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 = 3.52422 3.52422 3.52422 Created orthogonal box = (0 -52.1572 0) to (42.5833 52.1572 8.63254) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.25 5.00104 5.75503 Created 1756 atoms create_atoms CPU = 0.000689983 secs 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.25 5.00104 5.75503 Created 1756 atoms create_atoms CPU = 0.0006001 secs 1756 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 = 6.31717 ghost atom cutoff = 6.31717 binsize = 3.15858, bins = 14 34 3 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 6.31717 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 3472 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 = 6.31717 ghost atom cutoff = 6.31717 binsize = 3.15858, bins = 14 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.31717 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) = 6.1 | 6.1 | 6.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15363.121 0 -15363.121 4920.9912 37 0 -15422.839 0 -15422.839 -982.77448 Loop time of 0.484385 on 1 procs for 37 steps with 3472 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15363.1205707 -15422.8264181 -15422.8392089 Force two-norm initial, final = 64.5129 0.42893 Force max component initial, final = 7.7675 0.11029 Final line search alpha, max atom move = 0.505083 0.0557056 Iterations, force evaluations = 37 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46455 | 0.46455 | 0.46455 | 0.0 | 95.90 Neigh | 0.01038 | 0.01038 | 0.01038 | 0.0 | 2.14 Comm | 0.0042655 | 0.0042655 | 0.0042655 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005192 | | | 1.07 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8711 ave 8711 max 8711 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: 297438 ave 297438 max 297438 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297438 Ave neighs/atom = 85.6676 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 : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.107 | 6.107 | 6.107 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -15422.839 0 -15422.839 -982.77448 38346.228 39 0 -15422.874 0 -15422.874 585.39731 38315.083 Loop time of 0.0294421 on 1 procs for 2 steps with 3472 atoms 101.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15422.8392089 -15422.8692702 -15422.8736348 Force two-norm initial, final = 71.8366 0.458292 Force max component initial, final = 70.6222 0.143195 Final line search alpha, max atom move = 4.62614e-05 6.62442e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.028107 | 0.028107 | 0.028107 | 0.0 | 95.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023317 | 0.00023317 | 0.00023317 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001102 | | | 3.74 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8697 ave 8697 max 8697 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: 297406 ave 297406 max 297406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297406 Ave neighs/atom = 85.6584 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 = 6.31717 ghost atom cutoff = 6.31717 binsize = 3.15858, bins = 14 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.31717 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) = 6.245 | 6.245 | 6.245 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15422.874 0 -15422.874 585.39731 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3472 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: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8707 ave 8707 max 8707 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: 297410 ave 297410 max 297410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297410 Ave neighs/atom = 85.6596 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) = 6.245 | 6.245 | 6.245 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 -15422.874 -15422.874 42.540508 104.31445 8.6342105 585.39731 585.39731 -1.60177 1763.7827 -5.9889899 2.2397628 1528.8349 Loop time of 2.14577e-06 on 1 procs for 0 steps with 3472 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 | | 2.146e-06 | | |100.00 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8707 ave 8707 max 8707 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 148705 ave 148705 max 148705 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 297410 ave 297410 max 297410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297410 Ave neighs/atom = 85.6596 Neighbor list builds = 0 Dangerous builds = 0 3472 -15422.8736347591 eV 2.23976282959246 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00