LAMMPS (19 Mar 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 = 3.52 3.52 3.52 Created orthogonal box = (0 -43.1145 0) to (6.09682 43.1145 4.97803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.09682 5.74814 4.97803 Created 121 atoms create_atoms CPU = 0.000294924 secs 121 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.09682 5.74814 4.97803 Created 121 atoms create_atoms CPU = 0.000202179 secs 121 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 2 26 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 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 236 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 2 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 4.467 | 4.467 | 4.467 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1043.3778 0 -1043.3778 -6335.3967 23 0 -1046.8851 0 -1046.8851 -16836.49 Loop time of 0.0207679 on 1 procs for 23 steps with 236 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 = -1043.37777817 -1046.88418737 -1046.88511963 Force two-norm initial, final = 6.05109 0.101282 Force max component initial, final = 2.04755 0.0160379 Final line search alpha, max atom move = 1 0.0160379 Iterations, force evaluations = 23 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.019257 | 0.019257 | 0.019257 | 0.0 | 92.73 Neigh | 0.00072002 | 0.00072002 | 0.00072002 | 0.0 | 3.47 Comm | 0.00058055 | 0.00058055 | 0.00058055 | 0.0 | 2.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00021 | | | 1.01 Nlocal: 236 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3169 ave 3169 max 3169 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: 31120 ave 31120 max 31120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31120 Ave neighs/atom = 131.864 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Setting up cg style minimization ... Unit style : metal Current step : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.467 | 4.467 | 4.467 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -1046.8851 0 -1046.8851 -16836.49 2617.0661 27 0 -1046.931 0 -1046.931 -7928.1826 2603.7912 Loop time of 0.0039711 on 1 procs for 4 steps with 236 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 = -1046.88511963 -1046.93083327 -1046.93095262 Force two-norm initial, final = 24.9642 0.119061 Force max component initial, final = 19.3592 0.0194345 Final line search alpha, max atom move = 0.00133284 2.59032e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.003619 | 0.003619 | 0.003619 | 0.0 | 91.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.4652e-05 | 9.4652e-05 | 9.4652e-05 | 0.0 | 2.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002575 | | | 6.48 Nlocal: 236 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3169 ave 3169 max 3169 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: 31148 ave 31148 max 31148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31148 Ave neighs/atom = 131.983 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 2 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 4.605 | 4.605 | 4.605 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1046.931 0 -1046.931 -7928.1826 Loop time of 1.19209e-06 on 1 procs for 0 steps with 236 atoms 167.8% 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 | | 1.192e-06 | | |100.00 Nlocal: 236 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3169 ave 3169 max 3169 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: 31148 ave 31148 max 31148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31148 Ave neighs/atom = 131.983 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) = 4.605 | 4.605 | 4.605 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 -1046.931 -1046.931 6.0848456 86.229079 4.9625266 -7928.1826 -7928.1826 -6.6428153 -23784.135 6.2298069 2.4059552 115.94962 Loop time of 9.53674e-07 on 1 procs for 0 steps with 236 atoms 209.7% 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: 236 ave 236 max 236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3169 ave 3169 max 3169 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15574 ave 15574 max 15574 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31148 ave 31148 max 31148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31148 Ave neighs/atom = 131.983 Neighbor list builds = 0 Dangerous builds = 0 236 -1046.93095262194 eV 2.40595520149299 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00