LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.52733 3.52733 3.52733 Created orthogonal box = (0 -42.6244 0) to (52.1997 42.6244 8.64016) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.00545 5.25463 5.7601 Created 1758 atoms create_atoms CPU = 0.00208616 secs 1758 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.00545 5.25463 5.7601 Created 1758 atoms create_atoms CPU = 0.00183797 secs 1758 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 = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 11 17 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 10.1329 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 84 atoms, new total = 3432 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 11 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.1329 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) = 14.18 | 14.18 | 14.18 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14152.561 0 -14152.561 -3112.1072 83 0 -14310.009 0 -14310.009 -30190.68 Loop time of 11.0414 on 1 procs for 83 steps with 3432 atoms 59.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14152.5609529 -14309.9967802 -14310.0092753 Force two-norm initial, final = 41.6773 0.485808 Force max component initial, final = 4.27086 0.0318679 Final line search alpha, max atom move = 1 0.0318679 Iterations, force evaluations = 83 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.901 | 10.901 | 10.901 | 0.0 | 98.73 Neigh | 0.081483 | 0.081483 | 0.081483 | 0.0 | 0.74 Comm | 0.040527 | 0.040527 | 0.040527 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01874 | | | 0.17 Nlocal: 3432 ave 3432 max 3432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16342 ave 16342 max 16342 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: 1.29874e+06 ave 1.29874e+06 max 1.29874e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1298736 Ave neighs/atom = 378.42 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 14.18 | 14.18 | 14.18 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -14310.009 0 -14310.009 -30190.68 38448.385 96 0 -14316.86 0 -14316.86 -2724.9605 37853.147 Loop time of 1.94379 on 1 procs for 13 steps with 3432 atoms 33.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14310.0092753 -14316.8592577 -14316.8598264 Force two-norm initial, final = 1117.35 1.17778 Force max component initial, final = 970.454 0.136283 Final line search alpha, max atom move = 9.6956e-05 1.32135e-05 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.933 | 1.933 | 1.933 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002368 | 0.002368 | 0.002368 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00841 | | | 0.43 Nlocal: 3432 ave 3432 max 3432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16325 ave 16325 max 16325 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: 1.29882e+06 ave 1.29882e+06 max 1.29882e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1298820 Ave neighs/atom = 378.444 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 = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 11 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.1329 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) = 13.69 | 13.69 | 13.69 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14316.86 0 -14316.86 -2724.9605 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3432 atoms 314.6% 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 | | 9.537e-07 | | |100.00 Nlocal: 3432 ave 3432 max 3432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16498 ave 16498 max 16498 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: 1.30652e+06 ave 1.30652e+06 max 1.30652e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1306524 Ave neighs/atom = 380.689 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) = 13.69 | 13.69 | 13.69 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 -14316.86 -14316.86 51.58749 85.248821 8.6073449 -2724.9605 -2724.9605 -5.3516637 -8163.7835 -5.7464391 2.2884741 1724.938 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3432 atoms 157.3% 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 | | 1.907e-06 | | |100.00 Nlocal: 3432 ave 3432 max 3432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16498 ave 16498 max 16498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 653262 ave 653262 max 653262 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.30652e+06 ave 1.30652e+06 max 1.30652e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1306524 Ave neighs/atom = 380.689 Neighbor list builds = 0 Dangerous builds = 0 3432 -14316.8598263635 eV 2.28847406759142 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14