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 = 4.03299 4.03299 4.03299 Created orthogonal box = (0 -55.4485 0) to (15.0901 55.4485 9.87876) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.46717 6.16049 6.58584 Created 508 atoms create_atoms CPU = 0.000858068 secs 508 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.46717 6.16049 6.58584 Created 508 atoms create_atoms CPU = 0.00059104 secs 508 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 17 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1000 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 7.221 | 7.221 | 7.221 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2868.8882 0 -2868.8882 4310.3804 62 0 -2908.3615 0 -2908.3615 -3565.9601 Loop time of 2.7817 on 1 procs for 62 steps with 1000 atoms 96.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2868.88822681 -2908.3586685 -2908.36147738 Force two-norm initial, final = 36.1825 0.160573 Force max component initial, final = 7.55456 0.0154762 Final line search alpha, max atom move = 1 0.0154762 Iterations, force evaluations = 62 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7401 | 2.7401 | 2.7401 | 0.0 | 98.50 Neigh | 0.024176 | 0.024176 | 0.024176 | 0.0 | 0.87 Comm | 0.012819 | 0.012819 | 0.012819 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004639 | | | 0.17 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12244 ave 12244 max 12244 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: 664832 ave 664832 max 664832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 664832 Ave neighs/atom = 664.832 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.223 | 7.223 | 7.223 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -2908.3615 0 -2908.3615 -3565.9601 16531.531 65 0 -2908.4015 0 -2908.4015 -1528.035 16485.328 Loop time of 0.164809 on 1 procs for 3 steps with 1000 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2908.36147738 -2908.40125596 -2908.40151757 Force two-norm initial, final = 36.8359 0.16199 Force max component initial, final = 32.2005 0.0184141 Final line search alpha, max atom move = 0.000452508 8.33251e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16242 | 0.16242 | 0.16242 | 0.0 | 98.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064778 | 0.00064778 | 0.00064778 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001737 | | | 1.05 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12484 ave 12484 max 12484 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: 666448 ave 666448 max 666448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 666448 Ave neighs/atom = 666.448 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 7.361 | 7.361 | 7.361 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2908.4015 0 -2908.4015 -1528.035 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1000 atoms 209.7% 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: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12484 ave 12484 max 12484 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: 667296 ave 667296 max 667296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 667296 Ave neighs/atom = 667.296 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) = 7.361 | 7.361 | 7.361 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 -2908.4015 -2908.4015 15.078663 110.89692 9.8586014 -1528.035 -1528.035 -1.7882751 -4583.6159 1.2991132 2.6019218 461.89685 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1000 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: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12484 ave 12484 max 12484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 333648 ave 333648 max 333648 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 667296 ave 667296 max 667296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 667296 Ave neighs/atom = 667.296 Neighbor list builds = 0 Dangerous builds = 0 1000 -2908.40151756862 eV 2.60192184387739 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03