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 -41.5261 0) to (20.7618 41.5261 2.57518) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 2.87471 2.87471 2.57518 Created 522 atoms create_atoms CPU = 0.000192881 secs 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 2.87471 2.87471 2.57518 Created 522 atoms create_atoms CPU = 8.79765e-05 secs 522 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 = 8 29 1 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 20 atoms, new total = 1024 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 = 8 29 1 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) = 5.436 | 5.436 | 5.436 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -198275.02 0 -198275.02 -9005921.7 72 0 -59841222 0 -59841222 -2.9422485e+10 Loop time of 63.3033 on 1 procs for 72 steps with 1024 atoms 77.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -198275.015371 -59841221.7681 -59841221.7681 Force two-norm initial, final = 2024.28 2.05787e+06 Force max component initial, final = 348.753 1.15576e+06 Final line search alpha, max atom move = 2.45913e-21 2.84217e-15 Iterations, force evaluations = 72 172 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 63.231 | 63.231 | 63.231 | 0.0 | 99.89 Neigh | 0.018501 | 0.018501 | 0.018501 | 0.0 | 0.03 Comm | 0.049926 | 0.049926 | 0.049926 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004371 | | | 0.01 Nlocal: 1024 ave 1024 max 1024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8972 ave 8972 max 8972 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: 195672 ave 195672 max 195672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195672 Ave neighs/atom = 191.086 Neighbor list builds = 4 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 : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.437 | 5.437 | 5.437 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -59841222 0 -59841222 -2.9422485e+10 4440.4208 1072 0 -4.5490527e+14 0 -4.5490527e+14 9.1366075e+16 264.45835 Loop time of 949.17 on 1 procs for 1000 steps with 1024 atoms 76.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -59841221.7681 -4.5490510611e+14 -4.54905271375e+14 Force two-norm initial, final = 2.48934e+08 2.45827e+13 Force max component initial, final = 2.48913e+08 1.89043e+13 Final line search alpha, max atom move = 7.02848e-17 0.00132868 Iterations, force evaluations = 1000 1025 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 948.71 | 948.71 | 948.71 | 0.0 | 99.95 Neigh | 0.02641 | 0.02641 | 0.02641 | 0.0 | 0.00 Comm | 0.10173 | 0.10173 | 0.10173 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3318 | | | 0.03 Nlocal: 1024 ave 1024 max 1024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 38023 ave 38023 max 38023 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: 881620 ave 881620 max 881620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 881620 Ave neighs/atom = 860.957 Neighbor list builds = 2 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 = 8 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