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 = 3.61473 3.61473 3.61473 Created orthogonal box = (0 -47.2723 0) to (22.2827 47.2723 5.112) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.69109 5.80493 5.112 Created 458 atoms create_atoms CPU = 0.000381947 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.69109 5.80493 5.112 Created 458 atoms create_atoms CPU = 0.000261068 secs 458 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 6 22 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 8.6825 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 904 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 6 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.6825 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) = 5.409 | 5.409 | 5.409 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3157.6709 0 -3157.6709 6590.5985 56 0 -3174.4017 0 -3174.4017 -4160.2703 Loop time of 0.518154 on 1 procs for 56 steps with 904 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3157.67088837 -3174.39964687 -3174.4017329 Force two-norm initial, final = 24.1275 0.145328 Force max component initial, final = 4.07011 0.0191601 Final line search alpha, max atom move = 1 0.0191601 Iterations, force evaluations = 56 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.51041 | 0.51041 | 0.51041 | 0.0 | 98.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00506 | 0.00506 | 0.00506 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002685 | | | 0.52 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7185 ave 7185 max 7185 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: 201684 ave 201684 max 201684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201684 Ave neighs/atom = 223.102 Neighbor list builds = 0 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.411 | 5.411 | 5.411 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -3174.4017 0 -3174.4017 -4160.2703 10769.486 58 0 -3174.4212 0 -3174.4212 -1815.188 10751.171 Loop time of 0.019716 on 1 procs for 2 steps with 904 atoms 101.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3174.4017329 -3174.41834169 -3174.4211903 Force two-norm initial, final = 24.6665 0.222817 Force max component initial, final = 20.4728 0.119585 Final line search alpha, max atom move = 0.000253457 3.03096e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.019081 | 0.019081 | 0.019081 | 0.0 | 96.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016832 | 0.00016832 | 0.00016832 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004668 | | | 2.37 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7206 ave 7206 max 7206 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: 201964 ave 201964 max 201964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201964 Ave neighs/atom = 223.412 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 6 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.6825 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) = 5.549 | 5.549 | 5.549 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3174.4212 0 -3174.4212 -1815.188 Loop time of 9.53674e-07 on 1 procs for 0 steps with 904 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: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7206 ave 7206 max 7206 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: 201992 ave 201992 max 201992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201992 Ave neighs/atom = 223.442 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) = 5.549 | 5.549 | 5.549 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 -3174.4212 -3174.4212 22.244126 94.544638 5.1121494 -1815.188 -1815.188 -14.298575 -5413.4441 -17.821446 2.3840222 561.03318 Loop time of 1.90735e-06 on 1 procs for 0 steps with 904 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: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7206 ave 7206 max 7206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100996 ave 100996 max 100996 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 201992 ave 201992 max 201992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201992 Ave neighs/atom = 223.442 Neighbor list builds = 0 Dangerous builds = 0 904 -3174.42119029682 eV 2.38402217047946 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00