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 = 3.6584 3.6584 3.6584 Created orthogonal box = (0 -51.7413 0) to (25.8688 51.7413 3.6584) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.13901 4.13901 3.6584 Created 402 atoms create_atoms CPU = 0.000228882 secs 402 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.13901 4.13901 3.6584 Created 402 atoms create_atoms CPU = 0.000102997 secs 402 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 25 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 788 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.996 | 4.996 | 4.996 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3044.0877 0 -3044.0877 -4368.2531 55 0 -3059.6998 0 -3059.6998 -9946.1804 Loop time of 0.389616 on 1 procs for 55 steps with 788 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3044.08768648 -3059.69677052 -3059.6997771 Force two-norm initial, final = 7.67176 0.138177 Force max component initial, final = 2.0571 0.0266203 Final line search alpha, max atom move = 1 0.0266203 Iterations, force evaluations = 55 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37979 | 0.37979 | 0.37979 | 0.0 | 97.48 Neigh | 0.0032291 | 0.0032291 | 0.0032291 | 0.0 | 0.83 Comm | 0.0045195 | 0.0045195 | 0.0045195 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002076 | | | 0.53 Nlocal: 788 ave 788 max 788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7592 ave 7592 max 7592 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: 158704 ave 158704 max 158704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158704 Ave neighs/atom = 201.401 Neighbor list builds = 1 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 : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.997 | 4.997 | 4.997 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -3059.6998 0 -3059.6998 -9946.1804 9793.4419 326 0 -3093.2719 0 -3093.2719 43504.833 8883.2955 Loop time of 1.40641 on 1 procs for 271 steps with 788 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 = -3059.6997771 -3093.27133418 -3093.2719359 Force two-norm initial, final = 89.5143 3.82132 Force max component initial, final = 86.1672 2.21161 Final line search alpha, max atom move = 0.000351382 0.00077712 Iterations, force evaluations = 271 286 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3294 | 1.3294 | 1.3294 | 0.0 | 94.53 Neigh | 0.019559 | 0.019559 | 0.019559 | 0.0 | 1.39 Comm | 0.013858 | 0.013858 | 0.013858 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04357 | | | 3.10 Nlocal: 788 ave 788 max 788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8227 ave 8227 max 8227 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: 181524 ave 181524 max 181524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181524 Ave neighs/atom = 230.36 Neighbor list builds = 4 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.139 | 5.139 | 5.139 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3093.2719 0 -3093.2719 43504.833 Loop time of 1.90735e-06 on 1 procs for 0 steps with 788 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: 788 ave 788 max 788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8301 ave 8301 max 8301 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: 178568 ave 178568 max 178568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178568 Ave neighs/atom = 226.609 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) = 5.139 | 5.139 | 5.139 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 -3093.2719 -3093.2719 21.450748 103.48258 4.0018833 43504.833 43504.833 330.75812 129903.05 280.69119 2.1965522 425.66633 Loop time of 9.53674e-07 on 1 procs for 0 steps with 788 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: 788 ave 788 max 788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8301 ave 8301 max 8301 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89284 ave 89284 max 89284 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 178568 ave 178568 max 178568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178568 Ave neighs/atom = 226.609 Neighbor list builds = 0 Dangerous builds = 0 788 -3093.27193590341 eV 2.19655222367738 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01