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 = 3.63376 3.63376 3.63376 Created orthogonal box = (0 -62.0974 0) to (31.0469 62.0974 3.63376) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6783 4.6783 3.63376 Created 586 atoms create_atoms CPU = 0.0002141 secs 586 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6783 4.6783 3.63376 Created 586 atoms create_atoms CPU = 0.000108957 secs 586 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 41 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1160 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.628 | 4.628 | 4.628 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4730.9694 0 -4730.9694 -1406.6344 22 0 -4743.0339 0 -4743.0339 -6282.0701 Loop time of 22.4652 on 1 procs for 22 steps with 1160 atoms 83.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4730.96936654 -4743.02941266 -4743.03391714 Force two-norm initial, final = 25.0322 0.176813 Force max component initial, final = 6.82308 0.0257438 Final line search alpha, max atom move = 1 0.0257438 Iterations, force evaluations = 22 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.463 | 22.463 | 22.463 | 0.0 | 99.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014107 | 0.0014107 | 0.0014107 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001016 | | | 0.00 Nlocal: 1160 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5908 ave 5908 max 5908 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: 89944 ave 89944 max 89944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89944 Ave neighs/atom = 77.5379 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 : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.628 | 4.628 | 4.628 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -4743.0339 0 -4743.0339 -6282.0701 14011.272 25 0 -4743.1285 0 -4743.1285 -1020.8068 13959.458 Loop time of 3.33327 on 1 procs for 3 steps with 1160 atoms 91.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4743.03391714 -4743.12843356 -4743.12846043 Force two-norm initial, final = 72.1431 0.21964 Force max component initial, final = 53.1152 0.0735704 Final line search alpha, max atom move = 0.00295358 0.000217296 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3324 | 3.3324 | 3.3324 | 0.0 | 99.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019121 | 0.00019121 | 0.00019121 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006602 | | | 0.02 Nlocal: 1160 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5932 ave 5932 max 5932 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: 90168 ave 90168 max 90168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90168 Ave neighs/atom = 77.731 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.766 | 4.766 | 4.766 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4743.1285 0 -4743.1285 -1020.8068 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1160 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: 1160 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5932 ave 5932 max 5932 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: 90184 ave 90184 max 90184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90184 Ave neighs/atom = 77.7448 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) = 4.766 | 4.766 | 4.766 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 -4743.1285 -4743.1285 30.989387 124.19476 3.6270395 -1020.8068 -1020.8068 -6.0294312 -3064.8192 8.4283143 2.310726 449.38233 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1160 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: 1160 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5932 ave 5932 max 5932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45092 ave 45092 max 45092 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90184 ave 90184 max 90184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90184 Ave neighs/atom = 77.7448 Neighbor list builds = 0 Dangerous builds = 0 1160 -1786.14772044442 eV 2.31072596055254 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:28