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 = 3.60566 3.60566 3.60566 Created orthogonal box = (0 -49.5733 0) to (13.4912 49.5733 8.83204) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.78192 5.50774 5.88802 Created 508 atoms create_atoms CPU = 0.000411034 secs 508 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.78192 5.50774 5.88802 Created 508 atoms create_atoms CPU = 0.000263214 secs 508 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 = 7.67337 ghost atom cutoff = 7.67337 binsize = 3.83668, bins = 4 26 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 7.67337 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 992 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 = 7.67337 ghost atom cutoff = 7.67337 binsize = 3.83668, bins = 4 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.67337 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) = 5.041 | 5.041 | 5.041 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4119.8197 0 -4119.8197 -5285.8022 479 0 -4183.8756 0 -4183.8756 -36385.56 Loop time of 3.0013 on 1 procs for 479 steps with 992 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 = -4119.8197464 -4183.87185273 -4183.87558736 Force two-norm initial, final = 7.58815 0.195608 Force max component initial, final = 1.33609 0.0166506 Final line search alpha, max atom move = 1 0.0166506 Iterations, force evaluations = 479 906 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8839 | 2.8839 | 2.8839 | 0.0 | 96.09 Neigh | 0.066679 | 0.066679 | 0.066679 | 0.0 | 2.22 Comm | 0.029965 | 0.029965 | 0.029965 | 0.0 | 1.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02078 | | | 0.69 Nlocal: 992 ave 992 max 992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5709 ave 5709 max 5709 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: 154196 ave 154196 max 154196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154196 Ave neighs/atom = 155.44 Neighbor list builds = 15 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 : 479 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.042 | 5.042 | 5.042 Mbytes Step Temp E_pair E_mol TotEng Press Volume 479 0 -4183.8756 0 -4183.8756 -36385.56 11813.749 532 0 -4203.5732 0 -4203.5732 -16446.489 11797.328 Loop time of 0.15969 on 1 procs for 53 steps with 992 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4183.87558736 -4203.57068366 -4203.57322377 Force two-norm initial, final = 737.322 2.29109 Force max component initial, final = 694.957 0.720513 Final line search alpha, max atom move = 0.000191248 0.000137796 Iterations, force evaluations = 53 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15248 | 0.15248 | 0.15248 | 0.0 | 95.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015376 | 0.0015376 | 0.0015376 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005669 | | | 3.55 Nlocal: 992 ave 992 max 992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5732 ave 5732 max 5732 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: 154250 ave 154250 max 154250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154250 Ave neighs/atom = 155.494 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 = 7.67337 ghost atom cutoff = 7.67337 binsize = 3.83668, bins = 4 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.67337 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) = 5.179 | 5.179 | 5.179 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4203.5732 0 -4203.5732 -16446.489 Loop time of 9.53674e-07 on 1 procs for 0 steps with 992 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: 992 ave 992 max 992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5680 ave 5680 max 5680 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: 159588 ave 159588 max 159588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159588 Ave neighs/atom = 160.875 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) = 5.179 | 5.179 | 5.179 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 -4203.5732 -4203.5732 12.927388 99.146569 9.2043932 -16446.489 -16446.489 43.829544 -49281.319 -101.97708 2.3592804 644.33952 Loop time of 2.14577e-06 on 1 procs for 0 steps with 992 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: 992 ave 992 max 992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5680 ave 5680 max 5680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79794 ave 79794 max 79794 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 159588 ave 159588 max 159588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159588 Ave neighs/atom = 160.875 Neighbor list builds = 0 Dangerous builds = 0 992 -4203.57322377403 eV 2.35928042256901 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03