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 = 3.49194 3.49194 3.49194 Created orthogonal box = (0 -40.4256 0) to (28.5827 40.4256 4.93835) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.54591 6.03315 4.93835 Created 538 atoms create_atoms CPU = 0.000477076 secs 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.54591 6.03315 4.93835 Created 538 atoms create_atoms CPU = 0.000332117 secs 538 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 9 24 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 6.85342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1060 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85342 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) = 5.011 | 5.011 | 5.011 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4668.6608 0 -4668.6608 6138.4422 84 0 -4697.7366 0 -4697.7366 -15437.677 Loop time of 1.02598 on 1 procs for 84 steps with 1060 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 = -4668.6607963 -4697.73194488 -4697.73659694 Force two-norm initial, final = 39.555 0.259335 Force max component initial, final = 11.4004 0.0326664 Final line search alpha, max atom move = 1 0.0326664 Iterations, force evaluations = 84 154 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0096 | 1.0096 | 1.0096 | 0.0 | 98.41 Neigh | 0.0060811 | 0.0060811 | 0.0060811 | 0.0 | 0.59 Comm | 0.0062528 | 0.0062528 | 0.0062528 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004017 | | | 0.39 Nlocal: 1060 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6236 ave 6236 max 6236 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: 141148 ave 141148 max 141148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141148 Ave neighs/atom = 133.158 Neighbor list builds = 2 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 : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.011 | 5.011 | 5.011 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -4697.7366 0 -4697.7366 -15437.677 11412.272 92 0 -4698.3013 0 -4698.3013 -3318.4723 11333.65 Loop time of 0.0671201 on 1 procs for 8 steps with 1060 atoms 104.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4697.73659694 -4698.30106392 -4698.30125387 Force two-norm initial, final = 169.844 0.906503 Force max component initial, final = 160.208 0.817446 Final line search alpha, max atom move = 0.000318133 0.000260056 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.065622 | 0.065622 | 0.065622 | 0.0 | 97.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033283 | 0.00033283 | 0.00033283 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001165 | | | 1.74 Nlocal: 1060 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6228 ave 6228 max 6228 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: 141176 ave 141176 max 141176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141176 Ave neighs/atom = 133.185 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85342 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) = 5.149 | 5.149 | 5.149 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4698.3013 0 -4698.3013 -3318.4723 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1060 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: 1060 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6236 ave 6236 max 6236 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: 141420 ave 141420 max 141420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141420 Ave neighs/atom = 133.415 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) = 5.149 | 5.149 | 5.149 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 -4698.3013 -4698.3013 28.383565 80.851207 4.9387423 -3318.4723 -3318.4723 -114.7526 -9865.5217 24.857473 2.3148391 638.67777 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1060 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: 1060 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6236 ave 6236 max 6236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70710 ave 70710 max 70710 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 141420 ave 141420 max 141420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141420 Ave neighs/atom = 133.415 Neighbor list builds = 0 Dangerous builds = 0 1060 -4698.30125387059 eV 2.31483911377651 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01