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 = 3.51623 3.51623 3.51623 Created orthogonal box = (0 -45.5791 0) to (26.3131 45.5791 6.09029) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.63852 5.42566 6.09029 Created 676 atoms create_atoms CPU = 0.00050807 secs 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.63852 5.42566 6.09029 Created 676 atoms create_atoms CPU = 0.000356913 secs 676 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 6 21 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 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1328 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.926 | 5.926 | 5.926 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6397.7648 0 -6397.7648 14992.394 63 0 -6447.0379 0 -6447.0379 -13885.127 Loop time of 1.0379 on 1 procs for 63 steps with 1328 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 = -6397.76481192 -6447.03157944 -6447.03793893 Force two-norm initial, final = 97.0915 0.276103 Force max component initial, final = 19.3055 0.0368356 Final line search alpha, max atom move = 1 0.0368356 Iterations, force evaluations = 63 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0167 | 1.0167 | 1.0167 | 0.0 | 97.96 Neigh | 0.010099 | 0.010099 | 0.010099 | 0.0 | 0.97 Comm | 0.0070841 | 0.0070841 | 0.0070841 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004025 | | | 0.39 Nlocal: 1328 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9273 ave 9273 max 9273 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: 331824 ave 331824 max 331824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331824 Ave neighs/atom = 249.867 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.926 | 5.926 | 5.926 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -6447.0379 0 -6447.0379 -13885.127 14608.501 67 0 -6447.2013 0 -6447.2013 -7138.9367 14550.842 Loop time of 0.0517969 on 1 procs for 4 steps with 1328 atoms 96.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6447.03793893 -6447.20010846 -6447.20127099 Force two-norm initial, final = 105.718 0.316473 Force max component initial, final = 91.0627 0.0331437 Final line search alpha, max atom move = 0.000140831 4.66767e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.050549 | 0.050549 | 0.050549 | 0.0 | 97.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031948 | 0.00031948 | 0.00031948 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009286 | | | 1.79 Nlocal: 1328 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9279 ave 9279 max 9279 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: 333616 ave 333616 max 333616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 333616 Ave neighs/atom = 251.217 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 6.064 | 6.064 | 6.064 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6447.2013 0 -6447.2013 -7138.9367 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1328 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: 1328 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9298 ave 9298 max 9298 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: 334312 ave 334312 max 334312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334312 Ave neighs/atom = 251.741 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) = 6.064 | 6.064 | 6.064 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 -6447.2013 -6447.2013 26.233757 91.158204 6.0845979 -7138.9367 -7138.9367 -0.52445713 -21413.011 -3.2749361 2.2346962 782.81809 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1328 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: 1328 ave 1328 max 1328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9298 ave 9298 max 9298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 167156 ave 167156 max 167156 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 334312 ave 334312 max 334312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334312 Ave neighs/atom = 251.741 Neighbor list builds = 0 Dangerous builds = 0 1328 -6447.2012709856 eV 2.23469619041879 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01