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 = 3.61481 3.61481 3.61481 Created orthogonal box = (0 -43.6816 0) to (53.4944 43.6816 8.85445) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1296 5.38495 5.90297 Created 1757 atoms create_atoms CPU = 0.000658035 secs 1757 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1296 5.38495 5.90297 Created 1757 atoms create_atoms CPU = 0.000561953 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 10 16 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 11.0375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 3492 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.0375 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) = 15.35 | 15.35 | 15.35 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12215.006 0 -12215.006 10548.834 48 0 -12324.016 0 -12324.016 -2428.8461 Loop time of 3.0406 on 1 procs for 48 steps with 3492 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12215.0058135 -12324.0044973 -12324.015934 Force two-norm initial, final = 68.6612 0.296592 Force max component initial, final = 7.26477 0.032035 Final line search alpha, max atom move = 1 0.032035 Iterations, force evaluations = 48 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9469 | 2.9469 | 2.9469 | 0.0 | 96.92 Neigh | 0.077393 | 0.077393 | 0.077393 | 0.0 | 2.55 Comm | 0.010032 | 0.010032 | 0.010032 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006302 | | | 0.21 Nlocal: 3492 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17853 ave 17853 max 17853 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: 1.61163e+06 ave 1.61163e+06 max 1.61163e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1611634 Ave neighs/atom = 461.522 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 : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 15.36 | 15.36 | 15.36 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -12324.016 0 -12324.016 -2428.8461 41380.681 50 0 -12324.048 0 -12324.048 -829.63862 41331.616 Loop time of 0.215371 on 1 procs for 2 steps with 3492 atoms 102.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12324.015934 -12324.0457859 -12324.0477904 Force two-norm initial, final = 66.7657 0.304944 Force max component initial, final = 57.2003 0.0356973 Final line search alpha, max atom move = 0.000116024 4.14176e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21328 | 0.21328 | 0.21328 | 0.0 | 99.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005734 | 0.0005734 | 0.0005734 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001515 | | | 0.70 Nlocal: 3492 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17854 ave 17854 max 17854 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: 1.61133e+06 ave 1.61133e+06 max 1.61133e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1611334 Ave neighs/atom = 461.436 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.0375 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) = 14.87 | 14.87 | 14.87 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12324.048 0 -12324.048 -829.63862 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3492 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 | | 9.537e-07 | | |100.00 Nlocal: 3492 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17875 ave 17875 max 17875 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: 1.61202e+06 ave 1.61202e+06 max 1.61202e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1612020 Ave neighs/atom = 461.632 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) = 14.87 | 14.87 | 14.87 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 -12324.048 -12324.048 53.440804 87.363139 8.8528106 -829.63862 -829.63862 -1.0760764 -2486.4563 -1.3835138 2.3356099 1416.0181 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3492 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 | | 9.537e-07 | | |100.00 Nlocal: 3492 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17875 ave 17875 max 17875 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 806010 ave 806010 max 806010 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.61202e+06 ave 1.61202e+06 max 1.61202e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1612020 Ave neighs/atom = 461.632 Neighbor list builds = 0 Dangerous builds = 0 3492 -12324.0477903917 eV 2.3356098832413 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03