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 = 3.63857 3.63857 3.63857 Created orthogonal box = (0 -46.3151 0) to (32.7471 46.3151 5.14571) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.06428 6.2892 5.14571 Created 650 atoms create_atoms CPU = 0.000494003 secs 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.06428 6.2892 5.14571 Created 650 atoms create_atoms CPU = 0.000364065 secs 650 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 20 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1288 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 20 2 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) = 6.297 | 6.297 | 6.297 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4349.4797 0 -4349.4797 4816.6723 60 0 -4377.8004 0 -4377.8004 -6841.3373 Loop time of 0.974931 on 1 procs for 60 steps with 1288 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4349.47973716 -4377.79630447 -4377.80036307 Force two-norm initial, final = 40.4049 0.18096 Force max component initial, final = 12.2432 0.023318 Final line search alpha, max atom move = 1 0.023318 Iterations, force evaluations = 60 103 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95406 | 0.95406 | 0.95406 | 0.0 | 97.86 Neigh | 0.010761 | 0.010761 | 0.010761 | 0.0 | 1.10 Comm | 0.0066237 | 0.0066237 | 0.0066237 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00349 | | | 0.36 Nlocal: 1288 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10457 ave 10457 max 10457 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: 409252 ave 409252 max 409252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409252 Ave neighs/atom = 317.742 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 : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.297 | 6.297 | 6.297 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -4377.8004 0 -4377.8004 -6841.3373 15608.846 63 0 -4377.8637 0 -4377.8637 -2927.5819 15566.049 Loop time of 0.0668662 on 1 procs for 3 steps with 1288 atoms 89.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4377.80036307 -4377.86367899 -4377.86371864 Force two-norm initial, final = 64.9216 0.187079 Force max component initial, final = 48.2821 0.0433516 Final line search alpha, max atom move = 0.00136842 5.93234e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.065306 | 0.065306 | 0.065306 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037384 | 0.00037384 | 0.00037384 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001186 | | | 1.77 Nlocal: 1288 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10407 ave 10407 max 10407 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: 409228 ave 409228 max 409228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409228 Ave neighs/atom = 317.724 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 20 2 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) = 6.435 | 6.435 | 6.435 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4377.8637 0 -4377.8637 -2927.5819 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1288 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: 1288 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10407 ave 10407 max 10407 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: 409300 ave 409300 max 409300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409300 Ave neighs/atom = 317.78 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) = 6.435 | 6.435 | 6.435 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 -4377.8637 -4377.8637 32.697348 92.630109 5.1394152 -2927.5819 -2927.5819 0.29618525 -8778.5853 -4.4566173 2.3447637 495.60648 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1288 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: 1288 ave 1288 max 1288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10407 ave 10407 max 10407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 204650 ave 204650 max 204650 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 409300 ave 409300 max 409300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409300 Ave neighs/atom = 317.78 Neighbor list builds = 0 Dangerous builds = 0 1288 -4377.86371863762 eV 2.34476368750353 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01