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 = 3.63552 3.63552 3.63552 Created orthogonal box = (0 -39.1594 0) to (19.5779 39.1594 3.63552) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7257 4.7257 3.63552 Created 233 atoms create_atoms CPU = 0.000262976 secs 233 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7257 4.7257 3.63552 Created 233 atoms create_atoms CPU = 8.39233e-05 secs 233 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 7 27 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 460 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.454 | 4.454 | 4.454 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1857.1314 0 -1857.1314 15611.19 66 0 -1877.9541 0 -1877.9541 -1992.3366 Loop time of 7.92704 on 1 procs for 66 steps with 460 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1857.13140201 -1877.95253785 -1877.95409987 Force two-norm initial, final = 39.1543 0.110962 Force max component initial, final = 12.9207 0.0391456 Final line search alpha, max atom move = 1 0.0391456 Iterations, force evaluations = 66 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.9215 | 7.9215 | 7.9215 | 0.0 | 99.93 Neigh | 0.001236 | 0.001236 | 0.001236 | 0.0 | 0.02 Comm | 0.0027251 | 0.0027251 | 0.0027251 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001575 | | | 0.02 Nlocal: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3351 ave 3351 max 3351 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: 35248 ave 35248 max 35248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35248 Ave neighs/atom = 76.6261 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 : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.455 | 4.455 | 4.455 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -1877.9541 0 -1877.9541 -1992.3366 5574.4052 70 0 -1877.9738 0 -1877.9738 -220.15207 5567.4535 Loop time of 0.437968 on 1 procs for 4 steps with 460 atoms 100.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1877.95409987 -1877.9728916 -1877.97379596 Force two-norm initial, final = 13.1049 1.48693 Force max component initial, final = 13.0803 1.4341 Final line search alpha, max atom move = 0.000280049 0.000401618 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43743 | 0.43743 | 0.43743 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011754 | 0.00011754 | 0.00011754 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004203 | | | 0.10 Nlocal: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3361 ave 3361 max 3361 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: 35272 ave 35272 max 35272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35272 Ave neighs/atom = 76.6783 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.593 | 4.593 | 4.593 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1877.9738 0 -1877.9738 -220.15207 Loop time of 9.53674e-07 on 1 procs for 0 steps with 460 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: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3376 ave 3376 max 3376 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: 35276 ave 35276 max 35276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35276 Ave neighs/atom = 76.687 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) = 4.593 | 4.593 | 4.593 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 -1877.9738 -1877.9738 19.519266 78.318805 3.641892 -220.15207 -220.15207 104.59262 -1178.4702 413.42132 2.3311395 297.95112 Loop time of 9.53674e-07 on 1 procs for 0 steps with 460 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: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3376 ave 3376 max 3376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17638 ave 17638 max 17638 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35276 ave 35276 max 35276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35276 Ave neighs/atom = 76.687 Neighbor list builds = 0 Dangerous builds = 0 460 -1612.81536584405 eV 2.33113946665854 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08