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 = 3.99462 3.99462 3.99462 Created orthogonal box = (0 -42.4674 0) to (42.4634 42.4674 3.99462) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.63673 5.63673 3.99462 Created 454 atoms create_atoms CPU = 0.000279903 secs 454 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.63673 5.63673 3.99462 Created 454 atoms create_atoms CPU = 0.000134945 secs 454 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 12 23 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 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 902 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 12 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 4.948 | 4.948 | 4.948 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2926.8693 0 -2926.8693 6880.2332 90 0 -2958.4416 0 -2958.4416 -462.34145 Loop time of 0.945025 on 1 procs for 90 steps with 902 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2926.86934463 -2958.43916101 -2958.44160968 Force two-norm initial, final = 19.2769 0.110861 Force max component initial, final = 4.74635 0.0187332 Final line search alpha, max atom move = 1 0.0187332 Iterations, force evaluations = 90 149 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92719 | 0.92719 | 0.92719 | 0.0 | 98.11 Neigh | 0.0088398 | 0.0088398 | 0.0088398 | 0.0 | 0.94 Comm | 0.0054348 | 0.0054348 | 0.0054348 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003561 | | | 0.38 Nlocal: 902 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5598 ave 5598 max 5598 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: 117828 ave 117828 max 117828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117828 Ave neighs/atom = 130.63 Neighbor list builds = 3 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 : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.95 | 4.95 | 4.95 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -2958.4416 0 -2958.4416 -462.34145 14407.035 93 0 -2958.4561 0 -2958.4561 -508.01912 14408.904 Loop time of 0.0243859 on 1 procs for 3 steps with 902 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 = -2958.44160968 -2958.45493988 -2958.45606211 Force two-norm initial, final = 9.60463 0.716458 Force max component initial, final = 8.13477 0.532639 Final line search alpha, max atom move = 0.00049748 0.000264977 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.023818 | 0.023818 | 0.023818 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015974 | 0.00015974 | 0.00015974 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004084 | | | 1.67 Nlocal: 902 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5581 ave 5581 max 5581 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: 118572 ave 118572 max 118572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118572 Ave neighs/atom = 131.455 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 12 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 5.087 | 5.087 | 5.087 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2958.4561 0 -2958.4561 -508.01912 Loop time of 9.53674e-07 on 1 procs for 0 steps with 902 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: 902 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5581 ave 5581 max 5581 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: 118600 ave 118600 max 118600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118600 Ave neighs/atom = 131.486 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) = 5.087 | 5.087 | 5.087 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 -2958.4561 -2958.4561 42.370239 84.934704 4.0039151 -508.01912 -508.01912 59.096113 -1635.0193 51.86578 2.5274211 177.80116 Loop time of 1.90735e-06 on 1 procs for 0 steps with 902 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: 902 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5581 ave 5581 max 5581 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59300 ave 59300 max 59300 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 118600 ave 118600 max 118600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118600 Ave neighs/atom = 131.486 Neighbor list builds = 0 Dangerous builds = 0 902 -2958.45606210965 eV 2.52742106308166 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01