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 = 3.52264 3.52264 3.52264 Created orthogonal box = (0 -46.0681 0) to (21.715 46.0681 4.98177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.57158 5.65705 4.98177 Created 459 atoms create_atoms CPU = 0.000396013 secs 459 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.57158 5.65705 4.98177 Created 459 atoms create_atoms CPU = 0.000259876 secs 459 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 11.7548 ghost atom cutoff = 11.7548 binsize = 5.87738, bins = 4 16 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 11.7548 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 896 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 = 11.7548 ghost atom cutoff = 11.7548 binsize = 5.87738, bins = 4 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7548 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) = 6.695 | 6.695 | 6.695 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3733.2366 0 -3733.2366 765.71432 75 0 -3771.9555 0 -3771.9555 -23141.23 Loop time of 1.99645 on 1 procs for 75 steps with 896 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3733.2366052 -3771.95174545 -3771.95550182 Force two-norm initial, final = 24.9996 0.275879 Force max component initial, final = 3.45294 0.034114 Final line search alpha, max atom move = 1 0.034114 Iterations, force evaluations = 75 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9707 | 1.9707 | 1.9707 | 0.0 | 98.71 Neigh | 0.0084598 | 0.0084598 | 0.0084598 | 0.0 | 0.42 Comm | 0.012733 | 0.012733 | 0.012733 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004542 | | | 0.23 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12513 ave 12513 max 12513 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: 550234 ave 550234 max 550234 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 550234 Ave neighs/atom = 614.1 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 : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.695 | 6.695 | 6.695 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -3771.9555 0 -3771.9555 -23141.23 9967.2136 90 0 -3773.0876 0 -3773.0876 -7400.5293 9878.2039 Loop time of 0.182358 on 1 procs for 15 steps with 896 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3771.95550182 -3773.08740205 -3773.08756579 Force two-norm initial, final = 167.85 1.0396 Force max component initial, final = 166.9 0.513469 Final line search alpha, max atom move = 0.00125553 0.000644675 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17861 | 0.17861 | 0.17861 | 0.0 | 97.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010645 | 0.0010645 | 0.0010645 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00268 | | | 1.47 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12511 ave 12511 max 12511 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: 549608 ave 549608 max 549608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 549608 Ave neighs/atom = 613.402 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 = 11.7548 ghost atom cutoff = 11.7548 binsize = 5.87738, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7548 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) = 6.834 | 6.834 | 6.834 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3773.0876 0 -3773.0876 -7400.5293 Loop time of 1.90735e-06 on 1 procs for 0 steps with 896 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: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12649 ave 12649 max 12649 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: 551984 ave 551984 max 551984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 551984 Ave neighs/atom = 616.054 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) = 6.834 | 6.834 | 6.834 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 -3773.0876 -3773.0876 21.407663 92.136101 5.008168 -7400.5293 -7400.5293 65.043627 -22182.909 -83.722495 2.2644237 433.15718 Loop time of 2.14577e-06 on 1 procs for 0 steps with 896 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: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12649 ave 12649 max 12649 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 275992 ave 275992 max 275992 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 551984 ave 551984 max 551984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 551984 Ave neighs/atom = 616.054 Neighbor list builds = 0 Dangerous builds = 0 896 -3773.0875657915 eV 2.26442367198876 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02