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 = 3.61481 3.61481 3.61481 Created orthogonal box = (0 -38.5993 0) to (22.2832 38.5993 6.26104) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.864 5.41693 6.26104 Created 457 atoms create_atoms CPU = 0.00032711 secs 457 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.864 5.41693 6.26104 Created 457 atoms create_atoms CPU = 0.000244856 secs 457 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 5 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 11.0375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 900 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 5 14 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.0375 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 -3151.2508 0 -3151.2508 2428.2725 89 0 -3171.234 0 -3171.234 -13959.549 Loop time of 1.66755 on 1 procs for 89 steps with 900 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3151.25075299 -3171.23091678 -3171.23400403 Force two-norm initial, final = 22.8729 0.147593 Force max component initial, final = 5.89856 0.0187241 Final line search alpha, max atom move = 1 0.0187241 Iterations, force evaluations = 89 151 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6145 | 1.6145 | 1.6145 | 0.0 | 96.82 Neigh | 0.040197 | 0.040197 | 0.040197 | 0.0 | 2.41 Comm | 0.0090358 | 0.0090358 | 0.0090358 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003808 | | | 0.23 Nlocal: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9638 ave 9638 max 9638 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: 413210 ave 413210 max 413210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 413210 Ave neighs/atom = 459.122 Neighbor list builds = 4 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 : 89 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 89 0 -3171.234 0 -3171.234 -13959.549 10770.432 94 0 -3171.4427 0 -3171.4427 -5633.9255 10701.291 Loop time of 0.087781 on 1 procs for 5 steps with 900 atoms 102.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3171.23400403 -3171.44268332 -3171.44270948 Force two-norm initial, final = 91.1432 0.171635 Force max component initial, final = 67.9155 0.0465751 Final line search alpha, max atom move = 0.0021321 9.93026e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.086254 | 0.086254 | 0.086254 | 0.0 | 98.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004077 | 0.0004077 | 0.0004077 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001119 | | | 1.27 Nlocal: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9827 ave 9827 max 9827 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: 413202 ave 413202 max 413202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 413202 Ave neighs/atom = 459.113 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 5 14 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.0375 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 -3171.4427 0 -3171.4427 -5633.9255 Loop time of 9.53674e-07 on 1 procs for 0 steps with 900 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: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9860 ave 9860 max 9860 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: 413896 ave 413896 max 413896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 413896 Ave neighs/atom = 459.884 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 -3171.4427 -3171.4427 22.21789 77.198517 6.2391353 -5633.9255 -5633.9255 -6.9526884 -16896.998 2.1743259 2.3283308 618.05599 Loop time of 2.14577e-06 on 1 procs for 0 steps with 900 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 | | 2.146e-06 | | |100.00 Nlocal: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9860 ave 9860 max 9860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 206948 ave 206948 max 206948 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 413896 ave 413896 max 413896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 413896 Ave neighs/atom = 459.884 Neighbor list builds = 0 Dangerous builds = 0 900 -3171.44270947873 eV 2.32833082502257 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01