 94022.712 78 0 -10367.704 0 -10367.704 6666.5538 Loop time of 3.18506 on 1 procs for 78 steps with 2336 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9577.70041613235 -10367.6938962824 -10367.7040749649 Force two-norm initial, final = 1235.6440 0.42906217 Force max component initial, final = 206.01451 0.047247332 Final line search alpha, max atom move = 1.0000000 0.047247332 Iterations, force evaluations = 78 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0604 | 3.0604 | 3.0604 | 0.0 | 96.09 Neigh | 0.06595 | 0.06595 | 0.06595 | 0.0 | 2.07 Comm | 0.023836 | 0.023836 | 0.023836 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03487 | | | 1.09 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6442.00 ave 6442 max 6442 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: 200096.0 ave 200096 max 200096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200096 Ave neighs/atom = 85.657534 Neighbor list builds = 2 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 = 12 28 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 : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.536 | 5.536 | 5.536 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -10367.704 0 -10367.704 6666.5538 25737.51 85 0 -10368.398 0 -10368.398 45.050466 25822.449 Loop time of 0.212682 on 1 procs for 7 steps with 2336 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10367.7040749648 -10368.3983322963 -10368.3984543352 Force two-norm initial, final = 260.29491 1.4876206 Force max component initial, final = 255.91727 0.96775246 Final line search alpha, max atom move = 0.00040880016 0.00039561736 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2042 | 0.2042 | 0.2042 | 0.0 | 96.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015321 | 0.0015321 | 0.0015321 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006951 | | | 3.27 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6488.00 ave 6488 max 6488 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: 199824.0 ave 199824 max 199824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199824 Ave neighs/atom = 85.541096 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 = 12 28 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) = 5.674 | 5.674 | 5.674 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10368.398 0 -10368.398 45.050466 Loop time of 6.776e-06 on 1 procs for 0 steps with 2336 atoms 191.9% 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 | | 6.776e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6503.00 ave 6503 max 6503 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: 199696.0 ave 199696 max 199696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199696 Ave neighs/atom = 85.486301 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 = 12 28 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) = 5.674 | 5.674 | 5.674 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 -10368.398 -10368.398 34.831155 85.964786 8.6240043 45.050466 45.050466 37.52296 37.642774 59.985665 2.2635074 1365.8901 Loop time of 7.106e-06 on 1 procs for 0 steps with 2336 atoms 281.5% 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 | | 7.106e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6503.00 ave 6503 max 6503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 99848.0 ave 99848 max 99848 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 199696.0 ave 199696 max 199696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199696 Ave neighs/atom = 85.486301 Neighbor list builds = 0 Dangerous builds = 0 2336 -10368.3984543352 eV 2.26350742788413 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04