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 = 4.03204 4.03204 4.03204 Created orthogonal box = (0 -48.7233 0) to (59.6687 48.7233 9.87644) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.72166 6.00649 6.58429 Created 1755 atoms create_atoms CPU = 0.000729084 secs 1755 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.72166 6.00649 6.58429 Created 1755 atoms create_atoms CPU = 0.000609875 secs 1755 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 14 23 3 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 54 atoms, new total = 3456 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.398 | 7.398 | 7.398 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11535.007 0 -11535.007 266.4479 71 0 -11584.791 0 -11584.791 -7074.3444 Loop time of 1.61233 on 1 procs for 71 steps with 3456 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11535.0069566 -11584.7807636 -11584.7910749 Force two-norm initial, final = 35.7454 0.272308 Force max component initial, final = 6.08196 0.0519089 Final line search alpha, max atom move = 1 0.0519089 Iterations, force evaluations = 71 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5639 | 1.5639 | 1.5639 | 0.0 | 97.00 Neigh | 0.029543 | 0.029543 | 0.029543 | 0.0 | 1.83 Comm | 0.0090687 | 0.0090687 | 0.0090687 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009794 | | | 0.61 Nlocal: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10987 ave 10987 max 10987 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: 593456 ave 593456 max 593456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 593456 Ave neighs/atom = 171.718 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 : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.399 | 7.399 | 7.399 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -11584.791 0 -11584.791 -7074.3444 57426.714 76 0 -11585.517 0 -11585.517 -1724.2788 57054.637 Loop time of 0.0792139 on 1 procs for 5 steps with 3456 atoms 101.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11584.7910749 -11585.5153977 -11585.5174235 Force two-norm initial, final = 308.105 0.38337 Force max component initial, final = 234.339 0.0440987 Final line search alpha, max atom move = 0.000121848 5.37336e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.077017 | 0.077017 | 0.077017 | 0.0 | 97.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042582 | 0.00042582 | 0.00042582 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001771 | | | 2.24 Nlocal: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10973 ave 10973 max 10973 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: 593222 ave 593222 max 593222 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 593222 Ave neighs/atom = 171.65 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 7.537 | 7.537 | 7.537 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11585.517 0 -11585.517 -1724.2788 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3456 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: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10994 ave 10994 max 10994 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: 595062 ave 595062 max 595062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 595062 Ave neighs/atom = 172.182 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) = 7.537 | 7.537 | 7.537 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 -11585.517 -11585.517 59.519912 97.44667 9.8369772 -1724.2788 -1724.2788 -1.1557201 -5171.0466 -0.63426972 2.574786 2258.8733 Loop time of 2.14577e-06 on 1 procs for 0 steps with 3456 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 | | 2.146e-06 | | |100.00 Nlocal: 3456 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10994 ave 10994 max 10994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 297531 ave 297531 max 297531 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 595062 ave 595062 max 595062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 595062 Ave neighs/atom = 172.182 Neighbor list builds = 0 Dangerous builds = 0 3456 -11585.5174235498 eV 2.57478600100708 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01