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 = 3.60735 3.60735 3.60735 Created orthogonal box = (0 -38.856 0) to (19.4262 38.856 3.60735) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.68908 4.68908 3.60735 Created 233 atoms create_atoms CPU = 0.000482082 secs 233 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.68908 4.68908 3.60735 Created 233 atoms create_atoms CPU = 0.000249147 secs 233 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 13 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 460 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.365 | 5.365 | 5.365 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1579.4895 0 -1579.4895 15759.341 73 0 -1611.0733 0 -1611.0733 -3024.8498 Loop time of 1.53396 on 1 procs for 73 steps with 460 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1579.48949047 -1611.07181572 -1611.07331459 Force two-norm initial, final = 45.617 0.141607 Force max component initial, final = 13.4924 0.0275264 Final line search alpha, max atom move = 1 0.0275264 Iterations, force evaluations = 73 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5105 | 1.5105 | 1.5105 | 0.0 | 98.47 Neigh | 0.009249 | 0.009249 | 0.009249 | 0.0 | 0.60 Comm | 0.011125 | 0.011125 | 0.011125 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003112 | | | 0.20 Nlocal: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9740 ave 9740 max 9740 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: 287588 ave 287588 max 287588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287588 Ave neighs/atom = 625.191 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 : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.365 | 5.365 | 5.365 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -1611.0733 0 -1611.0733 -3024.8498 5445.8306 79 0 -1611.133 0 -1611.133 -420.91855 5435.3491 Loop time of 0.0727539 on 1 procs for 6 steps with 460 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1611.07331459 -1611.13220806 -1611.13299065 Force two-norm initial, final = 24.9293 1.11819 Force max component initial, final = 24.7282 0.918863 Final line search alpha, max atom move = 0.000579267 0.000532267 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071005 | 0.071005 | 0.071005 | 0.0 | 97.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052333 | 0.00052333 | 0.00052333 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001226 | | | 1.69 Nlocal: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9657 ave 9657 max 9657 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: 287192 ave 287192 max 287192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287192 Ave neighs/atom = 624.33 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.503 | 5.503 | 5.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1611.133 0 -1611.133 -420.91855 Loop time of 1.90735e-06 on 1 procs for 0 steps with 460 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: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9719 ave 9719 max 9719 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: 287564 ave 287564 max 287564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287564 Ave neighs/atom = 625.139 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) = 5.503 | 5.503 | 5.503 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 -1611.133 -1611.133 19.327655 77.71197 3.6187648 -420.91855 -420.91855 -269.47917 -824.16634 -169.11015 2.287309 274.08095 Loop time of 2.14577e-06 on 1 procs for 0 steps with 460 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: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9719 ave 9719 max 9719 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 143782 ave 143782 max 143782 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 287564 ave 287564 max 287564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 287564 Ave neighs/atom = 625.139 Neighbor list builds = 0 Dangerous builds = 0 460 -1611.13299064994 eV 2.28730895717939 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01