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 = 4.0333 4.0333 4.0333 Created orthogonal box = (0 -59.6914 0) to (48.7346 59.6914 9.87953) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.00837 5.72345 6.58635 Created 1758 atoms create_atoms CPU = 0.000730038 secs 1758 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.00837 5.72345 6.58635 Created 1758 atoms create_atoms CPU = 0.000613213 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 29 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 46 atoms, new total = 3470 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.636 | 6.636 | 6.636 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11634.75 0 -11634.75 383.51803 41 0 -11660.381 0 -11660.381 -3011.5278 Loop time of 0.970551 on 1 procs for 41 steps with 3470 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11634.7501098 -11660.3712061 -11660.3806884 Force two-norm initial, final = 28.3647 0.257726 Force max component initial, final = 3.916 0.0905199 Final line search alpha, max atom move = 0.912189 0.0825712 Iterations, force evaluations = 41 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95874 | 0.95874 | 0.95874 | 0.0 | 98.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0058045 | 0.0058045 | 0.0058045 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006002 | | | 0.62 Nlocal: 3470 ave 3470 max 3470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11173 ave 11173 max 11173 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: 484508 ave 484508 max 484508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 484508 Ave neighs/atom = 139.628 Neighbor list builds = 0 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.636 | 6.636 | 6.636 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -11660.381 0 -11660.381 -3011.5278 57479.85 44 0 -11660.569 0 -11660.569 -370.7416 57287.632 Loop time of 0.070457 on 1 procs for 3 steps with 3470 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11660.3806884 -11660.5666246 -11660.5691198 Force two-norm initial, final = 152.373 0.298833 Force max component initial, final = 120.658 0.0997995 Final line search alpha, max atom move = 0.000120832 1.2059e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.068555 | 0.068555 | 0.068555 | 0.0 | 97.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038576 | 0.00038576 | 0.00038576 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001516 | | | 2.15 Nlocal: 3470 ave 3470 max 3470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11200 ave 11200 max 11200 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: 488984 ave 488984 max 488984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 488984 Ave neighs/atom = 140.918 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.774 | 6.774 | 6.774 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11660.569 0 -11660.569 -370.7416 Loop time of 2.14577e-06 on 1 procs for 0 steps with 3470 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 | | 2.146e-06 | | |100.00 Nlocal: 3470 ave 3470 max 3470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11215 ave 11215 max 11215 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: 489830 ave 489830 max 489830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489830 Ave neighs/atom = 141.161 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) = 6.774 | 6.774 | 6.774 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 -11660.569 -11660.569 48.62242 119.3829 9.8692053 -370.7416 -370.7416 1.480441 -1114.9003 1.1950464 2.5638264 2163.6067 Loop time of 1.19209e-06 on 1 procs for 0 steps with 3470 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 | | 1.192e-06 | | |100.00 Nlocal: 3470 ave 3470 max 3470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11215 ave 11215 max 11215 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 244915 ave 244915 max 244915 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 489830 ave 489830 max 489830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489830 Ave neighs/atom = 141.161 Neighbor list builds = 0 Dangerous builds = 0 3470 -11660.5691198059 eV 2.56382637120555 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01