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 -65.2898 0) to (23.0822 65.2898 4.97803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.90474 6.07314 4.97803 Created 690 atoms create_atoms CPU = 0.000715017 secs 690 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.90474 6.07314 4.97803 Created 690 atoms create_atoms CPU = 0.000570059 secs 690 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 6 30 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 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1368 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 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) = 5.964 | 5.964 | 5.964 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6054.6182 0 -6054.6182 2173.576 80 0 -6076.1987 0 -6076.1987 -6572.3433 Loop time of 1.33803 on 1 procs for 80 steps with 1368 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6054.61822969 -6076.19278521 -6076.19867865 Force two-norm initial, final = 18.5224 0.260747 Force max component initial, final = 5.45614 0.0285669 Final line search alpha, max atom move = 1 0.0285669 Iterations, force evaluations = 80 144 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3117 | 1.3117 | 1.3117 | 0.0 | 98.03 Neigh | 0.0097132 | 0.0097132 | 0.0097132 | 0.0 | 0.73 Comm | 0.010897 | 0.010897 | 0.010897 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005697 | | | 0.43 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11581 ave 11581 max 11581 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: 337612 ave 337612 max 337612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337612 Ave neighs/atom = 246.792 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 : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.964 | 5.964 | 5.964 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -6076.1987 0 -6076.1987 -6572.3433 15004.097 82 0 -6076.2369 0 -6076.2369 -3143.6858 14975.262 Loop time of 0.041225 on 1 procs for 2 steps with 1368 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 = -6076.19867865 -6076.23610486 -6076.23693623 Force two-norm initial, final = 55.5702 2.52415 Force max component initial, final = 45.6764 2.51025 Final line search alpha, max atom move = 0.000139313 0.00034971 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040049 | 0.040049 | 0.040049 | 0.0 | 97.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032353 | 0.00032353 | 0.00032353 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008526 | | | 2.07 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11485 ave 11485 max 11485 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: 338340 ave 338340 max 338340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338340 Ave neighs/atom = 247.325 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 = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 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) = 6.102 | 6.102 | 6.102 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6076.2369 0 -6076.2369 -3143.6858 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1368 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: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11551 ave 11551 max 11551 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: 338432 ave 338432 max 338432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338432 Ave neighs/atom = 247.392 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) = 6.102 | 6.102 | 6.102 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 -6076.2369 -6076.2369 23.053778 130.57959 4.9745868 -3143.6858 -3143.6858 -0.12917424 -9699.31 268.38174 2.2894804 354.62024 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1368 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: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11551 ave 11551 max 11551 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 169216 ave 169216 max 169216 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 338432 ave 338432 max 338432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338432 Ave neighs/atom = 247.392 Neighbor list builds = 0 Dangerous builds = 0 1368 -6045.38901481885 eV 2.28948044927394 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01