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 = 3.61481 3.61481 3.61481 Created orthogonal box = (0 -49.6991 0) to (13.5254 49.6991 8.85445) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7966 5.52172 5.90297 Created 508 atoms create_atoms CPU = 0.000339985 secs 508 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7966 5.52172 5.90297 Created 508 atoms create_atoms CPU = 0.0002141 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 3 19 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 11.0375 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:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 3 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.0375 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) = 6.374 | 6.374 | 6.374 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3506.3977 0 -3506.3977 4273.0448 62 0 -3528.4294 0 -3528.4294 -7167.9968 Loop time of 1.42398 on 1 procs for 62 steps with 1000 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3506.39765007 -3528.42590544 -3528.4294223 Force two-norm initial, final = 29.1003 0.168645 Force max component initial, final = 6.32323 0.0285091 Final line search alpha, max atom move = 1 0.0285091 Iterations, force evaluations = 62 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4009 | 1.4009 | 1.4009 | 0.0 | 98.38 Neigh | 0.012162 | 0.012162 | 0.012162 | 0.0 | 0.85 Comm | 0.0078187 | 0.0078187 | 0.0078187 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00314 | | | 0.22 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10082 ave 10082 max 10082 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: 459416 ave 459416 max 459416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459416 Ave neighs/atom = 459.416 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.377 | 6.377 | 6.377 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -3528.4294 0 -3528.4294 -7167.9968 11903.912 65 0 -3528.5168 0 -3528.5168 -1889.8898 11856.762 Loop time of 0.0679159 on 1 procs for 3 steps with 1000 atoms 103.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3528.4294223 -3528.5160048 -3528.51679425 Force two-norm initial, final = 62.2846 1.70851 Force max component initial, final = 47.5819 1.6468 Final line search alpha, max atom move = 0.000188344 0.000310164 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.066759 | 0.066759 | 0.066759 | 0.0 | 98.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032783 | 0.00032783 | 0.00032783 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000829 | | | 1.22 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10221 ave 10221 max 10221 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: 458732 ave 458732 max 458732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 458732 Ave neighs/atom = 458.732 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 = 11.0375 ghost atom cutoff = 11.0375 binsize = 5.51875, bins = 3 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.0375 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) = 6.516 | 6.516 | 6.516 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3528.5168 0 -3528.5168 -1889.8898 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1000 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: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10284 ave 10284 max 10284 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: 459068 ave 459068 max 459068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459068 Ave neighs/atom = 459.068 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) = 6.516 | 6.516 | 6.516 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 -3528.5168 -3528.5168 13.50259 99.398161 8.8342698 -1889.8898 -1889.8898 222.15241 -5835.6812 -56.140686 2.2988945 357.75681 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1000 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: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10284 ave 10284 max 10284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 229534 ave 229534 max 229534 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 459068 ave 459068 max 459068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459068 Ave neighs/atom = 459.068 Neighbor list builds = 0 Dangerous builds = 0 1000 -3528.51679424984 eV 2.2988945417226 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01