LAMMPS (19 Mar 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.63909 3.63909 3.63909 Created orthogonal box = (0 -62.6129 0) to (31.3046 62.6129 3.63909) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.07642 5.07642 3.63909 Created 593 atoms create_atoms CPU = 0.000515938 secs 593 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.07642 5.07642 3.63909 Created 593 atoms create_atoms CPU = 0.000374079 secs 593 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 27 1 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1180 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.904 | 5.904 | 5.904 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3844.9954 0 -3844.9954 5279.6581 71 0 -3863.3241 0 -3863.3241 -464.25202 Loop time of 1.1756 on 1 procs for 71 steps with 1180 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3844.99542648 -3863.320492 -3863.32405519 Force two-norm initial, final = 20.9372 0.151883 Force max component initial, final = 7.38445 0.0122728 Final line search alpha, max atom move = 1 0.0122728 Iterations, force evaluations = 71 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1528 | 1.1528 | 1.1528 | 0.0 | 98.06 Neigh | 0.0093341 | 0.0093341 | 0.0093341 | 0.0 | 0.79 Comm | 0.0097616 | 0.0097616 | 0.0097616 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003754 | | | 0.32 Nlocal: 1180 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13071 ave 13071 max 13071 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: 375536 ave 375536 max 375536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 375536 Ave neighs/atom = 318.251 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) 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) = 5.907 | 5.907 | 5.907 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -3863.3241 0 -3863.3241 -464.25202 14265.744 72 0 -3863.3278 0 -3863.3278 553.6742 14255.681 Loop time of 0.0330889 on 1 procs for 1 steps with 1180 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3863.32405519 -3863.32405519 -3863.327796 Force two-norm initial, final = 14.9285 0.194333 Force max component initial, final = 11.4677 0.0947924 Final line search alpha, max atom move = 8.72012e-05 8.26601e-06 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.03239 | 0.03239 | 0.03239 | 0.0 | 97.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022078 | 0.00022078 | 0.00022078 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000478 | | | 1.44 Nlocal: 1180 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13077 ave 13077 max 13077 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: 375422 ave 375422 max 375422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 375422 Ave neighs/atom = 318.154 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.045 | 6.045 | 6.045 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3863.3278 0 -3863.3278 553.6742 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1180 atoms 209.7% 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: 1180 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13077 ave 13077 max 13077 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: 375454 ave 375454 max 375454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 375454 Ave neighs/atom = 318.181 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) = 6.045 | 6.045 | 6.045 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 -3863.3278 -3863.3278 31.292567 125.22573 3.6379204 553.6742 553.6742 8.3242735 1663.3485 -10.650176 2.2808435 313.919 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1180 atoms 209.7% 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: 1180 ave 1180 max 1180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13077 ave 13077 max 13077 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 187727 ave 187727 max 187727 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 375454 ave 375454 max 375454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 375454 Ave neighs/atom = 318.181 Neighbor list builds = 0 Dangerous builds = 0 1180 -3863.32779600006 eV 2.28084347210568 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01