LAMMPS (24 Dec 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 = 3.6041287 3.6041287 3.6041287 Created orthogonal box = (0.0000000 -38.485168 0.0000000) to (27.210575 38.485168 5.0970076) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2511635 6.0760364 5.0970076 Created 458 atoms create_atoms CPU = 0.000 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2511635 6.0760364 5.0970076 Created 458 atoms create_atoms CPU = 0.000 seconds 458 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 24 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 902 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.581 | 4.581 | 4.581 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3697.3233 0 -3697.3233 20599.11 243 0 -3794.1061 0 -3794.1061 -14664.545 Loop time of 6.36488 on 1 procs for 243 steps with 902 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 = -3697.32333757247 -3794.10305757522 -3794.10610378381 Force two-norm initial, final = 89.397046 0.21439960 Force max component initial, final = 29.269156 0.063740383 Final line search alpha, max atom move = 1.0000000 0.063740383 Iterations, force evaluations = 243 444 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3289 | 6.3289 | 6.3289 | 0.0 | 99.44 Neigh | 0.013196 | 0.013196 | 0.013196 | 0.0 | 0.21 Comm | 0.013239 | 0.013239 | 0.013239 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0095 | | | 0.15 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4627.00 ave 4627 max 4627 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 86486.0 ave 86486 max 86486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86486 Ave neighs/atom = 95.882483 Neighbor list builds = 5 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Setting up cg style minimization ... Unit style : metal Current step : 243 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.581 | 4.581 | 4.581 Mbytes Step Temp E_pair E_mol TotEng Press Volume 243 0 -3794.1061 0 -3794.1061 -14664.545 10675.209 264 0 -3797.7927 0 -3797.7927 7290.8158 10521.127 Loop time of 0.339378 on 1 procs for 21 steps with 902 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 = -3794.1061037838 -3797.79114363472 -3797.79265026887 Force two-norm initial, final = 356.21374 1.4400456 Force max component initial, final = 356.17588 0.62216606 Final line search alpha, max atom move = 0.00019268223 0.00011988034 Iterations, force evaluations = 21 22 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33625 | 0.33625 | 0.33625 | 0.0 | 99.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006271 | 0.0006271 | 0.0006271 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002505 | | | 0.74 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4630.00 ave 4630 max 4630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 86470.0 ave 86470 max 86470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86470 Ave neighs/atom = 95.864745 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.718 | 4.718 | 4.718 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3797.7927 0 -3797.7927 7290.8158 Loop time of 2.10002e-06 on 1 procs for 0 steps with 902 atoms 142.9% 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 | | 2.1e-06 | | |100.00 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4711.00 ave 4711 max 4711 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87712.0 ave 87712 max 87712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87712 Ave neighs/atom = 97.241685 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) = 4.718 | 4.718 | 4.718 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 -3797.7927 -3797.7927 27.372475 76.970336 4.9937273 7290.8158 7290.8158 -95.308307 22039.793 -72.036937 2.3176501 3325.6388 Loop time of 2.20002e-06 on 1 procs for 0 steps with 902 atoms 181.8% 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 | | 2.2e-06 | | |100.00 Nlocal: 902.000 ave 902 max 902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4711.00 ave 4711 max 4711 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43856.0 ave 43856 max 43856 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 87712.0 ave 87712 max 87712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87712 Ave neighs/atom = 97.241685 Neighbor list builds = 0 Dangerous builds = 0 902 -3797.79265026887 eV 2.31765008818481 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06