LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.52 3.52 3.52 Created orthogonal box = (0 -42.5358 0) to (52.0912 42.5358 8.6222) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.99505 5.24371 5.74814 Created 1756 atoms create_atoms CPU = 0.000741005 secs 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.99505 5.24371 5.74814 Created 1756 atoms create_atoms CPU = 0.000619888 secs 1756 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 13 21 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 56 atoms, new total = 3456 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 7.876 | 7.876 | 7.876 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15226.062 0 -15226.062 1184.5819 54 0 -15323.014 0 -15323.014 -15138.67 Loop time of 1.48064 on 1 procs for 54 steps with 3456 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 = -15226.0621811 -15323.0009988 -15323.0136244 Force two-norm initial, final = 37.8953 0.355833 Force max component initial, final = 4.31759 0.0215444 Final line search alpha, max atom move = 1 0.0215444 Iterations, force evaluations = 54 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4459 | 1.4459 | 1.4459 | 0.0 | 97.65 Neigh | 0.019589 | 0.019589 | 0.019589 | 0.0 | 1.32 Comm | 0.0077109 | 0.0077109 | 0.0077109 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007444 | | | 0.50 Nlocal: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12426 ave 12426 max 12426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 739648 ave 739648 max 739648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 739648 Ave neighs/atom = 214.019 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.877 | 7.877 | 7.877 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -15323.014 0 -15323.014 -15138.67 38209.21 59 0 -15324.109 0 -15324.109 -3467.1229 37953.612 Loop time of 0.107496 on 1 procs for 5 steps with 3456 atoms 93.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15323.0136244 -15324.1069902 -15324.1092103 Force two-norm initial, final = 454.986 0.544246 Force max component initial, final = 343.62 0.0472765 Final line search alpha, max atom move = 8.36356e-05 3.954e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10501 | 0.10501 | 0.10501 | 0.0 | 97.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053072 | 0.00053072 | 0.00053072 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001953 | | | 1.82 Nlocal: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12521 ave 12521 max 12521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 745560 ave 745560 max 745560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 745560 Ave neighs/atom = 215.729 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 8.016 | 8.016 | 8.016 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15324.109 0 -15324.109 -3467.1229 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3456 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12666 ave 12666 max 12666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 754170 ave 754170 max 754170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 754170 Ave neighs/atom = 218.22 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 8.016 | 8.016 | 8.016 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 -15324.109 -15324.109 51.881303 85.071685 8.5991832 -3467.1229 -3467.1229 -0.050948439 -10399.327 -1.9904046 2.2120836 1570.2472 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3456 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12666 ave 12666 max 12666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 377085 ave 377085 max 377085 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 754170 ave 754170 max 754170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 754170 Ave neighs/atom = 218.22 Neighbor list builds = 0 Dangerous builds = 0 3456 -15246.1887252158 eV 2.21208355839098 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01