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 = 2.57518 2.57518 2.57518 Created orthogonal box = (0 -41.8443 0) to (14.7933 41.8443 3.64186) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.03454 3.16983 3.64186 Created 530 atoms create_atoms CPU = 0.000260115 secs 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.03454 3.16983 3.64186 Created 530 atoms create_atoms CPU = 0.000149965 secs 530 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 29 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1046 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 5.453 | 5.453 | 5.453 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -202241.22 0 -202241.22 -1396411.1 64 0 -72831038 0 -72831038 -5.1759702e+10 Loop time of 23.0558 on 1 procs for 64 steps with 1046 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 = -202241.222533 -72830989.9811 -72831037.5731 Force two-norm initial, final = 2633.54 20016.2 Force max component initial, final = 551.349 7089.15 Final line search alpha, max atom move = 2.67586e-06 0.0189696 Iterations, force evaluations = 64 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.038 | 23.038 | 23.038 | 0.0 | 99.92 Neigh | 0.010786 | 0.010786 | 0.010786 | 0.0 | 0.05 Comm | 0.004235 | 0.004235 | 0.004235 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002535 | | | 0.01 Nlocal: 1046 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7941 ave 7941 max 7941 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: 205260 ave 205260 max 205260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205260 Ave neighs/atom = 196.233 Neighbor list builds = 2 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 : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.456 | 5.456 | 5.456 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -72831038 0 -72831038 -5.1759702e+10 4508.7328 1064 0 -1.8864951e+15 0 -1.8864951e+15 3.4446645e+18 213.89675 Loop time of 778.036 on 1 procs for 1000 steps with 1046 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -72831037.5731 -1.88590567715e+15 -1.88649506116e+15 Force two-norm initial, final = 4.36797e+08 1.79706e+15 Force max component initial, final = 4.36797e+08 1.68202e+15 Final line search alpha, max atom move = 8.8594e-19 0.00149017 Iterations, force evaluations = 1000 1016 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 777.66 | 777.66 | 777.66 | 0.0 | 99.95 Neigh | 0.025719 | 0.025719 | 0.025719 | 0.0 | 0.00 Comm | 0.090425 | 0.090425 | 0.090425 | 0.0 | 0.01 Output | 1.6928e-05 | 1.6928e-05 | 1.6928e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2577 | | | 0.03 Nlocal: 1046 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 39651 ave 39651 max 39651 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: 1.1297e+06 ave 1.1297e+06 max 1.1297e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1129704 Ave neighs/atom = 1080.02 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 6 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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 WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:931) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 ERROR on proc 0: Neighbor list overflow, boost neigh_modify one (src/npair_full_bin_atomonly.cpp:88) Last command: run 0