LAMMPS (24 Jan 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 = 3.60735 3.60735 3.60735 Created orthogonal box = (0 -53.3876 0) to (43.5878 53.3876 8.83617) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.37384 5.11901 5.89078 Created 1756 atoms create_atoms CPU = 0.00195885 secs 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.37384 5.11901 5.89078 Created 1756 atoms create_atoms CPU = 0.00177813 secs 1756 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 8 18 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 3472 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 8 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 17.37 | 17.37 | 17.37 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12099.367 0 -12099.367 3147.197 51 0 -12195.974 0 -12195.974 -6731.7988 Loop time of 7.78786 on 1 procs for 51 steps with 3472 atoms 83.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12099.3669092 -12195.962099 -12195.9737618 Force two-norm initial, final = 60.832 0.441967 Force max component initial, final = 8.70062 0.0440015 Final line search alpha, max atom move = 1 0.0440015 Iterations, force evaluations = 51 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.6842 | 7.6842 | 7.6842 | 0.0 | 98.67 Neigh | 0.074695 | 0.074695 | 0.074695 | 0.0 | 0.96 Comm | 0.018193 | 0.018193 | 0.018193 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01076 | | | 0.14 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21352 ave 21352 max 21352 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: 2.16521e+06 ave 2.16521e+06 max 2.16521e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2165210 Ave neighs/atom = 623.62 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 17.76 | 17.76 | 17.76 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -12195.974 0 -12195.974 -6731.7988 41124.371 54 0 -12196.198 0 -12196.198 -2250.3311 40989.522 Loop time of 0.597302 on 1 procs for 3 steps with 3472 atoms 74.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12195.9737618 -12196.1971604 -12196.1984219 Force two-norm initial, final = 191.903 0.489155 Force max component initial, final = 140.69 0.0594421 Final line search alpha, max atom move = 0.000130146 7.73614e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.5929 | 0.5929 | 0.5929 | 0.0 | 99.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011513 | 0.0011513 | 0.0011513 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003254 | | | 0.54 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21421 ave 21421 max 21421 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: 2.16895e+06 ave 2.16895e+06 max 2.16895e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2168952 Ave neighs/atom = 624.698 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 8 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 17.27 | 17.27 | 17.27 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12196.198 0 -12196.198 -2250.3311 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3472 atoms 419.4% 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: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21421 ave 21421 max 21421 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: 2.17009e+06 ave 2.17009e+06 max 2.17009e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2170092 Ave neighs/atom = 625.026 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) = 17.27 | 17.27 | 17.27 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 -12196.198 -12196.198 43.50283 106.7751 8.824403 -2250.3311 -2250.3311 -1.2773791 -6747.8892 -1.8266471 2.2584989 1503.4578 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3472 atoms 157.3% 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: 21421 ave 21421 max 21421 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.08505e+06 ave 1.08505e+06 max 1.08505e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.17009e+06 ave 2.17009e+06 max 2.17009e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2170092 Ave neighs/atom = 625.026 Neighbor list builds = 0 Dangerous builds = 0 3472 -12196.1984219125 eV 2.25849892688286 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09