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 = 4.0398 4.0398 4.0398 Created orthogonal box = (0 -73.1679 0) to (25.8673 73.1679 5.71314) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.94002 6.2457 5.71314 Created 658 atoms create_atoms CPU = 0.00169206 secs 658 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.94002 6.2457 5.71314 Created 658 atoms create_atoms CPU = 0.00140882 secs 658 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 5 25 1 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 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 5 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 6.775 | 6.775 | 6.775 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3723.1241 0 -3723.1241 2527.5623 48 0 -3757.2802 0 -3757.2802 -3448.1864 Loop time of 1.57453 on 1 procs for 48 steps with 1304 atoms 94.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3723.12407561 -3757.27692641 -3757.28017034 Force two-norm initial, final = 30.8728 0.177407 Force max component initial, final = 7.32617 0.0142337 Final line search alpha, max atom move = 1 0.0142337 Iterations, force evaluations = 48 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5455 | 1.5455 | 1.5455 | 0.0 | 98.16 Neigh | 0.015863 | 0.015863 | 0.015863 | 0.0 | 1.01 Comm | 0.0090458 | 0.0090458 | 0.0090458 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004091 | | | 0.26 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13176 ave 13176 max 13176 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: 537476 ave 537476 max 537476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 537476 Ave neighs/atom = 412.175 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 : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.775 | 6.775 | 6.775 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -3757.2802 0 -3757.2802 -3448.1864 21626.036 52 0 -3757.3916 0 -3757.3916 -1159.7658 21560.118 Loop time of 0.13632 on 1 procs for 4 steps with 1304 atoms 90.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3757.28017034 -3757.38996387 -3757.39156002 Force two-norm initial, final = 66.5823 0.4128 Force max component initial, final = 66.4652 0.313512 Final line search alpha, max atom move = 0.000155101 4.86259e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13379 | 0.13379 | 0.13379 | 0.0 | 98.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00065637 | 0.00065637 | 0.00065637 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001877 | | | 1.38 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13186 ave 13186 max 13186 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: 519448 ave 519448 max 519448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 519448 Ave neighs/atom = 398.35 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 5 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 6.913 | 6.913 | 6.913 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3757.3916 0 -3757.3916 -1159.7658 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1304 atoms 186.4% 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 | | 2.146e-06 | | |100.00 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13186 ave 13186 max 13186 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: 528744 ave 528744 max 528744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 528744 Ave neighs/atom = 405.479 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) = 6.913 | 6.913 | 6.913 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 -3757.3916 -3757.3916 25.875416 146.3358 5.6939441 -1159.7658 -1159.7658 23.304984 -3515.0245 12.422095 2.6471666 642.47863 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1304 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: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13186 ave 13186 max 13186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 264372 ave 264372 max 264372 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 528744 ave 528744 max 528744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 528744 Ave neighs/atom = 405.479 Neighbor list builds = 0 Dangerous builds = 0 1304 -3757.39156002418 eV 2.64716658084208 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02