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 = 3.52 3.52 3.52 Created orthogonal box = (0 -52.0948 0) to (42.5323 52.0948 8.6222) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.24371 4.99505 5.74814 Created 1757 atoms create_atoms CPU = 0.000767946 secs 1757 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.24371 4.99505 5.74814 Created 1757 atoms create_atoms CPU = 0.000646114 secs 1757 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 11 25 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 42 atoms, new total = 3472 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 11.78 | 11.78 | 11.78 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15350.085 0 -15350.085 1096.5667 41 0 -15395.461 0 -15395.461 -6921.2373 Loop time of 1.10893 on 1 procs for 41 steps with 3472 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15350.0845349 -15395.4497857 -15395.461185 Force two-norm initial, final = 48.9836 0.384107 Force max component initial, final = 7.61525 0.0927934 Final line search alpha, max atom move = 0.94421 0.0876165 Iterations, force evaluations = 41 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0561 | 1.0561 | 1.0561 | 0.0 | 95.24 Neigh | 0.041215 | 0.041215 | 0.041215 | 0.0 | 3.72 Comm | 0.0058262 | 0.0058262 | 0.0058262 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005745 | | | 0.52 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12971 ave 12971 max 12971 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: 774442 ave 774442 max 774442 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774442 Ave neighs/atom = 223.054 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.78 | 11.78 | 11.78 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -15395.461 0 -15395.461 -6921.2373 38208.628 44 0 -15395.672 0 -15395.672 -1748.7957 38097.92 Loop time of 0.103096 on 1 procs for 3 steps with 3472 atoms 97.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15395.461185 -15395.6706088 -15395.671625 Force two-norm initial, final = 202.933 0.40833 Force max component initial, final = 150.847 0.0795365 Final line search alpha, max atom move = 0.000138334 1.10026e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10085 | 0.10085 | 0.10085 | 0.0 | 97.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047874 | 0.00047874 | 0.00047874 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001767 | | | 1.71 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12968 ave 12968 max 12968 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: 774346 ave 774346 max 774346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774346 Ave neighs/atom = 223.026 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 11.29 | 11.29 | 11.29 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15395.672 0 -15395.672 -1748.7957 Loop time of 1.19209e-06 on 1 procs for 0 steps with 3472 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: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12990 ave 12990 max 12990 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: 774582 ave 774582 max 774582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774582 Ave neighs/atom = 223.094 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) = 11.29 | 11.29 | 11.29 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 -15395.672 -15395.672 42.45827 104.18953 8.612216 -1748.7957 -1748.7957 -1.7563528 -5242.2747 -2.3560593 2.2230345 1472.4464 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3472 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 | | 1.907e-06 | | |100.00 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12990 ave 12990 max 12990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 387291 ave 387291 max 387291 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 774582 ave 774582 max 774582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 774582 Ave neighs/atom = 223.094 Neighbor list builds = 0 Dangerous builds = 0 3472 -15395.6716249679 eV 2.22303446932665 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01