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 = 3.65836 3.65836 3.65836 Created orthogonal box = (0 -59.4451 0) to (12.1334 59.4451 8.96113) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.51519 5.40376 5.97408 Created 530 atoms create_atoms CPU = 0.00027895 secs 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.51519 5.40376 5.97408 Created 530 atoms create_atoms CPU = 0.000160933 secs 530 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 32 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1046 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 32 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.089 | 5.089 | 5.089 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4157.486 0 -4157.486 -603.8565 415 0 -4202.5491 0 -4202.5491 -45437.887 Loop time of 3.04281 on 1 procs for 415 steps with 1046 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 = -4157.48598139 -4202.54503664 -4202.54906505 Force two-norm initial, final = 21.2595 0.19795 Force max component initial, final = 8.42564 0.0281179 Final line search alpha, max atom move = 1 0.0281179 Iterations, force evaluations = 415 816 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9634 | 2.9634 | 2.9634 | 0.0 | 97.39 Neigh | 0.026308 | 0.026308 | 0.026308 | 0.0 | 0.86 Comm | 0.031409 | 0.031409 | 0.031409 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02172 | | | 0.71 Nlocal: 1046 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6153 ave 6153 max 6153 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: 156948 ave 156948 max 156948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156948 Ave neighs/atom = 150.046 Neighbor list builds = 6 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 : 415 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.089 | 5.089 | 5.089 Mbytes Step Temp E_pair E_mol TotEng Press Volume 415 0 -4202.5491 0 -4202.5491 -45437.887 12926.82 461 0 -4213.0332 0 -4213.0332 -21363.3 12668.543 Loop time of 0.203696 on 1 procs for 46 steps with 1046 atoms 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4202.54906505 -4213.02928528 -4213.03320517 Force two-norm initial, final = 476.899 5.08707 Force max component initial, final = 475.601 2.90102 Final line search alpha, max atom move = 0.000126917 0.000368189 Iterations, force evaluations = 46 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19473 | 0.19473 | 0.19473 | 0.0 | 95.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018628 | 0.0018628 | 0.0018628 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007103 | | | 3.49 Nlocal: 1046 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6141 ave 6141 max 6141 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: 157364 ave 157364 max 157364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157364 Ave neighs/atom = 150.444 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.226 | 5.226 | 5.226 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4213.0332 0 -4213.0332 -21363.3 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1046 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: 1046 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6197 ave 6197 max 6197 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: 160888 ave 160888 max 160888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160888 Ave neighs/atom = 153.813 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) = 5.226 | 5.226 | 5.226 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 -4213.0332 -4213.0332 11.645995 118.8901 9.1496476 -21363.3 -21363.3 -352.15055 -63406.014 -331.73536 2.3166511 1819.1852 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1046 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: 1046 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6197 ave 6197 max 6197 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80444 ave 80444 max 80444 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 160888 ave 160888 max 160888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160888 Ave neighs/atom = 153.813 Neighbor list builds = 0 Dangerous builds = 0 1046 -4213.03320516645 eV 2.31665108980555 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03