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 = 3.52733 3.52733 3.52733 Created orthogonal box = (0 -40.8353 0) to (28.8724 40.8353 4.9884) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.60211 6.0943 4.9884 Created 538 atoms create_atoms CPU = 0.00149107 secs 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.60211 6.0943 4.9884 Created 538 atoms create_atoms CPU = 0.00114202 secs 538 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 = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 6 17 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 10.1329 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1058 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 = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 6 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.1329 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) = 6.264 | 6.264 | 6.264 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4361.9565 0 -4361.9565 6324.1852 88 0 -4424.6788 0 -4424.6788 -20712.486 Loop time of 2.36669 on 1 procs for 88 steps with 1058 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4361.9564886 -4424.67483899 -4424.67880625 Force two-norm initial, final = 46.9671 0.270541 Force max component initial, final = 16.0155 0.0254919 Final line search alpha, max atom move = 1 0.0254919 Iterations, force evaluations = 88 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3282 | 2.3282 | 2.3282 | 0.0 | 98.37 Neigh | 0.016316 | 0.016316 | 0.016316 | 0.0 | 0.69 Comm | 0.015018 | 0.015018 | 0.015018 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00719 | | | 0.30 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10212 ave 10212 max 10212 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: 401008 ave 401008 max 401008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 401008 Ave neighs/atom = 379.025 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 : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.264 | 6.264 | 6.264 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -4424.6788 0 -4424.6788 -20712.486 11762.791 101 0 -4426.599 0 -4426.599 3275.2793 11606.366 Loop time of 0.260871 on 1 procs for 13 steps with 1058 atoms 97.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4424.67880625 -4426.5989527 -4426.59897357 Force two-norm initial, final = 333.231 0.526179 Force max component initial, final = 303.663 0.194774 Final line search alpha, max atom move = 0.00128296 0.000249887 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25455 | 0.25455 | 0.25455 | 0.0 | 97.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014529 | 0.0014529 | 0.0014529 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004873 | | | 1.87 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10192 ave 10192 max 10192 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: 404560 ave 404560 max 404560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 404560 Ave neighs/atom = 382.382 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 = 10.1329 ghost atom cutoff = 10.1329 binsize = 5.06647, bins = 6 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.1329 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) = 6.401 | 6.401 | 6.401 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4426.599 0 -4426.599 3275.2793 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1058 atoms 139.8% 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: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10192 ave 10192 max 10192 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: 407464 ave 407464 max 407464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407464 Ave neighs/atom = 385.127 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) = 6.401 | 6.401 | 6.401 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 -4426.599 -4426.599 28.533098 81.670634 4.9805971 3275.2793 3275.2793 -17.913017 9870.5959 -26.845064 2.2986543 1018.2217 Loop time of 3.09944e-06 on 1 procs for 0 steps with 1058 atoms 129.1% 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 | | 3.099e-06 | | |100.00 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10192 ave 10192 max 10192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 203732 ave 203732 max 203732 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 407464 ave 407464 max 407464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407464 Ave neighs/atom = 385.127 Neighbor list builds = 0 Dangerous builds = 0 1058 -4426.59897356558 eV 2.29865428502129 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02