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 = 2.86883 2.86883 2.86883 Created orthogonal box = (0 -49.3601 0) to (24.6786 49.3601 2.86883) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.00194 4.00194 2.86883 Created 298 atoms create_atoms CPU = 0.00051713 secs 298 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.00194 4.00194 2.86883 Created 298 atoms create_atoms CPU = 0.00028491 secs 298 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 20 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 588 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.363 | 5.363 | 5.363 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2360.2883 0 -2360.2883 16641.486 116 0 -2419.9657 0 -2419.9657 -6882.9907 Loop time of 1.37048 on 1 procs for 116 steps with 588 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 = -2360.28829749 -2419.96349131 -2419.9657403 Force two-norm initial, final = 113.993 0.200287 Force max component initial, final = 38.374 0.0216821 Final line search alpha, max atom move = 0.788496 0.0170963 Iterations, force evaluations = 116 221 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3439 | 1.3439 | 1.3439 | 0.0 | 98.06 Neigh | 0.006752 | 0.006752 | 0.006752 | 0.0 | 0.49 Comm | 0.015089 | 0.015089 | 0.015089 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004754 | | | 0.35 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9860 ave 9860 max 9860 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: 224768 ave 224768 max 224768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224768 Ave neighs/atom = 382.259 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 : 116 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.363 | 5.363 | 5.363 Mbytes Step Temp E_pair E_mol TotEng Press Volume 116 0 -2419.9657 0 -2419.9657 -6882.9907 6989.2649 137 0 -2421.0491 0 -2421.0491 9156.1902 6920.6327 Loop time of 0.158148 on 1 procs for 21 steps with 588 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 = -2419.9657403 -2421.04812572 -2421.04910997 Force two-norm initial, final = 93.868 0.973161 Force max component initial, final = 92.5687 0.251858 Final line search alpha, max atom move = 0.000470367 0.000118466 Iterations, force evaluations = 21 22 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1522 | 0.1522 | 0.1522 | 0.0 | 96.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015392 | 0.0015392 | 0.0015392 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004405 | | | 2.79 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9844 ave 9844 max 9844 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: 225112 ave 225112 max 225112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225112 Ave neighs/atom = 382.844 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.5 | 5.5 | 5.5 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2421.0491 0 -2421.0491 9156.1902 Loop time of 1.90735e-06 on 1 procs for 0 steps with 588 atoms 104.9% 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: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9732 ave 9732 max 9732 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: 224908 ave 224908 max 224908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224908 Ave neighs/atom = 382.497 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) = 5.5 | 5.5 | 5.5 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 -2421.0491 -2421.0491 24.949545 98.720181 2.8098118 9156.1902 9156.1902 -44.962194 27456.425 57.10743 2.3731443 219.70052 Loop time of 9.53674e-07 on 1 procs for 0 steps with 588 atoms 209.7% 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: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9732 ave 9732 max 9732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112454 ave 112454 max 112454 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 224908 ave 224908 max 224908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224908 Ave neighs/atom = 382.497 Neighbor list builds = 0 Dangerous builds = 0 588 -2421.04910997342 eV 2.37314431696339 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01