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 = 3.63552 3.63552 3.63552 Created orthogonal box = (0 -40.65 0) to (19.9126 40.65 8.90517) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.31002 4.87756 5.93678 Created 612 atoms create_atoms CPU = 0.000237942 secs 612 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.31002 4.87756 5.93678 Created 612 atoms create_atoms CPU = 0.000140905 secs 612 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 7 28 4 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 1176 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 7 28 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.548 | 4.548 | 4.548 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4789.7298 0 -4789.7298 -10218.109 26 0 -4800.9895 0 -4800.9895 -18367.737 Loop time of 5.30587 on 1 procs for 26 steps with 1176 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 = -4789.72983007 -4800.98514854 -4800.98949188 Force two-norm initial, final = 5.12266 0.151944 Force max component initial, final = 0.642677 0.0124684 Final line search alpha, max atom move = 1 0.0124684 Iterations, force evaluations = 26 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3039 | 5.3039 | 5.3039 | 0.0 | 99.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0009439 | 0.0009439 | 0.0009439 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001012 | | | 0.02 Nlocal: 1176 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3609 ave 3609 max 3609 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: 89760 ave 89760 max 89760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 89760 Ave neighs/atom = 76.3265 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 : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.549 | 4.549 | 4.549 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -4800.9895 0 -4800.9895 -18367.737 14416.516 32 0 -4801.6299 0 -4801.6299 -4967.6685 14277.47 Loop time of 0.874329 on 1 procs for 6 steps with 1176 atoms 100.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4800.98949188 -4801.62773487 -4801.62985961 Force two-norm initial, final = 188.742 4.20996 Force max component initial, final = 136.5 4.13227 Final line search alpha, max atom move = 0.000125519 0.000518679 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.87357 | 0.87357 | 0.87357 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014877 | 0.00014877 | 0.00014877 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006092 | | | 0.07 Nlocal: 1176 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3732 ave 3732 max 3732 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: 90192 ave 90192 max 90192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90192 Ave neighs/atom = 76.6939 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 7 28 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.687 | 4.687 | 4.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4801.6299 0 -4801.6299 -4967.6685 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1176 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: 1176 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3782 ave 3782 max 3782 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: 90288 ave 90288 max 90288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90288 Ave neighs/atom = 76.7755 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) = 4.687 | 4.687 | 4.687 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 -4801.6299 -4801.6299 19.802759 81.300008 8.8681895 -4967.6685 -4967.6685 82.240853 -15447.032 461.78529 2.3459903 660.55601 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1176 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: 1176 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3782 ave 3782 max 3782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45144 ave 45144 max 45144 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90288 ave 90288 max 90288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90288 Ave neighs/atom = 76.7755 Neighbor list builds = 0 Dangerous builds = 0 1176 -4123.7465687224 eV 2.34599030304712 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06