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 = 3.52 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 122 atoms create_atoms CPU = 0.000253201 secs 122 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.09682 5.74814 4.97803 Created 122 atoms create_atoms CPU = 0.000157118 secs 122 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 2 20 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 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 240 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 2 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 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) = 4.522 | 4.522 | 4.522 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1047.5581 0 -1047.5581 15881.792 85 0 -1064.2924 0 -1064.2924 6318.3162 Loop time of 0.309199 on 1 procs for 85 steps with 240 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1047.55806126 -1064.29132702 -1064.29236225 Force two-norm initial, final = 18.9199 0.106315 Force max component initial, final = 5.83475 0.0133047 Final line search alpha, max atom move = 1 0.0133047 Iterations, force evaluations = 85 158 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30023 | 0.30023 | 0.30023 | 0.0 | 97.10 Neigh | 0.0016661 | 0.0016661 | 0.0016661 | 0.0 | 0.54 Comm | 0.0052609 | 0.0052609 | 0.0052609 | 0.0 | 1.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002043 | | | 0.66 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5159 ave 5159 max 5159 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: 59180 ave 59180 max 59180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59180 Ave neighs/atom = 246.583 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 : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.522 | 4.522 | 4.522 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -1064.2924 0 -1064.2924 6318.3162 2617.0662 88 0 -1064.3115 0 -1064.3115 392.88076 2625.7336 Loop time of 0.012162 on 1 procs for 3 steps with 240 atoms 82.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1064.29236225 -1064.311457 -1064.3114693 Force two-norm initial, final = 16.3797 0.119998 Force max component initial, final = 11.6164 0.039509 Final line search alpha, max atom move = 0.00537323 0.000212291 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.011525 | 0.011525 | 0.011525 | 0.0 | 94.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017238 | 0.00017238 | 0.00017238 | 0.0 | 1.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004649 | | | 3.82 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5046 ave 5046 max 5046 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: 59584 ave 59584 max 59584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59584 Ave neighs/atom = 248.267 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 2 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 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) = 4.653 | 4.653 | 4.653 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1064.3115 0 -1064.3115 392.88076 Loop time of 9.53674e-07 on 1 procs for 0 steps with 240 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: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4448 ave 4448 max 4448 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: 59536 ave 59536 max 59536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59536 Ave neighs/atom = 248.067 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) = 4.653 | 4.653 | 4.653 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 -1064.3115 -1064.3115 6.1064442 86.22908 4.9866458 392.88076 392.88076 16.327646 1186.4641 -24.149441 2.3666093 125.9766 Loop time of 1.19209e-06 on 1 procs for 0 steps with 240 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 | | 1.192e-06 | | |100.00 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4448 ave 4448 max 4448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29768 ave 29768 max 29768 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 59536 ave 59536 max 59536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59536 Ave neighs/atom = 248.067 Neighbor list builds = 0 Dangerous builds = 0 240 -1058.89955325889 eV 2.36660928037378 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00