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 = 3.615 3.615 3.615 Created orthogonal box = (0 -71.577 0) to (43.8296 71.577 8.85491) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.06873 5.11238 5.90327 Created 2358 atoms create_atoms CPU = 0.000899076 secs 2358 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.06873 5.11238 5.90327 Created 2358 atoms create_atoms CPU = 0.000753164 secs 2358 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 11 34 3 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 4668 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 11 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 12.83 | 12.83 | 12.83 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16443.142 0 -16443.142 -1126.0986 24 0 -16478.559 0 -16478.559 -5566.7138 Loop time of 0.834102 on 1 procs for 24 steps with 4668 atoms 100.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -16443.1416265 -16478.5495952 -16478.5594635 Force two-norm initial, final = 43.2826 0.317992 Force max component initial, final = 8.51782 0.0423763 Final line search alpha, max atom move = 1 0.0423763 Iterations, force evaluations = 24 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82535 | 0.82535 | 0.82535 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0045011 | 0.0045011 | 0.0045011 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004252 | | | 0.51 Nlocal: 4668 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16410 ave 16410 max 16410 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: 930060 ave 930060 max 930060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 930060 Ave neighs/atom = 199.242 Neighbor list builds = 0 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 : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.83 | 12.83 | 12.83 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -16478.559 0 -16478.559 -5566.7138 55559.044 27 0 -16478.904 0 -16478.904 -614.27978 55359.098 Loop time of 0.11319 on 1 procs for 3 steps with 4668 atoms 97.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -16478.5594635 -16478.9032566 -16478.9041308 Force two-norm initial, final = 269.636 0.363021 Force max component initial, final = 192.664 0.0347463 Final line search alpha, max atom move = 0.000166225 5.7757e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11078 | 0.11078 | 0.11078 | 0.0 | 97.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052094 | 0.00052094 | 0.00052094 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00189 | | | 1.67 Nlocal: 4668 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16410 ave 16410 max 16410 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: 935832 ave 935832 max 935832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 935832 Ave neighs/atom = 200.478 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 11 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 12.34 | 12.34 | 12.34 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16478.904 0 -16478.904 -614.27978 Loop time of 1.19209e-06 on 1 procs for 0 steps with 4668 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 | | 1.192e-06 | | |100.00 Nlocal: 4668 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16410 ave 16410 max 16410 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: 937224 ave 937224 max 937224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 937224 Ave neighs/atom = 200.776 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) = 12.34 | 12.34 | 12.34 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 -16478.904 -16478.904 43.741705 143.15399 8.8407647 -614.27978 -614.27978 -0.46174117 -1841.4214 -0.95622813 2.2685959 1772.7267 Loop time of 1.90735e-06 on 1 procs for 0 steps with 4668 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: 4668 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16410 ave 16410 max 16410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 468612 ave 468612 max 468612 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 937224 ave 937224 max 937224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 937224 Ave neighs/atom = 200.776 Neighbor list builds = 0 Dangerous builds = 0 4668 -16478.9041307687 eV 2.26859587880613 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01