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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -54.139447 0.0000000) to (44.204674 54.139447 8.9612251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4498913 5.1914539 5.9741501 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -54.139447 0.0000000) to (44.204674 54.139447 8.9612251) create_atoms CPU = 0.002 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4498913 5.1914539 5.9741501 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -54.139447 0.0000000) to (44.204674 54.139447 8.9612251) create_atoms CPU = 0.002 seconds 1757 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 30 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3506 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_249706810527_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.548 | 6.548 | 6.548 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10951.26 0 -10951.26 155681.8 908 0 -13765.971 0 -13765.971 -55102.76 Loop time of 39.3482 on 1 procs for 908 steps with 3506 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 = -10951.2603801818 -13765.9593036564 -13765.9712546159 Force two-norm initial, final = 3523.1490 0.48299455 Force max component initial, final = 472.60432 0.11049423 Final line search alpha, max atom move = 0.45652819 0.050443732 Iterations, force evaluations = 908 1775 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 38.422 | 38.422 | 38.422 | 0.0 | 97.65 Neigh | 0.52328 | 0.52328 | 0.52328 | 0.0 | 1.33 Comm | 0.16932 | 0.16932 | 0.16932 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.234 | | | 0.59 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10373.0 ave 10373 max 10373 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: 483798.0 ave 483798 max 483798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 483798 Ave neighs/atom = 137.99144 Neighbor list builds = 17 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 908 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.549 | 6.549 | 6.549 Mbytes Step Temp E_pair E_mol TotEng Press Volume 908 0 -13765.971 0 -13765.971 -55102.76 42892.305 954 0 -13835.096 0 -13835.096 1516.6979 41307.188 Loop time of 1.14881 on 1 procs for 46 steps with 3506 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 = -13765.9712546158 -13835.084806323 -13835.0958206825 Force two-norm initial, final = 3061.2503 83.463465 Force max component initial, final = 2281.4506 75.296562 Final line search alpha, max atom move = 1.9972256e-05 0.0015038422 Iterations, force evaluations = 46 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0272 | 1.0272 | 1.0272 | 0.0 | 89.41 Neigh | 0.091203 | 0.091203 | 0.091203 | 0.0 | 7.94 Comm | 0.0044687 | 0.0044687 | 0.0044687 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02596 | | | 2.26 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10384.0 ave 10384 max 10384 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: 498060.0 ave 498060 max 498060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498060 Ave neighs/atom = 142.05933 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 7.067 | 7.067 | 7.067 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13835.096 0 -13835.096 1516.6979 Loop time of 1.813e-06 on 1 procs for 0 steps with 3506 atoms 220.6% 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 | | 1.813e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10317.0 ave 10317 max 10317 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: 498820.0 ave 498820 max 498820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498820 Ave neighs/atom = 142.27610 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 7.067 | 7.067 | 7.067 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 -13835.096 -13835.096 42.877465 104.67406 9.203594 1516.6979 1516.6979 2832.8318 374.50883 1342.7531 2.1988636 7925.1689 Loop time of 2.102e-06 on 1 procs for 0 steps with 3506 atoms 190.3% 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 | | 2.102e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10317.0 ave 10317 max 10317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 249410.0 ave 249410 max 249410 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 498820.0 ave 498820 max 498820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498820 Ave neighs/atom = 142.27610 Neighbor list builds = 0 Dangerous builds = 0 3506 -13835.0958206825 eV 2.19886361974971 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:41