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 = 3.63909 3.63909 3.63909 Created orthogonal box = (0 -41.8135 0) to (29.5641 41.8135 5.14644) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.27117 5.70135 5.14644 Created 532 atoms create_atoms CPU = 0.000414848 secs 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.27117 5.70135 5.14644 Created 532 atoms create_atoms CPU = 0.000272989 secs 532 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 18 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.844 | 5.844 | 5.844 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3409.9924 0 -3409.9924 1413.1716 61 0 -3429.0848 0 -3429.0848 -4977.3751 Loop time of 0.845853 on 1 procs for 61 steps with 1048 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3409.9924383 -3429.08191436 -3429.08478682 Force two-norm initial, final = 18.9346 0.143144 Force max component initial, final = 3.91141 0.00988243 Final line search alpha, max atom move = 1 0.00988243 Iterations, force evaluations = 61 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8295 | 0.8295 | 0.8295 | 0.0 | 98.07 Neigh | 0.0058429 | 0.0058429 | 0.0058429 | 0.0 | 0.69 Comm | 0.0073025 | 0.0073025 | 0.0073025 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00321 | | | 0.38 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9129 ave 9129 max 9129 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: 330880 ave 330880 max 330880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330880 Ave neighs/atom = 315.725 Neighbor list builds = 1 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 : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.845 | 5.845 | 5.845 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -3429.0848 0 -3429.0848 -4977.3751 12723.845 66 0 -3429.2122 0 -3429.2122 -1134.5889 12690.533 Loop time of 0.071449 on 1 procs for 5 steps with 1048 atoms 98.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3429.08478682 -3429.21217776 -3429.2121907 Force two-norm initial, final = 65.3506 0.189895 Force max component initial, final = 65.347 0.0329604 Final line search alpha, max atom move = 0.00158203 5.21443e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.069691 | 0.069691 | 0.069691 | 0.0 | 97.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042582 | 0.00042582 | 0.00042582 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001332 | | | 1.86 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9119 ave 9119 max 9119 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: 330848 ave 330848 max 330848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330848 Ave neighs/atom = 315.695 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.983 | 5.983 | 5.983 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3429.2122 0 -3429.2122 -1134.5889 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9119 ave 9119 max 9119 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: 330944 ave 330944 max 330944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330944 Ave neighs/atom = 315.786 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) = 5.983 | 5.983 | 5.983 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 -3429.2122 -3429.2122 29.601604 83.627087 5.1264611 -1134.5889 -1134.5889 -4.1665303 -3395.9844 -3.6158648 2.4193543 674.39509 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9119 ave 9119 max 9119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 165472 ave 165472 max 165472 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 330944 ave 330944 max 330944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 330944 Ave neighs/atom = 315.786 Neighbor list builds = 0 Dangerous builds = 0 1048 -3429.21219070422 eV 2.41935426240144 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01