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 = 3.16926 3.16926 3.16926 Created orthogonal box = (0 -41.0815 0) to (23.7166 41.0815 5.48932) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.08212 4.89027 5.48932 Created 340 atoms create_atoms CPU = 0.000315905 secs 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.08212 4.89027 5.48932 Created 339 atoms create_atoms CPU = 0.000180006 secs 339 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 8 25 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 672 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 8 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.51 | 4.51 | 4.51 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7215.478 0 -7215.478 25757.76 22 0 -7259.7977 0 -7259.7977 11603.761 Loop time of 5.68176 on 1 procs for 22 steps with 672 atoms 82.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7215.47802847 -7259.79321255 -7259.79768977 Force two-norm initial, final = 50.2858 0.195069 Force max component initial, final = 9.8906 0.0322739 Final line search alpha, max atom move = 0.946746 0.0305552 Iterations, force evaluations = 22 40 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6801 | 5.6801 | 5.6801 | 0.0 | 99.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00096393 | 0.00096393 | 0.00096393 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006723 | | | 0.01 Nlocal: 672 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3317 ave 3317 max 3317 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: 43738 ave 43738 max 43738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43738 Ave neighs/atom = 65.0863 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 : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.51 | 4.51 | 4.51 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -7259.7977 0 -7259.7977 11603.761 10696.6 26 0 -7259.9203 0 -7259.9203 3374.8685 10729.689 Loop time of 0.657992 on 1 procs for 4 steps with 672 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7259.79768977 -7259.91904947 -7259.92030433 Force two-norm initial, final = 91.6849 0.239816 Force max component initial, final = 81.2696 0.0398033 Final line search alpha, max atom move = 9.98781e-05 3.97548e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65736 | 0.65736 | 0.65736 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013733 | 0.00013733 | 0.00013733 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004926 | | | 0.07 Nlocal: 672 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3355 ave 3355 max 3355 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: 43350 ave 43350 max 43350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43350 Ave neighs/atom = 64.5089 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 8 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.648 | 4.648 | 4.648 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7259.9203 0 -7259.9203 3374.8685 Loop time of 9.53674e-07 on 1 procs for 0 steps with 672 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 | | 9.537e-07 | | |100.00 Nlocal: 672 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3337 ave 3337 max 3337 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: 43292 ave 43292 max 43292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43292 Ave neighs/atom = 64.4226 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) = 4.648 | 4.648 | 4.648 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 -7259.9203 -7259.9203 23.719918 82.162908 5.5055178 3374.8685 3374.8685 -0.51171697 10125.943 -0.82607125 2.5465452 452.04492 Loop time of 1.90735e-06 on 1 procs for 0 steps with 672 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 | | 1.907e-06 | | |100.00 Nlocal: 672 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3337 ave 3337 max 3337 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21646 ave 21646 max 21646 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43292 ave 43292 max 43292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43292 Ave neighs/atom = 64.4226 Neighbor list builds = 0 Dangerous builds = 0 672 -3661.62527826624 eV 2.54654519986585 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06