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 = 4.03299 4.03299 4.03299 Created orthogonal box = (0 -47.723 0) to (58.4436 47.723 9.87876) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.67926 6.1353 6.58584 Created 1689 atoms create_atoms CPU = 0.0200181 secs 1689 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.67926 6.1353 6.58584 Created 1689 atoms create_atoms CPU = 0.00171494 secs 1689 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 9 14 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 66 atoms, new total = 3312 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 9 14 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 17.7 | 17.7 | 17.7 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9503.9505 0 -9503.9505 1118.739 66 0 -9629.3528 0 -9629.3528 -8146.9123 Loop time of 16.9534 on 1 procs for 66 steps with 3312 atoms 49.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9503.95051799 -9629.34350371 -9629.35279046 Force two-norm initial, final = 42.7955 0.297664 Force max component initial, final = 4.43007 0.0280829 Final line search alpha, max atom move = 1 0.0280829 Iterations, force evaluations = 66 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.488 | 16.488 | 16.488 | 0.0 | 97.25 Neigh | 0.40042 | 0.40042 | 0.40042 | 0.0 | 2.36 Comm | 0.034555 | 0.034555 | 0.034555 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03088 | | | 0.18 Nlocal: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20289 ave 20289 max 20289 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: 2.18205e+06 ave 2.18205e+06 max 2.18205e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2182052 Ave neighs/atom = 658.832 Neighbor list builds = 2 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 : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 17.71 | 17.71 | 17.71 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -9629.3528 0 -9629.3528 -8146.9123 55105.753 72 0 -9630.5839 0 -9630.5839 -1857.9512 54628.876 Loop time of 0.587642 on 1 procs for 6 steps with 3312 atoms 88.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9629.35279046 -9630.57425048 -9630.58386659 Force two-norm initial, final = 382.929 3.97934 Force max component initial, final = 323.534 3.70723 Final line search alpha, max atom move = 3.11818e-05 0.000115598 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58263 | 0.58263 | 0.58263 | 0.0 | 99.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013223 | 0.0013223 | 0.0013223 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003693 | | | 0.63 Nlocal: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20348 ave 20348 max 20348 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: 2.18303e+06 ave 2.18303e+06 max 2.18303e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2183034 Ave neighs/atom = 659.129 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 9 14 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 17.22 | 17.22 | 17.22 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9630.5839 0 -9630.5839 -1857.9512 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3312 atoms 157.3% 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: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20404 ave 20404 max 20404 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: 2.19265e+06 ave 2.19265e+06 max 2.19265e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2192652 Ave neighs/atom = 662.033 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) = 17.22 | 17.22 | 17.22 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 -9630.5839 -9630.5839 58.120191 95.445993 9.8477618 -1857.9512 -1857.9512 -40.464418 -5641.7749 108.38577 2.6977101 2857.9335 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3312 atoms 157.3% 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: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20404 ave 20404 max 20404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.09633e+06 ave 1.09633e+06 max 1.09633e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.19265e+06 ave 2.19265e+06 max 2.19265e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2192652 Ave neighs/atom = 662.033 Neighbor list builds = 0 Dangerous builds = 0 3312 -9630.58386658838 eV 2.69771011864091 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19