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 = 3.39012 3.39012 3.39012 Created orthogonal box = (0 -43.4181 0) to (30.6988 43.4181 4.79435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.24126 5.82392 4.79435 Created 330 atoms create_atoms CPU = 0.000331879 secs 330 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.24126 5.82392 4.79435 Created 330 atoms create_atoms CPU = 0.000234842 secs 330 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.2653, bins = 3 9 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 20.5307 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 655 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.2653, bins = 3 9 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 13.3 | 13.3 | 13.3 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 6439.2841 0 6439.2841 15521332 267 0 -23623.511 0 -23623.511 -107409.5 Loop time of 3.52975 on 1 procs for 267 steps with 655 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 = 6439.2840961 -23623.4880457 -23623.5110798 Force two-norm initial, final = 110826 3.24124 Force max component initial, final = 28212.8 1.09366 Final line search alpha, max atom move = 0.0948099 0.10369 Iterations, force evaluations = 267 493 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1735 | 3.1735 | 3.1735 | 0.0 | 89.91 Neigh | 0.277 | 0.277 | 0.277 | 0.0 | 7.85 Comm | 0.06546 | 0.06546 | 0.06546 | 0.0 | 1.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01383 | | | 0.39 Nlocal: 655 ave 655 max 655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 21835 ave 21835 max 21835 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: 1.21391e+06 ave 1.21391e+06 max 1.21391e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1213914 Ave neighs/atom = 1853.3 Neighbor list builds = 12 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 : 267 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.31 | 13.31 | 13.31 Mbytes Step Temp E_pair E_mol TotEng Press Volume 267 0 -23623.511 0 -23623.511 -107409.5 12780.613 310 0 -23766.083 0 -23766.083 203457.19 12571.096 Loop time of 0.390602 on 1 procs for 43 steps with 655 atoms 102.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -23623.5110798 -23766.0620878 -23766.082735 Force two-norm initial, final = 7077.88 38.8045 Force max component initial, final = 6637.15 14.2645 Final line search alpha, max atom move = 1.00195e-05 0.000142923 Iterations, force evaluations = 43 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35141 | 0.35141 | 0.35141 | 0.0 | 89.97 Neigh | 0.016475 | 0.016475 | 0.016475 | 0.0 | 4.22 Comm | 0.0064042 | 0.0064042 | 0.0064042 | 0.0 | 1.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01631 | | | 4.18 Nlocal: 655 ave 655 max 655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19982 ave 19982 max 19982 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: 1.23617e+06 ave 1.23617e+06 max 1.23617e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1236172 Ave neighs/atom = 1887.29 Neighbor list builds = 1 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 = 20.5307 ghost atom cutoff = 20.5307 binsize = 10.2653, bins = 3 9 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 20.5307 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) = 12.81 | 12.81 | 12.81 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -23766.083 0 -23766.083 203457.19 Loop time of 1.19209e-06 on 1 procs for 0 steps with 655 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: 655 ave 655 max 655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19982 ave 19982 max 19982 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: 1.23606e+06 ave 1.23606e+06 max 1.23606e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1236060 Ave neighs/atom = 1887.11 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) = 12.81 | 12.81 | 12.81 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 -23766.083 -23766.083 29.70668 86.836133 4.8732485 203457.19 203457.19 -76.493392 612296 -1847.9205 2.7078451 4599.9577 Loop time of 9.53674e-07 on 1 procs for 0 steps with 655 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: 655 ave 655 max 655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19982 ave 19982 max 19982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 618030 ave 618030 max 618030 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.23606e+06 ave 1.23606e+06 max 1.23606e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1236060 Ave neighs/atom = 1887.11 Neighbor list builds = 0 Dangerous builds = 0 655 -23766.0827350227 eV 2.70784510562226 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04