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 = 3.51812 3.51812 3.51812 Created orthogonal box = (0 -64.8745 0) to (32.4355 64.8745 3.51812) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.96072 4.96072 3.51812 Created 682 atoms create_atoms CPU = 0.000334024 secs 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.96072 4.96072 3.51812 Created 682 atoms create_atoms CPU = 0.000215054 secs 682 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 28 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1356 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.343 | 6.343 | 6.343 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5883.0702 0 -5883.0702 23895.356 73 0 -5936.7822 0 -5936.7822 -1069.2997 Loop time of 1.47565 on 1 procs for 73 steps with 1356 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5883.07017843 -5936.77710647 -5936.78215376 Force two-norm initial, final = 72.3716 0.218016 Force max component initial, final = 20.927 0.0278936 Final line search alpha, max atom move = 1 0.0278936 Iterations, force evaluations = 73 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4532 | 1.4532 | 1.4532 | 0.0 | 98.48 Neigh | 0.0073819 | 0.0073819 | 0.0073819 | 0.0 | 0.50 Comm | 0.010547 | 0.010547 | 0.010547 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004519 | | | 0.31 Nlocal: 1356 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13518 ave 13518 max 13518 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: 441812 ave 441812 max 441812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 441812 Ave neighs/atom = 325.82 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 : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.343 | 6.343 | 6.343 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -5936.7822 0 -5936.7822 -1069.2997 14805.901 75 0 -5936.7913 0 -5936.7913 -505.73848 14801.34 Loop time of 0.0566211 on 1 procs for 2 steps with 1356 atoms 88.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5936.78215376 -5936.79061674 -5936.79131822 Force two-norm initial, final = 15.0573 0.377353 Force max component initial, final = 13.6362 0.304935 Final line search alpha, max atom move = 0.000133016 4.05611e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.055473 | 0.055473 | 0.055473 | 0.0 | 97.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032449 | 0.00032449 | 0.00032449 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008235 | | | 1.45 Nlocal: 1356 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13476 ave 13476 max 13476 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: 441984 ave 441984 max 441984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 441984 Ave neighs/atom = 325.947 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.481 | 6.481 | 6.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5936.7913 0 -5936.7913 -505.73848 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1356 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: 1356 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13476 ave 13476 max 13476 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: 442152 ave 442152 max 442152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 442152 Ave neighs/atom = 326.071 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) = 6.481 | 6.481 | 6.481 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 -5936.7913 -5936.7913 32.457863 129.74893 3.5146114 -505.73848 -505.73848 -2.642769 -1481.5978 -32.974859 2.2057664 128.21593 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1356 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: 1356 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13476 ave 13476 max 13476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 221076 ave 221076 max 221076 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 442152 ave 442152 max 442152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 442152 Ave neighs/atom = 326.071 Neighbor list builds = 0 Dangerous builds = 0 1356 -5936.79131821557 eV 2.20576643274953 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01